Starting phenix.real_space_refine on Mon May 12 07:04:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlr_36405/05_2025/8jlr_36405_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlr_36405/05_2025/8jlr_36405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jlr_36405/05_2025/8jlr_36405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlr_36405/05_2025/8jlr_36405.map" model { file = "/net/cci-nas-00/data/ceres_data/8jlr_36405/05_2025/8jlr_36405_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlr_36405/05_2025/8jlr_36405_neut.cif" } resolution = 3.0 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= -0.005 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 5695 2.51 5 N 1522 2.21 5 O 1650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8934 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1928 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2160 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 11, 'TRANS': 256} Chain breaks: 2 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1784 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'VRK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.36, per 1000 atoms: 0.60 Number of scatterers: 8934 At special positions: 0 Unit cell: (109.2, 102.96, 124.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1650 8.00 N 1522 7.00 C 5695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.0 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 37.9% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.555A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.628A pdb=" N PHE A 282 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 283' Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.606A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 removed outlier: 3.782A pdb=" N ARG A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'R' and resid 20 through 51 Processing helix chain 'R' and resid 56 through 84 removed outlier: 4.482A pdb=" N MET R 77 " --> pdb=" O GLY R 73 " (cutoff:3.500A) Proline residue: R 78 - end of helix removed outlier: 3.844A pdb=" N VAL R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG R 83 " --> pdb=" O TYR R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 127 removed outlier: 3.802A pdb=" N ILE R 98 " --> pdb=" O VAL R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 160 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 187 through 199 removed outlier: 3.637A pdb=" N VAL R 192 " --> pdb=" O LYS R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 228 removed outlier: 4.269A pdb=" N MET R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 277 removed outlier: 3.935A pdb=" N PHE R 260 " --> pdb=" O VAL R 256 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N CYS R 265 " --> pdb=" O LEU R 261 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 282 through 305 removed outlier: 4.194A pdb=" N ASN R 286 " --> pdb=" O PRO R 282 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP R 287 " --> pdb=" O PRO R 283 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 319 Processing helix chain 'Y' and resid 7 through 24 Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'Y' and resid 45 through 48 Processing helix chain 'S' and resid 28 through 32 removed outlier: 4.212A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.544A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 3.813A pdb=" N ASP A 200 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N ALA A 220 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.726A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.692A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.710A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.607A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.442A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.913A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.680A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 3.829A pdb=" N VAL S 48 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 147 Processing sheet with id=AB4, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AB5, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.585A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1236 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: 2.55 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1428 1.31 - 1.44: 2583 1.44 - 1.56: 5024 1.56 - 1.69: 0 1.69 - 1.81: 101 Bond restraints: 9136 Sorted by residual: bond pdb=" CA THR R 194 " pdb=" C THR R 194 " ideal model delta sigma weight residual 1.523 1.440 0.083 1.35e-02 5.49e+03 3.76e+01 bond pdb=" C THR R 194 " pdb=" O THR R 194 " ideal model delta sigma weight residual 1.236 1.187 0.049 1.26e-02 6.30e+03 1.51e+01 bond pdb=" N TRP B 332 " pdb=" CA TRP B 332 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.32e-02 5.74e+03 5.54e+00 bond pdb=" N ASP R 103 " pdb=" CA ASP R 103 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.17e-02 7.31e+03 5.47e+00 bond pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.40e-02 5.10e+03 5.18e+00 ... (remaining 9131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 12064 1.67 - 3.33: 257 3.33 - 5.00: 38 5.00 - 6.67: 15 6.67 - 8.34: 3 Bond angle restraints: 12377 Sorted by residual: angle pdb=" N ASP B 333 " pdb=" CA ASP B 333 " pdb=" C ASP B 333 " ideal model delta sigma weight residual 113.15 108.97 4.18 1.19e+00 7.06e-01 1.24e+01 angle pdb=" N SER S 193 " pdb=" CA SER S 193 " pdb=" C SER S 193 " ideal model delta sigma weight residual 114.56 110.81 3.75 1.27e+00 6.20e-01 8.71e+00 angle pdb=" N TRP B 332 " pdb=" CA TRP B 332 " pdb=" C TRP B 332 " ideal model delta sigma weight residual 113.16 109.69 3.47 1.24e+00 6.50e-01 7.85e+00 angle pdb=" CB MET R 273 " pdb=" CG MET R 273 " pdb=" SD MET R 273 " ideal model delta sigma weight residual 112.70 121.04 -8.34 3.00e+00 1.11e-01 7.72e+00 angle pdb=" N ILE R 201 " pdb=" CA ILE R 201 " pdb=" C ILE R 201 " ideal model delta sigma weight residual 112.35 109.18 3.17 1.20e+00 6.94e-01 6.96e+00 ... (remaining 12372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 4803 16.19 - 32.39: 484 32.39 - 48.58: 137 48.58 - 64.78: 16 64.78 - 80.97: 11 Dihedral angle restraints: 5451 sinusoidal: 2165 harmonic: 3286 Sorted by residual: dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 182 " pdb=" CB CYS R 182 " ideal model delta sinusoidal sigma weight residual -86.00 -161.05 75.05 1 1.00e+01 1.00e-02 7.12e+01 dihedral pdb=" CA TYR S 235 " pdb=" C TYR S 235 " pdb=" N PRO S 236 " pdb=" CA PRO S 236 " ideal model delta harmonic sigma weight residual 180.00 157.77 22.23 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA PHE S 32 " pdb=" C PHE S 32 " pdb=" N GLY S 33 " pdb=" CA GLY S 33 " ideal model delta harmonic sigma weight residual 180.00 160.12 19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1281 0.082 - 0.164: 102 0.164 - 0.246: 1 0.246 - 0.329: 0 0.329 - 0.411: 1 Chirality restraints: 1385 Sorted by residual: chirality pdb=" C3 VRK R 401 " pdb=" C14 VRK R 401 " pdb=" C4 VRK R 401 " pdb=" O1 VRK R 401 " both_signs ideal model delta sigma weight residual False 2.41 2.00 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C2 VRK R 401 " pdb=" C1 VRK R 401 " pdb=" C16 VRK R 401 " pdb=" O1 VRK R 401 " both_signs ideal model delta sigma weight residual False 2.45 2.20 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ILE A 255 " pdb=" N ILE A 255 " pdb=" C ILE A 255 " pdb=" CB ILE A 255 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 1382 not shown) Planarity restraints: 1561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 298 " -0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO A 299 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 292 " -0.043 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO A 293 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 293 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 293 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR R 308 " -0.042 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO R 309 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO R 309 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 309 " -0.035 5.00e-02 4.00e+02 ... (remaining 1558 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 710 2.74 - 3.28: 9244 3.28 - 3.82: 15591 3.82 - 4.36: 18651 4.36 - 4.90: 32163 Nonbonded interactions: 76359 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.200 3.040 nonbonded pdb=" O ARG A 250 " pdb=" OG1 THR A 251 " model vdw 2.226 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.242 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP Y 48 " model vdw 2.250 3.040 nonbonded pdb=" O PHE R 186 " pdb=" OH TYR R 279 " model vdw 2.261 3.040 ... (remaining 76354 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.700 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 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 : 0.003 0.083 9139 Z= 0.165 Angle : 0.613 8.335 12383 Z= 0.333 Chirality : 0.044 0.411 1385 Planarity : 0.005 0.069 1561 Dihedral : 14.183 80.969 3322 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.21 % Allowed : 0.31 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1112 helix: 1.60 (0.26), residues: 385 sheet: -0.84 (0.30), residues: 265 loop : -1.15 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 339 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE S 29 TYR 0.016 0.001 TYR S 228 ARG 0.003 0.000 ARG R 23 Details of bonding type rmsd hydrogen bonds : bond 0.14255 ( 429) hydrogen bonds : angle 6.38229 ( 1236) SS BOND : bond 0.00087 ( 3) SS BOND : angle 0.38851 ( 6) covalent geometry : bond 0.00312 ( 9136) covalent geometry : angle 0.61261 (12377) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 212 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7378 (m-80) cc_final: 0.7044 (m-10) REVERT: A 274 LYS cc_start: 0.7765 (mmpt) cc_final: 0.7504 (mmtt) REVERT: R 123 TYR cc_start: 0.7732 (m-80) cc_final: 0.7403 (m-80) REVERT: R 211 TYR cc_start: 0.7978 (t80) cc_final: 0.7480 (t80) REVERT: S 228 TYR cc_start: 0.7710 (m-80) cc_final: 0.7034 (m-80) REVERT: S 237 LEU cc_start: 0.5182 (mp) cc_final: 0.4929 (mp) outliers start: 2 outliers final: 1 residues processed: 213 average time/residue: 0.7913 time to fit residues: 184.8875 Evaluate side-chains 165 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 194 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN ** R 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.207322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.160576 restraints weight = 10211.912| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.43 r_work: 0.3704 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9139 Z= 0.156 Angle : 0.602 7.747 12383 Z= 0.317 Chirality : 0.044 0.205 1385 Planarity : 0.005 0.057 1561 Dihedral : 5.382 40.198 1279 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.16 % Allowed : 10.57 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1112 helix: 1.52 (0.25), residues: 397 sheet: -0.73 (0.31), residues: 258 loop : -1.08 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.003 0.001 HIS A 324 PHE 0.015 0.001 PHE R 299 TYR 0.018 0.002 TYR S 190 ARG 0.007 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 429) hydrogen bonds : angle 5.32970 ( 1236) SS BOND : bond 0.00342 ( 3) SS BOND : angle 0.87191 ( 6) covalent geometry : bond 0.00353 ( 9136) covalent geometry : angle 0.60155 (12377) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7805 (m-80) cc_final: 0.7517 (m-10) REVERT: A 274 LYS cc_start: 0.7189 (mmpt) cc_final: 0.6776 (mmtt) REVERT: B 76 ASP cc_start: 0.8737 (p0) cc_final: 0.8478 (p0) REVERT: B 163 ASP cc_start: 0.7271 (t0) cc_final: 0.6935 (t0) REVERT: R 97 LYS cc_start: 0.8154 (tppt) cc_final: 0.7936 (mttm) REVERT: R 123 TYR cc_start: 0.8609 (m-80) cc_final: 0.8261 (m-80) REVERT: R 211 TYR cc_start: 0.8075 (t80) cc_final: 0.7656 (t80) REVERT: R 248 LYS cc_start: 0.8074 (ttmt) cc_final: 0.7798 (ttmt) REVERT: S 79 LEU cc_start: 0.4763 (mt) cc_final: 0.4461 (pp) REVERT: S 228 TYR cc_start: 0.7519 (m-80) cc_final: 0.6556 (m-80) outliers start: 21 outliers final: 8 residues processed: 185 average time/residue: 0.7603 time to fit residues: 155.5083 Evaluate side-chains 176 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 155 ASN ** R 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.202476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.155235 restraints weight = 10352.702| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.33 r_work: 0.3610 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9139 Z= 0.222 Angle : 0.631 7.790 12383 Z= 0.332 Chirality : 0.046 0.188 1385 Planarity : 0.005 0.056 1561 Dihedral : 5.395 40.119 1279 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.67 % Allowed : 14.58 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1112 helix: 1.47 (0.25), residues: 395 sheet: -0.84 (0.32), residues: 250 loop : -1.15 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS A 324 PHE 0.014 0.002 PHE A 189 TYR 0.022 0.002 TYR B 85 ARG 0.006 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 429) hydrogen bonds : angle 5.23651 ( 1236) SS BOND : bond 0.00381 ( 3) SS BOND : angle 0.83078 ( 6) covalent geometry : bond 0.00517 ( 9136) covalent geometry : angle 0.63066 (12377) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7981 (m-80) cc_final: 0.7582 (m-10) REVERT: A 274 LYS cc_start: 0.7133 (mmpt) cc_final: 0.6708 (mmtt) REVERT: B 163 ASP cc_start: 0.7523 (t0) cc_final: 0.7249 (t0) REVERT: R 91 PHE cc_start: 0.7488 (m-80) cc_final: 0.7234 (m-80) REVERT: R 194 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8390 (p) REVERT: R 211 TYR cc_start: 0.8181 (t80) cc_final: 0.7912 (t80) REVERT: S 188 LEU cc_start: 0.7533 (mt) cc_final: 0.7181 (mt) REVERT: S 228 TYR cc_start: 0.7701 (m-80) cc_final: 0.6976 (m-80) outliers start: 26 outliers final: 9 residues processed: 194 average time/residue: 0.7715 time to fit residues: 165.1573 Evaluate side-chains 173 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.204904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.155273 restraints weight = 10247.064| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.64 r_work: 0.3640 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9139 Z= 0.150 Angle : 0.598 12.916 12383 Z= 0.308 Chirality : 0.043 0.196 1385 Planarity : 0.005 0.057 1561 Dihedral : 5.197 35.739 1279 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.16 % Allowed : 16.84 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.25), residues: 1112 helix: 1.56 (0.25), residues: 391 sheet: -0.84 (0.31), residues: 256 loop : -1.12 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 211 HIS 0.003 0.001 HIS R 55 PHE 0.014 0.001 PHE A 189 TYR 0.018 0.002 TYR B 85 ARG 0.006 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 429) hydrogen bonds : angle 4.99185 ( 1236) SS BOND : bond 0.00353 ( 3) SS BOND : angle 0.76340 ( 6) covalent geometry : bond 0.00348 ( 9136) covalent geometry : angle 0.59783 (12377) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.966 Fit side-chains REVERT: A 53 MET cc_start: 0.6014 (OUTLIER) cc_final: 0.5643 (mtm) REVERT: A 274 LYS cc_start: 0.7013 (mmpt) cc_final: 0.6685 (mmtt) REVERT: A 290 ASP cc_start: 0.7103 (p0) cc_final: 0.6557 (t0) REVERT: B 163 ASP cc_start: 0.7569 (t0) cc_final: 0.7268 (t0) REVERT: B 211 TRP cc_start: 0.8540 (m100) cc_final: 0.8318 (m100) REVERT: R 123 TYR cc_start: 0.8630 (m-80) cc_final: 0.8364 (m-80) REVERT: R 158 MET cc_start: 0.7293 (tmm) cc_final: 0.6946 (ttm) REVERT: R 194 THR cc_start: 0.8557 (m) cc_final: 0.8244 (p) REVERT: R 211 TYR cc_start: 0.8145 (t80) cc_final: 0.7783 (t80) REVERT: R 248 LYS cc_start: 0.8069 (ttmt) cc_final: 0.7759 (ttmt) REVERT: S 188 LEU cc_start: 0.7412 (mt) cc_final: 0.7051 (mt) REVERT: S 228 TYR cc_start: 0.7635 (m-80) cc_final: 0.7061 (m-80) outliers start: 21 outliers final: 12 residues processed: 190 average time/residue: 0.8270 time to fit residues: 172.7930 Evaluate side-chains 181 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 80 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.206322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.158351 restraints weight = 10223.178| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.40 r_work: 0.3652 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9139 Z= 0.135 Angle : 0.578 9.326 12383 Z= 0.299 Chirality : 0.042 0.184 1385 Planarity : 0.005 0.056 1561 Dihedral : 5.003 33.166 1278 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.67 % Allowed : 17.66 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.25), residues: 1112 helix: 1.65 (0.26), residues: 390 sheet: -0.81 (0.31), residues: 257 loop : -1.09 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS A 324 PHE 0.016 0.001 PHE R 91 TYR 0.015 0.001 TYR S 190 ARG 0.006 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 429) hydrogen bonds : angle 4.86623 ( 1236) SS BOND : bond 0.00329 ( 3) SS BOND : angle 0.68799 ( 6) covalent geometry : bond 0.00308 ( 9136) covalent geometry : angle 0.57840 (12377) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6035 (OUTLIER) cc_final: 0.5821 (mtm) REVERT: A 274 LYS cc_start: 0.7154 (mmpt) cc_final: 0.6817 (mmtt) REVERT: A 290 ASP cc_start: 0.7089 (p0) cc_final: 0.6536 (t0) REVERT: B 76 ASP cc_start: 0.8569 (p0) cc_final: 0.8353 (p0) REVERT: B 163 ASP cc_start: 0.7509 (t0) cc_final: 0.7234 (t0) REVERT: B 211 TRP cc_start: 0.8494 (m100) cc_final: 0.8219 (m100) REVERT: B 239 ASN cc_start: 0.7655 (m-40) cc_final: 0.7096 (m110) REVERT: R 123 TYR cc_start: 0.8589 (m-80) cc_final: 0.8193 (m-80) REVERT: R 158 MET cc_start: 0.7224 (tmm) cc_final: 0.6805 (ttm) REVERT: R 194 THR cc_start: 0.8533 (m) cc_final: 0.8174 (p) REVERT: R 211 TYR cc_start: 0.8127 (t80) cc_final: 0.7777 (t80) REVERT: R 248 LYS cc_start: 0.8092 (ttmt) cc_final: 0.7804 (ttmt) REVERT: S 188 LEU cc_start: 0.7535 (mt) cc_final: 0.7210 (mt) REVERT: S 228 TYR cc_start: 0.7662 (m-80) cc_final: 0.7252 (m-80) outliers start: 26 outliers final: 15 residues processed: 186 average time/residue: 0.7970 time to fit residues: 162.9667 Evaluate side-chains 178 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.204506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.157617 restraints weight = 10256.691| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.44 r_work: 0.3622 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9139 Z= 0.178 Angle : 0.609 9.122 12383 Z= 0.316 Chirality : 0.044 0.192 1385 Planarity : 0.005 0.056 1561 Dihedral : 5.012 31.940 1278 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.87 % Allowed : 18.99 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1112 helix: 1.59 (0.26), residues: 392 sheet: -0.91 (0.31), residues: 260 loop : -1.03 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.008 0.001 HIS A 197 PHE 0.015 0.002 PHE R 91 TYR 0.016 0.002 TYR B 85 ARG 0.008 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 429) hydrogen bonds : angle 4.89784 ( 1236) SS BOND : bond 0.00289 ( 3) SS BOND : angle 0.68193 ( 6) covalent geometry : bond 0.00415 ( 9136) covalent geometry : angle 0.60908 (12377) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5839 (mtm) REVERT: A 197 HIS cc_start: 0.8239 (OUTLIER) cc_final: 0.7951 (m-70) REVERT: A 274 LYS cc_start: 0.7161 (mmpt) cc_final: 0.6828 (mmtt) REVERT: A 290 ASP cc_start: 0.7099 (p0) cc_final: 0.6533 (t0) REVERT: B 163 ASP cc_start: 0.7550 (t0) cc_final: 0.7263 (t0) REVERT: B 197 ARG cc_start: 0.7943 (mmm160) cc_final: 0.7678 (tpt-90) REVERT: B 211 TRP cc_start: 0.8545 (m100) cc_final: 0.8330 (m100) REVERT: B 214 ARG cc_start: 0.8474 (mmt90) cc_final: 0.8261 (mpt-90) REVERT: R 91 PHE cc_start: 0.7262 (m-80) cc_final: 0.7012 (m-80) REVERT: R 158 MET cc_start: 0.7091 (tmm) cc_final: 0.6706 (ttm) REVERT: R 194 THR cc_start: 0.8588 (m) cc_final: 0.8114 (p) REVERT: R 211 TYR cc_start: 0.8174 (t80) cc_final: 0.7812 (t80) REVERT: R 248 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7836 (ttmt) REVERT: S 188 LEU cc_start: 0.7568 (mt) cc_final: 0.7269 (mt) REVERT: S 228 TYR cc_start: 0.7721 (m-80) cc_final: 0.7320 (m-80) outliers start: 28 outliers final: 16 residues processed: 186 average time/residue: 0.8157 time to fit residues: 166.0437 Evaluate side-chains 185 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** R 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.204914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.156747 restraints weight = 10300.520| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.32 r_work: 0.3618 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9139 Z= 0.146 Angle : 0.593 9.021 12383 Z= 0.307 Chirality : 0.043 0.194 1385 Planarity : 0.005 0.057 1561 Dihedral : 4.964 31.633 1278 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.16 % Allowed : 20.53 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.15 (0.25), residues: 1112 helix: 1.62 (0.26), residues: 391 sheet: -0.92 (0.31), residues: 260 loop : -1.07 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS A 197 PHE 0.016 0.001 PHE R 91 TYR 0.014 0.001 TYR S 190 ARG 0.011 0.000 ARG A 54 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 429) hydrogen bonds : angle 4.85254 ( 1236) SS BOND : bond 0.00285 ( 3) SS BOND : angle 0.60558 ( 6) covalent geometry : bond 0.00337 ( 9136) covalent geometry : angle 0.59311 (12377) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 197 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.7970 (m-70) REVERT: A 274 LYS cc_start: 0.7071 (mmpt) cc_final: 0.6725 (mmtt) REVERT: A 290 ASP cc_start: 0.7143 (p0) cc_final: 0.6491 (t0) REVERT: B 163 ASP cc_start: 0.7537 (t0) cc_final: 0.7251 (t0) REVERT: B 197 ARG cc_start: 0.7945 (mmm160) cc_final: 0.7655 (tpt-90) REVERT: B 211 TRP cc_start: 0.8478 (m100) cc_final: 0.8128 (m100) REVERT: B 254 ASP cc_start: 0.7592 (t70) cc_final: 0.7177 (p0) REVERT: R 123 TYR cc_start: 0.8621 (m-80) cc_final: 0.8329 (m-80) REVERT: R 158 MET cc_start: 0.7282 (tmm) cc_final: 0.6837 (ttm) REVERT: R 194 THR cc_start: 0.8462 (m) cc_final: 0.8041 (p) REVERT: R 211 TYR cc_start: 0.8101 (t80) cc_final: 0.7727 (t80) REVERT: R 248 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7668 (ttmt) REVERT: S 188 LEU cc_start: 0.7440 (mt) cc_final: 0.7161 (mt) REVERT: S 228 TYR cc_start: 0.7644 (m-80) cc_final: 0.7326 (m-80) outliers start: 21 outliers final: 13 residues processed: 183 average time/residue: 0.8591 time to fit residues: 172.0701 Evaluate side-chains 181 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 20.0000 chunk 64 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 66 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 chunk 82 optimal weight: 8.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN R 63 HIS ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.206710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.158185 restraints weight = 10422.792| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.39 r_work: 0.3645 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9139 Z= 0.126 Angle : 0.591 10.814 12383 Z= 0.302 Chirality : 0.043 0.193 1385 Planarity : 0.005 0.059 1561 Dihedral : 4.860 30.484 1278 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.26 % Allowed : 21.05 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1112 helix: 1.66 (0.26), residues: 392 sheet: -0.91 (0.31), residues: 262 loop : -1.02 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS A 197 PHE 0.013 0.001 PHE A 189 TYR 0.014 0.001 TYR S 190 ARG 0.008 0.000 ARG A 54 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 429) hydrogen bonds : angle 4.80463 ( 1236) SS BOND : bond 0.00290 ( 3) SS BOND : angle 0.57063 ( 6) covalent geometry : bond 0.00284 ( 9136) covalent geometry : angle 0.59144 (12377) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 1.053 Fit side-chains REVERT: A 235 GLU cc_start: 0.7925 (tp30) cc_final: 0.7684 (mp0) REVERT: A 274 LYS cc_start: 0.6953 (mmpt) cc_final: 0.6607 (mmtt) REVERT: A 290 ASP cc_start: 0.7142 (p0) cc_final: 0.6444 (t0) REVERT: B 163 ASP cc_start: 0.7541 (t0) cc_final: 0.7247 (t0) REVERT: B 175 GLN cc_start: 0.8141 (pt0) cc_final: 0.7713 (pm20) REVERT: B 197 ARG cc_start: 0.7902 (mmm160) cc_final: 0.7602 (tpt-90) REVERT: B 211 TRP cc_start: 0.8441 (m100) cc_final: 0.8118 (m100) REVERT: B 254 ASP cc_start: 0.7547 (t70) cc_final: 0.7134 (p0) REVERT: R 123 TYR cc_start: 0.8599 (m-80) cc_final: 0.8200 (m-80) REVERT: R 158 MET cc_start: 0.7259 (tmm) cc_final: 0.6826 (ttm) REVERT: R 194 THR cc_start: 0.8440 (m) cc_final: 0.7964 (p) REVERT: R 211 TYR cc_start: 0.8111 (t80) cc_final: 0.7692 (t80) REVERT: S 140 MET cc_start: 0.5613 (ptm) cc_final: 0.5277 (ppp) REVERT: S 188 LEU cc_start: 0.7438 (mt) cc_final: 0.7171 (mt) REVERT: S 228 TYR cc_start: 0.7620 (m-80) cc_final: 0.7314 (m-80) outliers start: 22 outliers final: 13 residues processed: 181 average time/residue: 0.8152 time to fit residues: 161.7326 Evaluate side-chains 179 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 17 optimal weight: 0.0170 chunk 26 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.205685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.157982 restraints weight = 10334.684| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.41 r_work: 0.3649 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9139 Z= 0.144 Angle : 0.600 9.620 12383 Z= 0.308 Chirality : 0.043 0.196 1385 Planarity : 0.005 0.060 1561 Dihedral : 4.810 28.626 1278 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.95 % Allowed : 22.38 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1112 helix: 1.60 (0.26), residues: 394 sheet: -0.93 (0.31), residues: 264 loop : -0.96 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.011 0.001 HIS A 197 PHE 0.019 0.001 PHE R 91 TYR 0.019 0.002 TYR B 59 ARG 0.007 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 429) hydrogen bonds : angle 4.81374 ( 1236) SS BOND : bond 0.00277 ( 3) SS BOND : angle 0.51480 ( 6) covalent geometry : bond 0.00332 ( 9136) covalent geometry : angle 0.60012 (12377) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 1.110 Fit side-chains REVERT: A 274 LYS cc_start: 0.7043 (mmpt) cc_final: 0.6714 (mmtt) REVERT: A 290 ASP cc_start: 0.7136 (p0) cc_final: 0.6439 (t0) REVERT: B 59 TYR cc_start: 0.8295 (m-80) cc_final: 0.7986 (m-80) REVERT: B 163 ASP cc_start: 0.7540 (t0) cc_final: 0.7259 (t0) REVERT: B 175 GLN cc_start: 0.8153 (pt0) cc_final: 0.7831 (pm20) REVERT: B 197 ARG cc_start: 0.7884 (mmm160) cc_final: 0.7620 (tpt-90) REVERT: B 211 TRP cc_start: 0.8484 (m100) cc_final: 0.8239 (m100) REVERT: B 254 ASP cc_start: 0.7578 (t70) cc_final: 0.7195 (p0) REVERT: R 123 TYR cc_start: 0.8621 (m-80) cc_final: 0.8240 (m-80) REVERT: R 158 MET cc_start: 0.7147 (tmm) cc_final: 0.6723 (ttm) REVERT: R 194 THR cc_start: 0.8588 (m) cc_final: 0.8126 (p) REVERT: R 211 TYR cc_start: 0.8193 (t80) cc_final: 0.7852 (t80) REVERT: S 172 THR cc_start: 0.6555 (OUTLIER) cc_final: 0.6345 (t) REVERT: S 188 LEU cc_start: 0.7567 (mt) cc_final: 0.7291 (mt) REVERT: S 228 TYR cc_start: 0.7732 (m-80) cc_final: 0.7435 (m-80) outliers start: 19 outliers final: 14 residues processed: 177 average time/residue: 0.8863 time to fit residues: 171.5796 Evaluate side-chains 177 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.206406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.157935 restraints weight = 10347.244| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.37 r_work: 0.3639 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9139 Z= 0.137 Angle : 0.604 10.473 12383 Z= 0.309 Chirality : 0.043 0.192 1385 Planarity : 0.005 0.061 1561 Dihedral : 4.758 27.860 1278 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.05 % Allowed : 22.07 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.25), residues: 1112 helix: 1.61 (0.26), residues: 395 sheet: -0.89 (0.31), residues: 264 loop : -0.94 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS A 197 PHE 0.019 0.001 PHE R 91 TYR 0.017 0.002 TYR B 59 ARG 0.010 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 429) hydrogen bonds : angle 4.80170 ( 1236) SS BOND : bond 0.00279 ( 3) SS BOND : angle 0.49819 ( 6) covalent geometry : bond 0.00313 ( 9136) covalent geometry : angle 0.60364 (12377) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 1.018 Fit side-chains REVERT: A 274 LYS cc_start: 0.6965 (mmpt) cc_final: 0.6621 (mmtt) REVERT: A 290 ASP cc_start: 0.7272 (p0) cc_final: 0.6525 (t0) REVERT: B 59 TYR cc_start: 0.8235 (m-80) cc_final: 0.7881 (m-80) REVERT: B 163 ASP cc_start: 0.7527 (t0) cc_final: 0.7253 (t0) REVERT: B 175 GLN cc_start: 0.8162 (pt0) cc_final: 0.7716 (pm20) REVERT: B 197 ARG cc_start: 0.7850 (mmm160) cc_final: 0.7562 (tpt-90) REVERT: B 211 TRP cc_start: 0.8453 (m100) cc_final: 0.8156 (m100) REVERT: B 254 ASP cc_start: 0.7495 (t70) cc_final: 0.7062 (p0) REVERT: R 91 PHE cc_start: 0.7097 (m-80) cc_final: 0.6852 (m-80) REVERT: R 123 TYR cc_start: 0.8609 (m-80) cc_final: 0.8217 (m-80) REVERT: R 158 MET cc_start: 0.7262 (tmm) cc_final: 0.6841 (ttm) REVERT: R 194 THR cc_start: 0.8476 (m) cc_final: 0.7990 (p) REVERT: R 211 TYR cc_start: 0.8113 (t80) cc_final: 0.7702 (t80) REVERT: S 172 THR cc_start: 0.6286 (OUTLIER) cc_final: 0.6082 (t) REVERT: S 188 LEU cc_start: 0.7364 (mt) cc_final: 0.7134 (mt) REVERT: S 228 TYR cc_start: 0.7637 (m-80) cc_final: 0.7405 (m-80) outliers start: 20 outliers final: 13 residues processed: 182 average time/residue: 0.8374 time to fit residues: 166.7310 Evaluate side-chains 180 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.206038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.159958 restraints weight = 10337.898| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.26 r_work: 0.3665 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9139 Z= 0.137 Angle : 0.601 11.159 12383 Z= 0.307 Chirality : 0.043 0.190 1385 Planarity : 0.005 0.060 1561 Dihedral : 4.700 26.491 1278 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.95 % Allowed : 22.48 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1112 helix: 1.65 (0.26), residues: 394 sheet: -0.85 (0.31), residues: 264 loop : -0.95 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS B 142 PHE 0.019 0.001 PHE R 91 TYR 0.015 0.002 TYR B 59 ARG 0.009 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 429) hydrogen bonds : angle 4.79662 ( 1236) SS BOND : bond 0.00250 ( 3) SS BOND : angle 0.43928 ( 6) covalent geometry : bond 0.00314 ( 9136) covalent geometry : angle 0.60112 (12377) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6959.51 seconds wall clock time: 120 minutes 34.75 seconds (7234.75 seconds total)