Starting phenix.real_space_refine on Wed Sep 17 13:10:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nab_49184/09_2025/9nab_49184.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nab_49184/09_2025/9nab_49184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nab_49184/09_2025/9nab_49184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nab_49184/09_2025/9nab_49184.map" model { file = "/net/cci-nas-00/data/ceres_data/9nab_49184/09_2025/9nab_49184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nab_49184/09_2025/9nab_49184.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 31 5.16 5 C 5389 2.51 5 N 1401 2.21 5 O 1677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8498 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2793 Classifications: {'peptide': 357} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 343} Chain breaks: 2 Chain: "B" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3196 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 29, 'TRANS': 393} Chain breaks: 3 Chain: "D" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1418 Classifications: {'peptide': 182} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 170} Chain breaks: 3 Chain: "C" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1091 Classifications: {'peptide': 144} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 136} Chain breaks: 2 Time building chain proxies: 2.01, per 1000 atoms: 0.24 Number of scatterers: 8498 At special positions: 0 Unit cell: (66.96, 110.16, 132.48, 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 31 16.00 O 1677 8.00 N 1401 7.00 C 5389 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 213 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 401 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 156 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS D 167 " - pdb=" SG CYS D 223 " distance=2.03 Simple disulfide: pdb=" SG CYS C 51 " - pdb=" SG CYS C 116 " 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: 0.60 Conformation dependent library (CDL) restraints added in 415.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 23 sheets defined 12.9% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.869A pdb=" N GLU A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 199 through 205 removed outlier: 4.281A pdb=" N ARG A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 239 removed outlier: 3.546A pdb=" N PHE A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.921A pdb=" N LEU A 290 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 Processing helix chain 'A' and resid 341 through 352 removed outlier: 4.356A pdb=" N GLU A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 380 Processing helix chain 'A' and resid 401 through 405 removed outlier: 3.668A pdb=" N VAL A 405 " --> pdb=" O LYS A 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 237 through 244 Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 295 through 300 removed outlier: 3.640A pdb=" N THR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 110 removed outlier: 3.625A pdb=" N THR D 110 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.574A pdb=" N GLU C 111 " --> pdb=" O PRO C 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.856A pdb=" N GLN A 129 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A 428 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.509A pdb=" N ARG A 446 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 220 through 226 removed outlier: 5.371A pdb=" N ASN A 221 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER A 186 " --> pdb=" O ASN A 221 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU A 225 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 182 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG A 272 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE A 334 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 274 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA A 336 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE A 276 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N THR A 338 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR A 278 " --> pdb=" O THR A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 51 removed outlier: 3.703A pdb=" N ALA B 50 " --> pdb=" O VAL B 486 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 459 " --> pdb=" O GLY B 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 78 through 80 removed outlier: 3.654A pdb=" N VAL B 78 " --> pdb=" O TYR B 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 135 through 136 removed outlier: 3.898A pdb=" N SER B 161 " --> pdb=" O TYR B 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 149 removed outlier: 4.363A pdb=" N ALA B 155 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 175 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 185 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 210 through 213 Processing sheet with id=AB1, first strand: chain 'B' and resid 276 through 279 removed outlier: 3.584A pdb=" N THR B 304 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 330 through 333 removed outlier: 3.787A pdb=" N ALA B 347 " --> pdb=" O ARG B 364 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG B 364 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 381 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 370 through 371 Processing sheet with id=AB4, first strand: chain 'B' and resid 397 through 400 removed outlier: 5.517A pdb=" N ASP B 409 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 430 through 431 Processing sheet with id=AB6, first strand: chain 'D' and resid 22 through 25 Processing sheet with id=AB7, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.731A pdb=" N GLY D 31 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY D 68 " --> pdb=" O TRP D 55 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS D 57 " --> pdb=" O TRP D 66 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TRP D 66 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.731A pdb=" N GLY D 31 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR D 129 " --> pdb=" O ARG D 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AC1, first strand: chain 'D' and resid 147 through 148 removed outlier: 3.500A pdb=" N SER D 147 " --> pdb=" O LYS D 170 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LYS D 170 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU D 205 " --> pdb=" O LYS D 170 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER D 204 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 222 through 225 Processing sheet with id=AC3, first strand: chain 'C' and resid 38 through 39 removed outlier: 3.691A pdb=" N LEU C 39 " --> pdb=" O LYS C 131 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU C 61 " --> pdb=" O TYR C 77 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N TYR C 77 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP C 63 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 47 through 50 removed outlier: 3.541A pdb=" N GLN C 98 " --> pdb=" O SER C 95 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 161 through 165 removed outlier: 3.818A pdb=" N CYS C 162 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER C 205 " --> pdb=" O CYS C 162 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 573 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2740 1.34 - 1.46: 1718 1.46 - 1.58: 4188 1.58 - 1.70: 0 1.70 - 1.82: 43 Bond restraints: 8689 Sorted by residual: bond pdb=" N LEU A 123 " pdb=" CA LEU A 123 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.18e-02 7.18e+03 1.28e+01 bond pdb=" N ILE A 89 " pdb=" CA ILE A 89 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.24e-02 6.50e+03 8.65e+00 bond pdb=" N VAL A 393 " pdb=" CA VAL A 393 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.01e+00 bond pdb=" N VAL A 95 " pdb=" CA VAL A 95 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.19e-02 7.06e+03 7.69e+00 bond pdb=" N ARG A 124 " pdb=" CA ARG A 124 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.09e+00 ... (remaining 8684 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 11641 3.06 - 6.13: 126 6.13 - 9.19: 15 9.19 - 12.25: 2 12.25 - 15.31: 1 Bond angle restraints: 11785 Sorted by residual: angle pdb=" N ASN A 386 " pdb=" CA ASN A 386 " pdb=" C ASN A 386 " ideal model delta sigma weight residual 113.15 103.93 9.22 1.19e+00 7.06e-01 6.00e+01 angle pdb=" N GLN A 117 " pdb=" CA GLN A 117 " pdb=" C GLN A 117 " ideal model delta sigma weight residual 113.16 105.53 7.63 1.24e+00 6.50e-01 3.78e+01 angle pdb=" N HIS B 386 " pdb=" CA HIS B 386 " pdb=" C HIS B 386 " ideal model delta sigma weight residual 113.88 107.20 6.68 1.23e+00 6.61e-01 2.95e+01 angle pdb=" C THR A 394 " pdb=" N ILE A 395 " pdb=" CA ILE A 395 " ideal model delta sigma weight residual 123.12 116.27 6.85 1.30e+00 5.92e-01 2.77e+01 angle pdb=" CA ASN A 386 " pdb=" CB ASN A 386 " pdb=" CG ASN A 386 " ideal model delta sigma weight residual 112.60 117.38 -4.78 1.00e+00 1.00e+00 2.28e+01 ... (remaining 11780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 4432 17.80 - 35.61: 525 35.61 - 53.41: 137 53.41 - 71.21: 38 71.21 - 89.02: 13 Dihedral angle restraints: 5145 sinusoidal: 2009 harmonic: 3136 Sorted by residual: dihedral pdb=" CB CYS B 99 " pdb=" SG CYS B 99 " pdb=" SG CYS B 108 " pdb=" CB CYS B 108 " ideal model delta sinusoidal sigma weight residual -86.00 -149.84 63.84 1 1.00e+01 1.00e-02 5.37e+01 dihedral pdb=" CD ARG A 122 " pdb=" NE ARG A 122 " pdb=" CZ ARG A 122 " pdb=" NH1 ARG A 122 " ideal model delta sinusoidal sigma weight residual 0.00 37.79 -37.79 1 1.00e+01 1.00e-02 2.01e+01 dihedral pdb=" CA ARG A 446 " pdb=" C ARG A 446 " pdb=" N PRO A 447 " pdb=" CA PRO A 447 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 5142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1122 0.078 - 0.156: 148 0.156 - 0.235: 12 0.235 - 0.313: 3 0.313 - 0.391: 1 Chirality restraints: 1286 Sorted by residual: chirality pdb=" CB VAL A 120 " pdb=" CA VAL A 120 " pdb=" CG1 VAL A 120 " pdb=" CG2 VAL A 120 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CA ILE A 383 " pdb=" N ILE A 383 " pdb=" C ILE A 383 " pdb=" CB ILE A 383 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA LYS A 90 " pdb=" N LYS A 90 " pdb=" C LYS A 90 " pdb=" CB LYS A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1283 not shown) Planarity restraints: 1535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 122 " -0.646 9.50e-02 1.11e+02 2.90e-01 5.15e+01 pdb=" NE ARG A 122 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG A 122 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 122 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 122 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 382 " -0.022 2.00e-02 2.50e+03 4.46e-02 1.98e+01 pdb=" C VAL A 382 " 0.077 2.00e-02 2.50e+03 pdb=" O VAL A 382 " -0.030 2.00e-02 2.50e+03 pdb=" N ILE A 383 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 124 " 0.340 9.50e-02 1.11e+02 1.52e-01 1.44e+01 pdb=" NE ARG A 124 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 124 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 124 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 124 " 0.010 2.00e-02 2.50e+03 ... (remaining 1532 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 3656 2.91 - 3.41: 8535 3.41 - 3.91: 14927 3.91 - 4.40: 17659 4.40 - 4.90: 28332 Nonbonded interactions: 73109 Sorted by model distance: nonbonded pdb=" O ASN A 386 " pdb=" ND2 ASN A 386 " model vdw 2.416 3.120 nonbonded pdb=" O GLY B 363 " pdb=" N GLY B 385 " model vdw 2.432 3.120 nonbonded pdb=" O THR B 382 " pdb=" OG1 THR B 382 " model vdw 2.456 3.040 nonbonded pdb=" O ASP D 120 " pdb=" OD1 ASP D 120 " model vdw 2.476 3.040 nonbonded pdb=" O GLN A 369 " pdb=" OE1 GLN A 369 " model vdw 2.483 3.040 ... (remaining 73104 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.660 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.240 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 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 : 0.004 0.042 8698 Z= 0.256 Angle : 0.801 15.314 11803 Z= 0.478 Chirality : 0.052 0.391 1286 Planarity : 0.010 0.290 1535 Dihedral : 17.253 89.017 3134 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.47 % Favored : 94.43 % Rotamer: Outliers : 5.35 % Allowed : 22.03 % Favored : 72.62 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 11.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.26), residues: 1078 helix: -0.49 (0.51), residues: 101 sheet: -1.51 (0.30), residues: 293 loop : -1.04 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 122 TYR 0.020 0.001 TYR C 122 PHE 0.019 0.002 PHE B 60 TRP 0.011 0.002 TRP D 66 HIS 0.003 0.001 HIS B 386 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 8689) covalent geometry : angle 0.80153 (11785) SS BOND : bond 0.00108 ( 9) SS BOND : angle 0.53145 ( 18) hydrogen bonds : bond 0.24318 ( 227) hydrogen bonds : angle 11.49636 ( 573) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 122 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.7690 (p0) cc_final: 0.7462 (p0) REVERT: A 393 VAL cc_start: 0.6681 (OUTLIER) cc_final: 0.6424 (p) REVERT: A 441 ASP cc_start: 0.6909 (t70) cc_final: 0.6514 (t0) REVERT: B 248 GLU cc_start: 0.8126 (mp0) cc_final: 0.7819 (mp0) REVERT: B 488 ARG cc_start: 0.7343 (mtm180) cc_final: 0.6860 (mtp85) REVERT: D 62 GLN cc_start: 0.6499 (mp10) cc_final: 0.6146 (mp10) REVERT: D 172 TYR cc_start: 0.6583 (p90) cc_final: 0.6164 (p90) REVERT: D 173 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.7099 (t80) REVERT: D 227 HIS cc_start: 0.4343 (OUTLIER) cc_final: 0.3535 (m-70) outliers start: 50 outliers final: 25 residues processed: 161 average time/residue: 0.4049 time to fit residues: 71.1929 Evaluate side-chains 131 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 407 TYR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 161 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 129 GLN ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN B 238 GLN B 321 GLN ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.193396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.167726 restraints weight = 13075.208| |-----------------------------------------------------------------------------| r_work (start): 0.4446 rms_B_bonded: 3.18 r_work: 0.4340 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8698 Z= 0.172 Angle : 0.637 14.102 11803 Z= 0.329 Chirality : 0.046 0.175 1286 Planarity : 0.005 0.051 1535 Dihedral : 7.467 59.331 1224 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 7.17 % Allowed : 22.99 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.25), residues: 1078 helix: -0.17 (0.51), residues: 100 sheet: -1.52 (0.29), residues: 307 loop : -1.09 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 117 TYR 0.017 0.002 TYR C 122 PHE 0.018 0.002 PHE A 187 TRP 0.012 0.002 TRP D 55 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 8689) covalent geometry : angle 0.63723 (11785) SS BOND : bond 0.00215 ( 9) SS BOND : angle 0.70204 ( 18) hydrogen bonds : bond 0.03966 ( 227) hydrogen bonds : angle 7.97030 ( 573) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 121 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.7659 (p0) cc_final: 0.7408 (p0) REVERT: A 127 GLU cc_start: 0.4831 (OUTLIER) cc_final: 0.4517 (mm-30) REVERT: A 394 THR cc_start: 0.7189 (OUTLIER) cc_final: 0.6757 (p) REVERT: B 135 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.4409 (pm20) REVERT: B 212 GLU cc_start: 0.5907 (OUTLIER) cc_final: 0.5647 (tm-30) REVERT: B 246 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.6938 (t80) REVERT: B 322 MET cc_start: 0.7502 (ttt) cc_final: 0.7225 (ttt) REVERT: B 383 LEU cc_start: 0.6134 (OUTLIER) cc_final: 0.5925 (pp) REVERT: B 444 GLN cc_start: 0.6301 (pm20) cc_final: 0.5885 (mp10) REVERT: B 488 ARG cc_start: 0.6720 (mtm180) cc_final: 0.6223 (mtp85) REVERT: D 62 GLN cc_start: 0.6058 (mp10) cc_final: 0.5527 (mp10) REVERT: D 173 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.6725 (t80) REVERT: D 227 HIS cc_start: 0.3306 (OUTLIER) cc_final: 0.2786 (m-70) REVERT: C 32 MET cc_start: 0.3963 (OUTLIER) cc_final: 0.2890 (mpt) REVERT: C 98 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7095 (mp10) outliers start: 67 outliers final: 19 residues processed: 170 average time/residue: 0.3607 time to fit residues: 67.5193 Evaluate side-chains 131 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 162 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 10 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 30 optimal weight: 0.0370 chunk 104 optimal weight: 0.1980 chunk 58 optimal weight: 0.9990 chunk 81 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 71 optimal weight: 0.0770 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN B 238 GLN ** C 59 ASN ** 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 = 0.4772 r_free = 0.4772 target = 0.199075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.174163 restraints weight = 12976.630| |-----------------------------------------------------------------------------| r_work (start): 0.4496 rms_B_bonded: 3.17 r_work: 0.4394 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8698 Z= 0.121 Angle : 0.595 15.153 11803 Z= 0.297 Chirality : 0.045 0.298 1286 Planarity : 0.004 0.052 1535 Dihedral : 6.499 58.462 1209 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 6.20 % Allowed : 24.81 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.25), residues: 1078 helix: -0.06 (0.51), residues: 100 sheet: -1.31 (0.30), residues: 303 loop : -1.05 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 117 TYR 0.017 0.001 TYR B 204 PHE 0.012 0.001 PHE A 232 TRP 0.013 0.001 TRP D 55 HIS 0.002 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8689) covalent geometry : angle 0.59505 (11785) SS BOND : bond 0.00062 ( 9) SS BOND : angle 0.47135 ( 18) hydrogen bonds : bond 0.03326 ( 227) hydrogen bonds : angle 7.23595 ( 573) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 133 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8028 (tptt) cc_final: 0.7824 (tptt) REVERT: A 394 THR cc_start: 0.6768 (OUTLIER) cc_final: 0.6414 (p) REVERT: B 64 VAL cc_start: 0.4642 (OUTLIER) cc_final: 0.4210 (t) REVERT: B 135 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.4443 (pm20) REVERT: B 212 GLU cc_start: 0.5965 (OUTLIER) cc_final: 0.5660 (tm-30) REVERT: B 246 TYR cc_start: 0.7179 (OUTLIER) cc_final: 0.6926 (t80) REVERT: B 322 MET cc_start: 0.7443 (ttt) cc_final: 0.6739 (ttt) REVERT: B 444 GLN cc_start: 0.6269 (pm20) cc_final: 0.5915 (mp10) REVERT: B 488 ARG cc_start: 0.6699 (mtm180) cc_final: 0.6273 (mtp180) REVERT: D 62 GLN cc_start: 0.5996 (mp10) cc_final: 0.5447 (mp10) REVERT: D 173 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6558 (t80) REVERT: C 32 MET cc_start: 0.4042 (OUTLIER) cc_final: 0.3159 (mpt) outliers start: 58 outliers final: 23 residues processed: 177 average time/residue: 0.3642 time to fit residues: 70.9637 Evaluate side-chains 136 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 162 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 38 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 238 GLN B 240 GLN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.192625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.167376 restraints weight = 13201.767| |-----------------------------------------------------------------------------| r_work (start): 0.4420 rms_B_bonded: 3.18 r_work: 0.4319 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8698 Z= 0.208 Angle : 0.661 13.216 11803 Z= 0.338 Chirality : 0.047 0.251 1286 Planarity : 0.005 0.054 1535 Dihedral : 6.098 58.327 1199 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 7.91 % Allowed : 24.60 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.25), residues: 1078 helix: -0.20 (0.51), residues: 92 sheet: -1.34 (0.30), residues: 297 loop : -1.07 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 117 TYR 0.019 0.002 TYR A 375 PHE 0.032 0.002 PHE A 131 TRP 0.016 0.002 TRP B 141 HIS 0.006 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 8689) covalent geometry : angle 0.66048 (11785) SS BOND : bond 0.00228 ( 9) SS BOND : angle 0.67942 ( 18) hydrogen bonds : bond 0.03771 ( 227) hydrogen bonds : angle 7.34057 ( 573) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 117 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 373 ASP cc_start: 0.8423 (t0) cc_final: 0.8163 (t0) REVERT: A 394 THR cc_start: 0.6899 (OUTLIER) cc_final: 0.6510 (p) REVERT: B 212 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5692 (tm-30) REVERT: B 238 GLN cc_start: 0.6764 (OUTLIER) cc_final: 0.5653 (mp10) REVERT: B 246 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.6891 (t80) REVERT: B 322 MET cc_start: 0.7545 (ttt) cc_final: 0.6795 (ttt) REVERT: B 444 GLN cc_start: 0.6473 (pm20) cc_final: 0.6127 (mp10) REVERT: B 488 ARG cc_start: 0.6752 (mtm180) cc_final: 0.6269 (mtp180) REVERT: D 62 GLN cc_start: 0.6077 (mp10) cc_final: 0.5446 (mp10) REVERT: D 173 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6693 (t80) REVERT: D 227 HIS cc_start: 0.3602 (OUTLIER) cc_final: 0.2889 (m-70) REVERT: C 32 MET cc_start: 0.4057 (OUTLIER) cc_final: 0.3189 (mpt) REVERT: C 98 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7044 (mp10) REVERT: C 194 GLN cc_start: 0.5976 (pm20) cc_final: 0.5762 (pm20) outliers start: 74 outliers final: 33 residues processed: 170 average time/residue: 0.3568 time to fit residues: 67.0646 Evaluate side-chains 144 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 103 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 162 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 106 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 68 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 7 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN B 321 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.194265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.168651 restraints weight = 13038.714| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 3.19 r_work: 0.4335 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8698 Z= 0.167 Angle : 0.640 13.311 11803 Z= 0.322 Chirality : 0.046 0.204 1286 Planarity : 0.004 0.053 1535 Dihedral : 6.034 59.974 1199 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 6.31 % Allowed : 26.63 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.25), residues: 1078 helix: -0.26 (0.51), residues: 92 sheet: -1.34 (0.29), residues: 307 loop : -1.04 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 391 TYR 0.022 0.002 TYR B 204 PHE 0.021 0.002 PHE A 443 TRP 0.014 0.002 TRP B 141 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8689) covalent geometry : angle 0.63978 (11785) SS BOND : bond 0.00157 ( 9) SS BOND : angle 0.56862 ( 18) hydrogen bonds : bond 0.03387 ( 227) hydrogen bonds : angle 7.09005 ( 573) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 109 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 394 THR cc_start: 0.6799 (OUTLIER) cc_final: 0.6402 (p) REVERT: B 116 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6985 (pttt) REVERT: B 212 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5699 (tm-30) REVERT: B 238 GLN cc_start: 0.6805 (OUTLIER) cc_final: 0.5952 (mp10) REVERT: B 246 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.6861 (t80) REVERT: B 444 GLN cc_start: 0.6513 (pm20) cc_final: 0.6068 (mp10) REVERT: B 488 ARG cc_start: 0.6726 (mtm180) cc_final: 0.5827 (mtp180) REVERT: D 62 GLN cc_start: 0.6134 (mp10) cc_final: 0.5489 (mp10) REVERT: D 173 PHE cc_start: 0.7187 (OUTLIER) cc_final: 0.6708 (t80) REVERT: D 227 HIS cc_start: 0.3556 (OUTLIER) cc_final: 0.2878 (m-70) REVERT: C 32 MET cc_start: 0.4064 (OUTLIER) cc_final: 0.3305 (mpt) REVERT: C 66 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.7081 (tp-100) REVERT: C 98 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7014 (mp10) REVERT: C 194 GLN cc_start: 0.5951 (pm20) cc_final: 0.5654 (pm20) outliers start: 59 outliers final: 28 residues processed: 154 average time/residue: 0.3743 time to fit residues: 63.2154 Evaluate side-chains 140 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 162 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 9 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 100 optimal weight: 0.3980 chunk 92 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 20 optimal weight: 0.0040 chunk 106 optimal weight: 10.0000 chunk 79 optimal weight: 0.0270 chunk 83 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.4450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 238 GLN B 240 GLN C 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.198126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.172949 restraints weight = 12910.823| |-----------------------------------------------------------------------------| r_work (start): 0.4469 rms_B_bonded: 3.18 r_work: 0.4369 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8698 Z= 0.138 Angle : 0.609 13.702 11803 Z= 0.305 Chirality : 0.045 0.203 1286 Planarity : 0.004 0.055 1535 Dihedral : 5.896 59.091 1199 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 6.95 % Allowed : 26.42 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.26), residues: 1078 helix: -0.19 (0.51), residues: 92 sheet: -1.30 (0.28), residues: 335 loop : -0.93 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 464 TYR 0.023 0.002 TYR B 204 PHE 0.020 0.002 PHE A 443 TRP 0.011 0.002 TRP B 141 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8689) covalent geometry : angle 0.60916 (11785) SS BOND : bond 0.00136 ( 9) SS BOND : angle 0.64539 ( 18) hydrogen bonds : bond 0.03080 ( 227) hydrogen bonds : angle 6.82184 ( 573) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 116 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7032 (tm-30) REVERT: A 394 THR cc_start: 0.6723 (OUTLIER) cc_final: 0.6308 (p) REVERT: A 444 LYS cc_start: 0.8206 (mtpt) cc_final: 0.7859 (mtpt) REVERT: B 135 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.4531 (pm20) REVERT: B 212 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.5645 (tm-30) REVERT: B 246 TYR cc_start: 0.7128 (OUTLIER) cc_final: 0.6738 (t80) REVERT: B 306 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7246 (mp) REVERT: B 321 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: B 322 MET cc_start: 0.7486 (ttt) cc_final: 0.7277 (ttt) REVERT: B 444 GLN cc_start: 0.6382 (pm20) cc_final: 0.5993 (mp10) REVERT: B 488 ARG cc_start: 0.6708 (mtm180) cc_final: 0.6147 (mtp180) REVERT: D 62 GLN cc_start: 0.5956 (mp10) cc_final: 0.5326 (mp10) REVERT: D 173 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6724 (t80) REVERT: D 227 HIS cc_start: 0.3697 (OUTLIER) cc_final: 0.2925 (m170) REVERT: C 66 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.7095 (tp-100) outliers start: 65 outliers final: 27 residues processed: 164 average time/residue: 0.3726 time to fit residues: 67.2297 Evaluate side-chains 141 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 191 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN B 252 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.194922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.169043 restraints weight = 13096.638| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 3.20 r_work: 0.4328 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8698 Z= 0.181 Angle : 0.648 14.053 11803 Z= 0.329 Chirality : 0.046 0.236 1286 Planarity : 0.004 0.056 1535 Dihedral : 6.074 59.615 1199 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 6.31 % Allowed : 27.81 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.25), residues: 1078 helix: -0.21 (0.52), residues: 92 sheet: -1.28 (0.29), residues: 312 loop : -1.05 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 117 TYR 0.024 0.002 TYR B 204 PHE 0.023 0.002 PHE B 60 TRP 0.012 0.002 TRP B 447 HIS 0.005 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 8689) covalent geometry : angle 0.64843 (11785) SS BOND : bond 0.00213 ( 9) SS BOND : angle 0.65026 ( 18) hydrogen bonds : bond 0.03341 ( 227) hydrogen bonds : angle 6.88823 ( 573) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 117 time to evaluate : 0.398 Fit side-chains REVERT: A 347 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7057 (tm-30) REVERT: A 394 THR cc_start: 0.6808 (OUTLIER) cc_final: 0.6374 (p) REVERT: A 444 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7574 (mtpt) REVERT: B 212 GLU cc_start: 0.5994 (OUTLIER) cc_final: 0.5726 (tm-30) REVERT: B 246 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.6872 (t80) REVERT: B 306 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7311 (mp) REVERT: B 322 MET cc_start: 0.7480 (ttt) cc_final: 0.7239 (ttt) REVERT: B 444 GLN cc_start: 0.6491 (pm20) cc_final: 0.6041 (mp10) REVERT: B 447 TRP cc_start: 0.7755 (p90) cc_final: 0.7289 (p90) REVERT: B 488 ARG cc_start: 0.6793 (mtm180) cc_final: 0.5998 (mtp180) REVERT: D 62 GLN cc_start: 0.5932 (mp10) cc_final: 0.5311 (mp10) REVERT: D 173 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6588 (t80) REVERT: C 66 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.7064 (tp-100) REVERT: C 98 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.6998 (mp10) outliers start: 59 outliers final: 33 residues processed: 165 average time/residue: 0.3590 time to fit residues: 65.5164 Evaluate side-chains 146 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 191 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 104 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 40 optimal weight: 0.0060 chunk 61 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN B 240 GLN C 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.196431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.171514 restraints weight = 12820.526| |-----------------------------------------------------------------------------| r_work (start): 0.4466 rms_B_bonded: 3.11 r_work: 0.4368 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8698 Z= 0.140 Angle : 0.644 14.263 11803 Z= 0.320 Chirality : 0.046 0.239 1286 Planarity : 0.004 0.057 1535 Dihedral : 5.949 58.197 1199 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 5.88 % Allowed : 28.88 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.26), residues: 1078 helix: -0.20 (0.52), residues: 92 sheet: -1.29 (0.28), residues: 337 loop : -0.94 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 391 TYR 0.025 0.002 TYR B 204 PHE 0.040 0.002 PHE A 187 TRP 0.011 0.002 TRP D 55 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8689) covalent geometry : angle 0.64419 (11785) SS BOND : bond 0.00108 ( 9) SS BOND : angle 0.55304 ( 18) hydrogen bonds : bond 0.03044 ( 227) hydrogen bonds : angle 6.70209 ( 573) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 119 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7145 (tm-30) REVERT: A 394 THR cc_start: 0.6747 (OUTLIER) cc_final: 0.6316 (p) REVERT: B 212 GLU cc_start: 0.5994 (OUTLIER) cc_final: 0.5626 (tm-30) REVERT: B 246 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6810 (t80) REVERT: B 306 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7337 (mp) REVERT: B 444 GLN cc_start: 0.6373 (pm20) cc_final: 0.6001 (mp10) REVERT: B 488 ARG cc_start: 0.6699 (mtm180) cc_final: 0.5921 (mtp180) REVERT: D 62 GLN cc_start: 0.5905 (mp10) cc_final: 0.5294 (mp10) REVERT: D 173 PHE cc_start: 0.7272 (OUTLIER) cc_final: 0.6592 (t80) REVERT: C 66 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.7063 (tp-100) REVERT: C 194 GLN cc_start: 0.6637 (pm20) cc_final: 0.6287 (pm20) outliers start: 55 outliers final: 33 residues processed: 159 average time/residue: 0.3628 time to fit residues: 63.4231 Evaluate side-chains 147 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 191 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 14 optimal weight: 0.0980 chunk 59 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.191063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.165589 restraints weight = 13069.623| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 3.11 r_work: 0.4326 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8698 Z= 0.191 Angle : 0.684 14.505 11803 Z= 0.345 Chirality : 0.047 0.264 1286 Planarity : 0.005 0.058 1535 Dihedral : 6.141 59.709 1199 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 5.13 % Allowed : 29.73 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.25), residues: 1078 helix: -0.16 (0.53), residues: 92 sheet: -1.30 (0.29), residues: 312 loop : -1.10 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.028 0.002 TYR B 204 PHE 0.055 0.003 PHE A 187 TRP 0.022 0.003 TRP D 126 HIS 0.005 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 8689) covalent geometry : angle 0.68381 (11785) SS BOND : bond 0.00208 ( 9) SS BOND : angle 0.76108 ( 18) hydrogen bonds : bond 0.03443 ( 227) hydrogen bonds : angle 6.81657 ( 573) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 112 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7108 (tm-30) REVERT: A 394 THR cc_start: 0.6777 (OUTLIER) cc_final: 0.6359 (p) REVERT: A 444 LYS cc_start: 0.8314 (mtpt) cc_final: 0.7833 (mtpt) REVERT: B 212 GLU cc_start: 0.5980 (OUTLIER) cc_final: 0.5720 (tm-30) REVERT: B 246 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.6802 (t80) REVERT: B 306 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7374 (mp) REVERT: B 444 GLN cc_start: 0.6542 (pm20) cc_final: 0.6120 (mp10) REVERT: B 488 ARG cc_start: 0.6767 (mtm180) cc_final: 0.5993 (mtp180) REVERT: D 62 GLN cc_start: 0.5898 (mp10) cc_final: 0.5410 (mp10) REVERT: D 173 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6563 (t80) REVERT: C 66 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.7084 (tp-100) outliers start: 48 outliers final: 35 residues processed: 148 average time/residue: 0.3543 time to fit residues: 57.8551 Evaluate side-chains 145 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 0.0570 chunk 72 optimal weight: 0.0010 chunk 52 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 56 optimal weight: 0.0030 chunk 30 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 overall best weight: 0.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN C 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.199857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.174899 restraints weight = 12905.229| |-----------------------------------------------------------------------------| r_work (start): 0.4506 rms_B_bonded: 3.15 r_work: 0.4403 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8698 Z= 0.123 Angle : 0.642 14.496 11803 Z= 0.320 Chirality : 0.045 0.255 1286 Planarity : 0.005 0.057 1535 Dihedral : 5.825 56.107 1199 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.60 % Allowed : 30.37 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.26), residues: 1078 helix: -0.19 (0.52), residues: 92 sheet: -1.16 (0.29), residues: 328 loop : -0.96 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.026 0.001 TYR B 204 PHE 0.041 0.002 PHE A 187 TRP 0.029 0.002 TRP D 126 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8689) covalent geometry : angle 0.64161 (11785) SS BOND : bond 0.00158 ( 9) SS BOND : angle 0.70237 ( 18) hydrogen bonds : bond 0.02915 ( 227) hydrogen bonds : angle 6.47854 ( 573) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7107 (tm-30) REVERT: A 394 THR cc_start: 0.6583 (OUTLIER) cc_final: 0.6176 (p) REVERT: B 212 GLU cc_start: 0.5949 (OUTLIER) cc_final: 0.5663 (tm-30) REVERT: B 246 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.6777 (t80) REVERT: B 352 ASP cc_start: 0.5574 (t0) cc_final: 0.5073 (p0) REVERT: B 444 GLN cc_start: 0.6252 (pm20) cc_final: 0.5900 (mp10) REVERT: B 488 ARG cc_start: 0.6780 (mtm180) cc_final: 0.6022 (mtp180) REVERT: D 62 GLN cc_start: 0.5717 (mp10) cc_final: 0.5202 (mp10) REVERT: D 117 ARG cc_start: 0.6283 (ttp-170) cc_final: 0.5980 (ttp80) REVERT: D 173 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6641 (t80) outliers start: 43 outliers final: 27 residues processed: 158 average time/residue: 0.3337 time to fit residues: 58.5172 Evaluate side-chains 145 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 162 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 75 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 81 optimal weight: 0.2980 chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN ** C 118 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 = 0.4715 r_free = 0.4715 target = 0.194033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.168266 restraints weight = 12934.401| |-----------------------------------------------------------------------------| r_work (start): 0.4451 rms_B_bonded: 3.18 r_work: 0.4344 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8698 Z= 0.173 Angle : 0.700 14.634 11803 Z= 0.351 Chirality : 0.047 0.259 1286 Planarity : 0.005 0.057 1535 Dihedral : 6.068 59.169 1199 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.85 % Allowed : 31.55 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.26), residues: 1078 helix: -0.10 (0.54), residues: 91 sheet: -1.23 (0.28), residues: 328 loop : -0.95 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.026 0.002 TYR B 204 PHE 0.052 0.002 PHE C 126 TRP 0.049 0.003 TRP D 126 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8689) covalent geometry : angle 0.69966 (11785) SS BOND : bond 0.00195 ( 9) SS BOND : angle 0.74433 ( 18) hydrogen bonds : bond 0.03287 ( 227) hydrogen bonds : angle 6.58304 ( 573) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3652.73 seconds wall clock time: 63 minutes 3.14 seconds (3783.14 seconds total)