Starting phenix.real_space_refine on Sun Apr 5 02:32:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u32_63808/04_2026/9u32_63808_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u32_63808/04_2026/9u32_63808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u32_63808/04_2026/9u32_63808_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u32_63808/04_2026/9u32_63808_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u32_63808/04_2026/9u32_63808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u32_63808/04_2026/9u32_63808.map" } resolution = 2.51 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= 0.130 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 30 5.16 5 C 4810 2.51 5 N 1110 2.21 5 O 1258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7208 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3557 Classifications: {'peptide': 473} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 450} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 2.55, per 1000 atoms: 0.35 Number of scatterers: 7208 At special positions: 0 Unit cell: (75.492, 101.588, 77.356, 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 30 16.00 O 1258 8.00 N 1110 7.00 C 4810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.61 Conformation dependent library (CDL) restraints added in 247.6 milliseconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 84.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 95 through 112 removed outlier: 4.056A pdb=" N GLY A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 139 Processing helix chain 'A' and resid 143 through 158 removed outlier: 3.613A pdb=" N ILE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 168 through 171 removed outlier: 3.548A pdb=" N THR A 171 " --> pdb=" O SER A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'A' and resid 172 through 192 removed outlier: 3.639A pdb=" N PHE A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 208 through 224 removed outlier: 3.864A pdb=" N LEU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.958A pdb=" N ARG A 259 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 280 removed outlier: 4.173A pdb=" N GLY A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 296 removed outlier: 3.584A pdb=" N LEU A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 312 through 331 removed outlier: 3.647A pdb=" N ALA A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 319 " --> pdb=" O PRO A 315 " (cutoff:3.500A) Proline residue: A 324 - end of helix removed outlier: 3.723A pdb=" N LYS A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 353 removed outlier: 3.539A pdb=" N LYS A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 382 through 397 Processing helix chain 'A' and resid 401 through 407 removed outlier: 3.613A pdb=" N CYS A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 431 removed outlier: 3.631A pdb=" N TRP A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 448 Processing helix chain 'A' and resid 451 through 456 Processing helix chain 'A' and resid 457 through 464 Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 472 through 491 removed outlier: 6.398A pdb=" N SER A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 509 removed outlier: 3.502A pdb=" N ALA A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 525 removed outlier: 3.519A pdb=" N ALA A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 560 removed outlier: 3.537A pdb=" N ILE A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A 555 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A 558 " --> pdb=" O THR A 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 112 removed outlier: 4.056A pdb=" N GLY B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 109 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 139 Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.613A pdb=" N ILE B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 168 through 171 removed outlier: 3.548A pdb=" N THR B 171 " --> pdb=" O SER B 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 168 through 171' Processing helix chain 'B' and resid 172 through 192 removed outlier: 3.639A pdb=" N PHE B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 199 through 206 Processing helix chain 'B' and resid 208 through 224 removed outlier: 3.865A pdb=" N LEU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 Processing helix chain 'B' and resid 237 through 248 Processing helix chain 'B' and resid 255 through 260 removed outlier: 3.958A pdb=" N ARG B 259 " --> pdb=" O SER B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 280 removed outlier: 4.173A pdb=" N GLY B 274 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 284 through 296 removed outlier: 3.584A pdb=" N LEU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 312 Processing helix chain 'B' and resid 312 through 331 removed outlier: 3.647A pdb=" N ALA B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 319 " --> pdb=" O PRO B 315 " (cutoff:3.500A) Proline residue: B 324 - end of helix removed outlier: 3.722A pdb=" N LYS B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 353 removed outlier: 3.539A pdb=" N LYS B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 375 Processing helix chain 'B' and resid 382 through 397 Processing helix chain 'B' and resid 401 through 407 removed outlier: 3.613A pdb=" N CYS B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 431 removed outlier: 3.631A pdb=" N TRP B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 448 Processing helix chain 'B' and resid 451 through 456 Processing helix chain 'B' and resid 457 through 464 Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 472 through 491 removed outlier: 6.398A pdb=" N SER B 482 " --> pdb=" O GLY B 478 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.502A pdb=" N ALA B 503 " --> pdb=" O ALA B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 525 removed outlier: 3.519A pdb=" N ALA B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 560 removed outlier: 3.536A pdb=" N ILE B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE B 555 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS B 558 " --> pdb=" O THR B 554 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1500 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: 0.87 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1084 1.27 - 1.41: 1853 1.41 - 1.54: 4310 1.54 - 1.68: 109 1.68 - 1.81: 48 Bond restraints: 7404 Sorted by residual: bond pdb=" C LYS A 536 " pdb=" O LYS A 536 " ideal model delta sigma weight residual 1.235 1.138 0.097 1.10e-02 8.26e+03 7.82e+01 bond pdb=" C LYS B 536 " pdb=" O LYS B 536 " ideal model delta sigma weight residual 1.235 1.138 0.097 1.10e-02 8.26e+03 7.82e+01 bond pdb=" CA ASN B 303 " pdb=" CB ASN B 303 " ideal model delta sigma weight residual 1.525 1.561 -0.036 8.30e-03 1.45e+04 1.89e+01 bond pdb=" C LYS B 536 " pdb=" N ILE B 537 " ideal model delta sigma weight residual 1.335 1.282 0.053 1.23e-02 6.61e+03 1.85e+01 bond pdb=" C LYS A 536 " pdb=" N ILE A 537 " ideal model delta sigma weight residual 1.335 1.282 0.053 1.23e-02 6.61e+03 1.84e+01 ... (remaining 7399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 9930 2.78 - 5.55: 166 5.55 - 8.33: 34 8.33 - 11.11: 2 11.11 - 13.88: 2 Bond angle restraints: 10134 Sorted by residual: angle pdb=" C ASN A 303 " pdb=" CA ASN A 303 " pdb=" CB ASN A 303 " ideal model delta sigma weight residual 111.20 119.03 -7.83 7.10e-01 1.98e+00 1.21e+02 angle pdb=" C ASN B 303 " pdb=" CA ASN B 303 " pdb=" CB ASN B 303 " ideal model delta sigma weight residual 111.20 119.02 -7.82 7.10e-01 1.98e+00 1.21e+02 angle pdb=" C GLU B 601 " pdb=" CA GLU B 601 " pdb=" CB GLU B 601 " ideal model delta sigma weight residual 110.10 123.98 -13.88 1.90e+00 2.77e-01 5.34e+01 angle pdb=" C GLU A 601 " pdb=" CA GLU A 601 " pdb=" CB GLU A 601 " ideal model delta sigma weight residual 110.10 123.94 -13.84 1.90e+00 2.77e-01 5.31e+01 angle pdb=" C SER A 302 " pdb=" N ASN A 303 " pdb=" CA ASN A 303 " ideal model delta sigma weight residual 124.21 130.69 -6.48 1.21e+00 6.83e-01 2.87e+01 ... (remaining 10129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 3940 17.44 - 34.88: 324 34.88 - 52.32: 46 52.32 - 69.76: 20 69.76 - 87.20: 8 Dihedral angle restraints: 4338 sinusoidal: 1640 harmonic: 2698 Sorted by residual: dihedral pdb=" CA ASN B 303 " pdb=" C ASN B 303 " pdb=" N PRO B 304 " pdb=" CA PRO B 304 " ideal model delta harmonic sigma weight residual 180.00 -153.98 -26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA ASN A 303 " pdb=" C ASN A 303 " pdb=" N PRO A 304 " pdb=" CA PRO A 304 " ideal model delta harmonic sigma weight residual -180.00 -154.03 -25.97 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ALA A 198 " pdb=" C ALA A 198 " pdb=" N THR A 199 " pdb=" CA THR A 199 " ideal model delta harmonic sigma weight residual 180.00 155.98 24.02 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 4335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 940 0.053 - 0.105: 215 0.105 - 0.158: 51 0.158 - 0.211: 6 0.211 - 0.263: 4 Chirality restraints: 1216 Sorted by residual: chirality pdb=" CA ASN B 303 " pdb=" N ASN B 303 " pdb=" C ASN B 303 " pdb=" CB ASN B 303 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ASN A 303 " pdb=" N ASN A 303 " pdb=" C ASN A 303 " pdb=" CB ASN A 303 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CBB Y01 B 602 " pdb=" CAC Y01 B 602 " pdb=" CAO Y01 B 602 " pdb=" CBE Y01 B 602 " both_signs ideal model delta sigma weight residual False 2.58 2.36 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1213 not shown) Planarity restraints: 1212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 142 " -0.046 5.00e-02 4.00e+02 6.87e-02 7.54e+00 pdb=" N PRO B 143 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 143 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 143 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 142 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO A 143 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 143 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 143 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 239 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO B 240 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 240 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 240 " 0.037 5.00e-02 4.00e+02 ... (remaining 1209 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2367 2.83 - 3.34: 6698 3.34 - 3.86: 12781 3.86 - 4.38: 15723 4.38 - 4.90: 25388 Nonbonded interactions: 62957 Sorted by model distance: nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 199 " model vdw 2.307 3.040 nonbonded pdb=" O ASP A 195 " pdb=" OG1 THR A 199 " model vdw 2.308 3.040 nonbonded pdb=" OH TYR A 214 " pdb=" O LEU A 321 " model vdw 2.314 3.040 nonbonded pdb=" OH TYR B 214 " pdb=" O LEU B 321 " model vdw 2.314 3.040 nonbonded pdb=" O GLY A 550 " pdb=" OG1 THR A 554 " model vdw 2.343 3.040 ... (remaining 62952 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.510 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 : 0.006 0.097 7404 Z= 0.340 Angle : 0.897 13.883 10134 Z= 0.526 Chirality : 0.050 0.263 1216 Planarity : 0.008 0.069 1212 Dihedral : 13.776 87.203 2610 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.99 (0.16), residues: 942 helix: -4.04 (0.08), residues: 744 sheet: None (None), residues: 0 loop : -2.27 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 259 TYR 0.011 0.002 TYR B 331 PHE 0.020 0.003 PHE B 238 TRP 0.020 0.002 TRP A 417 HIS 0.005 0.002 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00591 ( 7404) covalent geometry : angle 0.89670 (10134) hydrogen bonds : bond 0.28133 ( 508) hydrogen bonds : angle 10.87917 ( 1500) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.210 Fit side-chains REVERT: A 131 LEU cc_start: 0.8344 (tp) cc_final: 0.7931 (mp) REVERT: A 195 ASP cc_start: 0.7096 (t70) cc_final: 0.6829 (t70) REVERT: A 350 LYS cc_start: 0.7545 (mtmt) cc_final: 0.7325 (mttt) REVERT: A 351 GLN cc_start: 0.6943 (mt0) cc_final: 0.6717 (tm-30) REVERT: B 131 LEU cc_start: 0.8371 (tp) cc_final: 0.7958 (mp) REVERT: B 195 ASP cc_start: 0.7111 (t70) cc_final: 0.6854 (t70) REVERT: B 350 LYS cc_start: 0.7537 (mtmt) cc_final: 0.7303 (mttt) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.4602 time to fit residues: 44.1500 Evaluate side-chains 60 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN B 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.144462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.124182 restraints weight = 7575.502| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.20 r_work: 0.3265 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7404 Z= 0.148 Angle : 0.622 7.652 10134 Z= 0.323 Chirality : 0.041 0.163 1216 Planarity : 0.006 0.046 1212 Dihedral : 9.342 56.626 1126 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.73 % Allowed : 6.93 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.24), residues: 942 helix: -1.11 (0.15), residues: 766 sheet: None (None), residues: 0 loop : -1.41 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 196 TYR 0.011 0.001 TYR B 331 PHE 0.034 0.002 PHE A 509 TRP 0.018 0.002 TRP B 417 HIS 0.005 0.002 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7404) covalent geometry : angle 0.62170 (10134) hydrogen bonds : bond 0.04885 ( 508) hydrogen bonds : angle 5.19198 ( 1500) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.248 Fit side-chains REVERT: A 195 ASP cc_start: 0.7540 (t70) cc_final: 0.7292 (t70) REVERT: A 350 LYS cc_start: 0.7663 (mtmt) cc_final: 0.7357 (mttm) REVERT: A 351 GLN cc_start: 0.6934 (mt0) cc_final: 0.6341 (tm-30) REVERT: B 131 LEU cc_start: 0.8676 (tp) cc_final: 0.8164 (mp) REVERT: B 195 ASP cc_start: 0.7504 (t70) cc_final: 0.7259 (t70) REVERT: B 350 LYS cc_start: 0.7686 (mtmt) cc_final: 0.7372 (mttm) REVERT: B 351 GLN cc_start: 0.7058 (mt0) cc_final: 0.6446 (tm-30) REVERT: B 437 MET cc_start: 0.7993 (mtm) cc_final: 0.7758 (mtm) outliers start: 13 outliers final: 4 residues processed: 85 average time/residue: 0.3767 time to fit residues: 34.6024 Evaluate side-chains 74 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 509 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 34 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.143379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.122891 restraints weight = 7563.749| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.20 r_work: 0.3230 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7404 Z= 0.153 Angle : 0.596 7.196 10134 Z= 0.307 Chirality : 0.042 0.157 1216 Planarity : 0.005 0.037 1212 Dihedral : 9.177 57.847 1126 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.00 % Allowed : 8.40 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.27), residues: 942 helix: 0.24 (0.18), residues: 770 sheet: None (None), residues: 0 loop : -0.71 (0.50), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 196 TYR 0.010 0.001 TYR A 331 PHE 0.035 0.002 PHE A 509 TRP 0.018 0.002 TRP A 452 HIS 0.004 0.002 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7404) covalent geometry : angle 0.59608 (10134) hydrogen bonds : bond 0.04333 ( 508) hydrogen bonds : angle 4.72435 ( 1500) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.209 Fit side-chains REVERT: A 195 ASP cc_start: 0.7563 (t70) cc_final: 0.7319 (t70) REVERT: A 350 LYS cc_start: 0.7771 (mtmt) cc_final: 0.7480 (mttm) REVERT: A 351 GLN cc_start: 0.6977 (mt0) cc_final: 0.6436 (tm-30) REVERT: A 437 MET cc_start: 0.8061 (mtm) cc_final: 0.7796 (mtm) REVERT: A 446 GLN cc_start: 0.7674 (tt0) cc_final: 0.7237 (mm-40) REVERT: A 482 SER cc_start: 0.7816 (OUTLIER) cc_final: 0.7349 (m) REVERT: B 195 ASP cc_start: 0.7583 (t70) cc_final: 0.7359 (t70) REVERT: B 350 LYS cc_start: 0.7659 (mtmt) cc_final: 0.7361 (mttm) REVERT: B 351 GLN cc_start: 0.6978 (mt0) cc_final: 0.6424 (tm-30) REVERT: B 443 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7375 (mttp) REVERT: B 482 SER cc_start: 0.7703 (OUTLIER) cc_final: 0.7242 (m) outliers start: 15 outliers final: 6 residues processed: 78 average time/residue: 0.4238 time to fit residues: 35.5035 Evaluate side-chains 78 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 443 LYS Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 509 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 52 optimal weight: 0.4980 chunk 40 optimal weight: 0.3980 chunk 93 optimal weight: 0.5980 chunk 91 optimal weight: 0.0370 chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.145944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.125664 restraints weight = 7714.417| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.20 r_work: 0.3283 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7404 Z= 0.111 Angle : 0.541 6.975 10134 Z= 0.276 Chirality : 0.039 0.148 1216 Planarity : 0.004 0.034 1212 Dihedral : 9.254 59.454 1126 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.93 % Allowed : 10.13 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.28), residues: 942 helix: 1.04 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -0.43 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 196 TYR 0.008 0.001 TYR A 264 PHE 0.033 0.002 PHE A 509 TRP 0.019 0.001 TRP B 417 HIS 0.003 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 7404) covalent geometry : angle 0.54128 (10134) hydrogen bonds : bond 0.03510 ( 508) hydrogen bonds : angle 4.45062 ( 1500) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.268 Fit side-chains REVERT: A 195 ASP cc_start: 0.7491 (t70) cc_final: 0.7276 (t70) REVERT: A 351 GLN cc_start: 0.6951 (mt0) cc_final: 0.6419 (tm-30) REVERT: A 446 GLN cc_start: 0.7665 (tt0) cc_final: 0.7211 (mm-40) REVERT: B 195 ASP cc_start: 0.7532 (t70) cc_final: 0.7326 (t70) REVERT: B 350 LYS cc_start: 0.7749 (mtmt) cc_final: 0.7535 (mttm) REVERT: B 351 GLN cc_start: 0.6971 (mt0) cc_final: 0.6411 (tm-30) REVERT: B 437 MET cc_start: 0.7954 (mtm) cc_final: 0.7658 (mtm) REVERT: B 446 GLN cc_start: 0.7701 (tt0) cc_final: 0.7255 (mm-40) outliers start: 7 outliers final: 0 residues processed: 84 average time/residue: 0.4050 time to fit residues: 36.6784 Evaluate side-chains 69 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 6 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.124329 restraints weight = 7590.537| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.21 r_work: 0.3258 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7404 Z= 0.132 Angle : 0.564 7.266 10134 Z= 0.287 Chirality : 0.041 0.157 1216 Planarity : 0.004 0.033 1212 Dihedral : 9.194 59.961 1126 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.33 % Allowed : 9.60 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.28), residues: 942 helix: 1.19 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -0.17 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 196 TYR 0.006 0.001 TYR B 523 PHE 0.018 0.002 PHE A 238 TRP 0.020 0.002 TRP A 417 HIS 0.004 0.002 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7404) covalent geometry : angle 0.56438 (10134) hydrogen bonds : bond 0.03768 ( 508) hydrogen bonds : angle 4.43520 ( 1500) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.267 Fit side-chains REVERT: A 195 ASP cc_start: 0.7505 (t70) cc_final: 0.7295 (t70) REVERT: A 351 GLN cc_start: 0.6975 (mt0) cc_final: 0.6404 (tm-30) REVERT: A 446 GLN cc_start: 0.7643 (tt0) cc_final: 0.7195 (mm-40) REVERT: A 482 SER cc_start: 0.7807 (OUTLIER) cc_final: 0.7453 (m) REVERT: B 195 ASP cc_start: 0.7527 (t70) cc_final: 0.7316 (t70) REVERT: B 351 GLN cc_start: 0.6972 (mt0) cc_final: 0.6431 (tm-30) REVERT: B 446 GLN cc_start: 0.7640 (tt0) cc_final: 0.7204 (mm-40) REVERT: B 482 SER cc_start: 0.7805 (OUTLIER) cc_final: 0.7442 (m) outliers start: 10 outliers final: 4 residues processed: 78 average time/residue: 0.3892 time to fit residues: 32.8735 Evaluate side-chains 78 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 509 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 16 optimal weight: 0.0470 chunk 81 optimal weight: 0.8980 chunk 21 optimal weight: 0.0980 chunk 38 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.0050 chunk 92 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 0.3092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.148068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.129245 restraints weight = 7554.079| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.13 r_work: 0.3315 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7404 Z= 0.106 Angle : 0.532 6.398 10134 Z= 0.270 Chirality : 0.039 0.141 1216 Planarity : 0.004 0.032 1212 Dihedral : 9.188 58.733 1126 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.33 % Allowed : 9.87 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.28), residues: 942 helix: 1.51 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -0.08 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 196 TYR 0.006 0.001 TYR A 264 PHE 0.016 0.001 PHE A 238 TRP 0.021 0.001 TRP A 417 HIS 0.002 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 7404) covalent geometry : angle 0.53233 (10134) hydrogen bonds : bond 0.03324 ( 508) hydrogen bonds : angle 4.27232 ( 1500) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.155 Fit side-chains REVERT: A 195 ASP cc_start: 0.7411 (t70) cc_final: 0.7207 (t70) REVERT: A 291 LEU cc_start: 0.8092 (tp) cc_final: 0.7864 (tp) REVERT: A 351 GLN cc_start: 0.6921 (mt0) cc_final: 0.6437 (tm-30) REVERT: A 446 GLN cc_start: 0.7631 (tt0) cc_final: 0.7223 (mm-40) REVERT: A 482 SER cc_start: 0.7728 (OUTLIER) cc_final: 0.7513 (m) REVERT: B 291 LEU cc_start: 0.8102 (tp) cc_final: 0.7880 (tp) REVERT: B 351 GLN cc_start: 0.6932 (mt0) cc_final: 0.6415 (tm-30) REVERT: B 437 MET cc_start: 0.7941 (mtm) cc_final: 0.7647 (mtm) REVERT: B 446 GLN cc_start: 0.7645 (tt0) cc_final: 0.7246 (mm-40) REVERT: B 482 SER cc_start: 0.7718 (OUTLIER) cc_final: 0.7489 (m) outliers start: 10 outliers final: 8 residues processed: 84 average time/residue: 0.3692 time to fit residues: 33.6545 Evaluate side-chains 85 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 509 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 82 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.144133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.123821 restraints weight = 7579.985| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.20 r_work: 0.3253 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7404 Z= 0.145 Angle : 0.581 7.296 10134 Z= 0.295 Chirality : 0.041 0.158 1216 Planarity : 0.004 0.033 1212 Dihedral : 9.107 59.265 1126 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.47 % Allowed : 10.53 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.28), residues: 942 helix: 1.42 (0.19), residues: 774 sheet: None (None), residues: 0 loop : 0.09 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 196 TYR 0.007 0.001 TYR B 523 PHE 0.019 0.002 PHE B 238 TRP 0.022 0.002 TRP A 417 HIS 0.004 0.002 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 7404) covalent geometry : angle 0.58143 (10134) hydrogen bonds : bond 0.03821 ( 508) hydrogen bonds : angle 4.37466 ( 1500) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.285 Fit side-chains REVERT: A 195 ASP cc_start: 0.7459 (t70) cc_final: 0.7255 (t70) REVERT: A 291 LEU cc_start: 0.8152 (tp) cc_final: 0.7950 (tp) REVERT: A 351 GLN cc_start: 0.6944 (mt0) cc_final: 0.6393 (tm-30) REVERT: A 446 GLN cc_start: 0.7657 (tt0) cc_final: 0.7245 (mm-40) REVERT: A 482 SER cc_start: 0.7804 (OUTLIER) cc_final: 0.7479 (m) REVERT: B 291 LEU cc_start: 0.8156 (tp) cc_final: 0.7956 (tp) REVERT: B 351 GLN cc_start: 0.6967 (mt0) cc_final: 0.6411 (tm-30) REVERT: B 446 GLN cc_start: 0.7634 (tt0) cc_final: 0.7228 (mm-40) REVERT: B 482 SER cc_start: 0.7805 (OUTLIER) cc_final: 0.7472 (m) outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 0.3787 time to fit residues: 35.0137 Evaluate side-chains 86 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 509 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 3 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.143956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.123543 restraints weight = 7650.351| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.21 r_work: 0.3253 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7404 Z= 0.136 Angle : 0.577 7.124 10134 Z= 0.292 Chirality : 0.041 0.148 1216 Planarity : 0.004 0.032 1212 Dihedral : 9.116 59.984 1126 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.33 % Allowed : 11.20 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.28), residues: 942 helix: 1.47 (0.19), residues: 774 sheet: None (None), residues: 0 loop : 0.09 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 196 TYR 0.015 0.001 TYR A 563 PHE 0.018 0.002 PHE A 238 TRP 0.020 0.002 TRP A 417 HIS 0.004 0.002 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7404) covalent geometry : angle 0.57701 (10134) hydrogen bonds : bond 0.03724 ( 508) hydrogen bonds : angle 4.37797 ( 1500) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.221 Fit side-chains REVERT: A 195 ASP cc_start: 0.7460 (t70) cc_final: 0.7249 (t70) REVERT: A 351 GLN cc_start: 0.6942 (mt0) cc_final: 0.6380 (tm-30) REVERT: A 443 LYS cc_start: 0.7644 (mttp) cc_final: 0.7311 (mttm) REVERT: A 446 GLN cc_start: 0.7640 (tt0) cc_final: 0.7237 (mm-40) REVERT: A 482 SER cc_start: 0.7784 (OUTLIER) cc_final: 0.7470 (m) REVERT: B 330 LEU cc_start: 0.7491 (mt) cc_final: 0.7158 (mt) REVERT: B 351 GLN cc_start: 0.6970 (mt0) cc_final: 0.6399 (tm-30) REVERT: B 446 GLN cc_start: 0.7643 (tt0) cc_final: 0.7242 (mm-40) REVERT: B 482 SER cc_start: 0.7787 (OUTLIER) cc_final: 0.7467 (m) outliers start: 10 outliers final: 6 residues processed: 77 average time/residue: 0.3896 time to fit residues: 32.4715 Evaluate side-chains 77 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 509 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 58 optimal weight: 0.0980 chunk 53 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.145045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.124734 restraints weight = 7485.394| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.19 r_work: 0.3256 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7404 Z= 0.128 Angle : 0.574 7.841 10134 Z= 0.289 Chirality : 0.040 0.147 1216 Planarity : 0.004 0.033 1212 Dihedral : 9.078 59.979 1126 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.33 % Allowed : 10.67 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.28), residues: 942 helix: 1.53 (0.19), residues: 774 sheet: None (None), residues: 0 loop : 0.11 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 196 TYR 0.013 0.001 TYR A 563 PHE 0.018 0.002 PHE A 238 TRP 0.022 0.002 TRP A 452 HIS 0.004 0.002 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7404) covalent geometry : angle 0.57397 (10134) hydrogen bonds : bond 0.03621 ( 508) hydrogen bonds : angle 4.35305 ( 1500) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.256 Fit side-chains REVERT: A 351 GLN cc_start: 0.6939 (mt0) cc_final: 0.6383 (tm-30) REVERT: A 443 LYS cc_start: 0.7635 (mttp) cc_final: 0.7309 (mttm) REVERT: A 446 GLN cc_start: 0.7616 (tt0) cc_final: 0.7231 (mm-40) REVERT: A 482 SER cc_start: 0.7767 (OUTLIER) cc_final: 0.7472 (m) REVERT: B 330 LEU cc_start: 0.7453 (mt) cc_final: 0.7130 (mt) REVERT: B 351 GLN cc_start: 0.6972 (mt0) cc_final: 0.6437 (tm-30) REVERT: B 443 LYS cc_start: 0.7668 (mttp) cc_final: 0.7335 (mttm) REVERT: B 446 GLN cc_start: 0.7623 (tt0) cc_final: 0.7235 (mm-40) REVERT: B 482 SER cc_start: 0.7773 (OUTLIER) cc_final: 0.7480 (m) outliers start: 10 outliers final: 5 residues processed: 80 average time/residue: 0.3712 time to fit residues: 32.2409 Evaluate side-chains 78 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 509 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 83 optimal weight: 0.0570 chunk 77 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 76 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.124584 restraints weight = 7560.821| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.20 r_work: 0.3261 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7404 Z= 0.124 Angle : 0.573 8.192 10134 Z= 0.288 Chirality : 0.040 0.146 1216 Planarity : 0.004 0.035 1212 Dihedral : 9.049 59.974 1126 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.93 % Allowed : 11.33 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.28), residues: 942 helix: 1.58 (0.19), residues: 774 sheet: None (None), residues: 0 loop : 0.13 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 196 TYR 0.013 0.001 TYR A 563 PHE 0.018 0.002 PHE B 238 TRP 0.023 0.002 TRP A 452 HIS 0.004 0.002 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7404) covalent geometry : angle 0.57323 (10134) hydrogen bonds : bond 0.03575 ( 508) hydrogen bonds : angle 4.33934 ( 1500) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.267 Fit side-chains REVERT: A 104 SER cc_start: 0.8894 (m) cc_final: 0.8656 (m) REVERT: A 330 LEU cc_start: 0.7464 (mt) cc_final: 0.7101 (mt) REVERT: A 351 GLN cc_start: 0.6940 (mt0) cc_final: 0.6386 (tm-30) REVERT: A 443 LYS cc_start: 0.7632 (mttp) cc_final: 0.7310 (mttm) REVERT: A 446 GLN cc_start: 0.7640 (tt0) cc_final: 0.7251 (mm-40) REVERT: A 482 SER cc_start: 0.7760 (OUTLIER) cc_final: 0.7482 (m) REVERT: B 104 SER cc_start: 0.8895 (m) cc_final: 0.8656 (m) REVERT: B 330 LEU cc_start: 0.7459 (mt) cc_final: 0.7156 (mt) REVERT: B 351 GLN cc_start: 0.6965 (mt0) cc_final: 0.6445 (tm-30) REVERT: B 443 LYS cc_start: 0.7677 (mttp) cc_final: 0.7351 (mttm) REVERT: B 446 GLN cc_start: 0.7653 (tt0) cc_final: 0.7272 (mm-40) REVERT: B 482 SER cc_start: 0.7762 (OUTLIER) cc_final: 0.7485 (m) outliers start: 7 outliers final: 4 residues processed: 76 average time/residue: 0.3939 time to fit residues: 32.3346 Evaluate side-chains 78 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 509 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 69 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 0.0050 chunk 87 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.145319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.124883 restraints weight = 7629.726| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.20 r_work: 0.3258 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7404 Z= 0.122 Angle : 0.570 8.209 10134 Z= 0.287 Chirality : 0.040 0.146 1216 Planarity : 0.004 0.037 1212 Dihedral : 9.014 59.663 1126 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.80 % Allowed : 11.87 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.28), residues: 942 helix: 1.61 (0.19), residues: 774 sheet: None (None), residues: 0 loop : 0.14 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 196 TYR 0.013 0.001 TYR A 563 PHE 0.018 0.001 PHE B 238 TRP 0.023 0.002 TRP A 452 HIS 0.003 0.002 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7404) covalent geometry : angle 0.57019 (10134) hydrogen bonds : bond 0.03538 ( 508) hydrogen bonds : angle 4.32106 ( 1500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2036.78 seconds wall clock time: 35 minutes 32.84 seconds (2132.84 seconds total)