Starting phenix.real_space_refine on Mon May 12 09:55:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fv6_50790/05_2025/9fv6_50790.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fv6_50790/05_2025/9fv6_50790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fv6_50790/05_2025/9fv6_50790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fv6_50790/05_2025/9fv6_50790.map" model { file = "/net/cci-nas-00/data/ceres_data/9fv6_50790/05_2025/9fv6_50790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fv6_50790/05_2025/9fv6_50790.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 54 5.16 5 C 5590 2.51 5 N 1536 2.21 5 O 1642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8822 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4411 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 13, 'TRANS': 555} Chain: "B" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4411 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 13, 'TRANS': 555} Time building chain proxies: 6.08, per 1000 atoms: 0.69 Number of scatterers: 8822 At special positions: 0 Unit cell: (116.96, 106.08, 134.64, 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 54 16.00 O 1642 8.00 N 1536 7.00 C 5590 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: 2.34 Conformation dependent library (CDL) restraints added in 1.0 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 4 sheets defined 69.0% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 Processing helix chain 'A' and resid 23 through 47 Processing helix chain 'A' and resid 47 through 54 removed outlier: 3.607A pdb=" N LEU A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 111 removed outlier: 3.871A pdb=" N TRP A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Proline residue: A 68 - end of helix removed outlier: 3.902A pdb=" N GLY A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 removed outlier: 4.447A pdb=" N PHE A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 129 removed outlier: 4.004A pdb=" N LEU A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 164 Processing helix chain 'A' and resid 164 through 213 removed outlier: 3.590A pdb=" N SER A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) Proline residue: A 176 - end of helix removed outlier: 3.918A pdb=" N THR A 199 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 223 through 250 Processing helix chain 'A' and resid 250 through 271 Processing helix chain 'A' and resid 282 through 324 removed outlier: 4.394A pdb=" N VAL A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 3.650A pdb=" N ASN A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASN A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.615A pdb=" N SER A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.579A pdb=" N ASP A 471 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 515 through 527 Processing helix chain 'A' and resid 538 through 545 Processing helix chain 'A' and resid 561 through 568 Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.935A pdb=" N ILE B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 47 Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 61 through 111 removed outlier: 3.592A pdb=" N MET B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 120 through 129 removed outlier: 3.748A pdb=" N LEU B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 164 removed outlier: 3.553A pdb=" N ALA B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 213 Proline residue: B 176 - end of helix removed outlier: 3.678A pdb=" N ASN B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 207 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 220 removed outlier: 4.103A pdb=" N ILE B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 272 removed outlier: 3.549A pdb=" N ARG B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 247 " --> pdb=" O LYS B 243 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 248 " --> pdb=" O MET B 244 " (cutoff:3.500A) Proline residue: B 253 - end of helix removed outlier: 3.554A pdb=" N SER B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 303 removed outlier: 4.155A pdb=" N ARG B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Proline residue: B 297 - end of helix removed outlier: 3.823A pdb=" N ASN B 303 " --> pdb=" O LYS B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 324 Processing helix chain 'B' and resid 381 through 390 removed outlier: 3.793A pdb=" N ILE B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.540A pdb=" N ASN B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 459 through 465 removed outlier: 3.854A pdb=" N ILE B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 472 removed outlier: 3.845A pdb=" N ASP B 471 " --> pdb=" O ASN B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 514 through 527 removed outlier: 3.943A pdb=" N ALA B 518 " --> pdb=" O GLU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 545 Processing helix chain 'B' and resid 561 through 568 Processing helix chain 'B' and resid 571 through 579 removed outlier: 3.834A pdb=" N MET B 578 " --> pdb=" O GLN B 574 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.517A pdb=" N GLU A 399 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL A 347 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU A 397 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 422 removed outlier: 6.677A pdb=" N LEU A 502 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR A 371 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL A 549 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL A 551 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 550 " --> pdb=" O GLU A 558 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU A 558 " --> pdb=" O VAL A 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 365 through 366 removed outlier: 3.853A pdb=" N VAL B 342 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE B 344 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU B 401 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASN B 346 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLU B 399 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 419 through 422 removed outlier: 6.346A pdb=" N ALA B 420 " --> pdb=" O ILE B 503 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU B 502 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE B 535 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU B 504 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 372 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR B 371 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL B 549 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ALA B 373 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL B 551 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL B 375 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE B 548 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG B 559 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B 550 " --> pdb=" O VAL B 557 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2928 1.35 - 1.47: 1943 1.47 - 1.59: 3975 1.59 - 1.71: 0 1.71 - 1.83: 104 Bond restraints: 8950 Sorted by residual: bond pdb=" N ARG A 148 " pdb=" CA ARG A 148 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.28e-02 6.10e+03 6.89e+00 bond pdb=" N PHE A 115 " pdb=" CA PHE A 115 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.76e+00 bond pdb=" N ASN A 303 " pdb=" CA ASN A 303 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.31e-02 5.83e+03 6.63e+00 bond pdb=" N MET A 159 " pdb=" CA MET A 159 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.80e+00 bond pdb=" C MET A 111 " pdb=" N PRO A 112 " ideal model delta sigma weight residual 1.331 1.360 -0.029 1.21e-02 6.83e+03 5.55e+00 ... (remaining 8945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 11754 2.33 - 4.66: 272 4.66 - 6.99: 51 6.99 - 9.32: 12 9.32 - 11.65: 3 Bond angle restraints: 12092 Sorted by residual: angle pdb=" CB MET B 456 " pdb=" CG MET B 456 " pdb=" SD MET B 456 " ideal model delta sigma weight residual 112.70 124.35 -11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" CA MET B 196 " pdb=" CB MET B 196 " pdb=" CG MET B 196 " ideal model delta sigma weight residual 114.10 121.65 -7.55 2.00e+00 2.50e-01 1.43e+01 angle pdb=" CA MET B 460 " pdb=" CB MET B 460 " pdb=" CG MET B 460 " ideal model delta sigma weight residual 114.10 121.63 -7.53 2.00e+00 2.50e-01 1.42e+01 angle pdb=" CB MET A 244 " pdb=" CG MET A 244 " pdb=" SD MET A 244 " ideal model delta sigma weight residual 112.70 123.05 -10.35 3.00e+00 1.11e-01 1.19e+01 angle pdb=" CA PRO A 273 " pdb=" N PRO A 273 " pdb=" CD PRO A 273 " ideal model delta sigma weight residual 112.00 107.52 4.48 1.40e+00 5.10e-01 1.02e+01 ... (remaining 12087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4808 17.91 - 35.82: 499 35.82 - 53.72: 119 53.72 - 71.63: 18 71.63 - 89.54: 10 Dihedral angle restraints: 5454 sinusoidal: 2164 harmonic: 3290 Sorted by residual: dihedral pdb=" CA MET B 276 " pdb=" C MET B 276 " pdb=" N ASP B 277 " pdb=" CA ASP B 277 " ideal model delta harmonic sigma weight residual 180.00 152.25 27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA GLN A 119 " pdb=" C GLN A 119 " pdb=" N SER A 120 " pdb=" CA SER A 120 " ideal model delta harmonic sigma weight residual 180.00 157.88 22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA VAL B 534 " pdb=" C VAL B 534 " pdb=" N ILE B 535 " pdb=" CA ILE B 535 " ideal model delta harmonic sigma weight residual 180.00 158.06 21.94 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 5451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1100 0.044 - 0.089: 262 0.089 - 0.133: 68 0.133 - 0.177: 8 0.177 - 0.221: 2 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CB ILE B 144 " pdb=" CA ILE B 144 " pdb=" CG1 ILE B 144 " pdb=" CG2 ILE B 144 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA MET A 159 " pdb=" N MET A 159 " pdb=" C MET A 159 " pdb=" CB MET A 159 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE B 170 " pdb=" CA ILE B 170 " pdb=" CG1 ILE B 170 " pdb=" CG2 ILE B 170 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 1437 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 272 " -0.061 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO A 273 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 273 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 273 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 17 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO B 18 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 18 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 18 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 287 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C VAL A 287 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL A 287 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 288 " 0.012 2.00e-02 2.50e+03 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 947 2.74 - 3.28: 9908 3.28 - 3.82: 15438 3.82 - 4.36: 17373 4.36 - 4.90: 28694 Nonbonded interactions: 72360 Sorted by model distance: nonbonded pdb=" O MET B 196 " pdb=" OG1 THR B 199 " model vdw 2.203 3.040 nonbonded pdb=" O ASP B 231 " pdb=" OG SER B 234 " model vdw 2.205 3.040 nonbonded pdb=" O MET A 196 " pdb=" OG1 THR A 199 " model vdw 2.213 3.040 nonbonded pdb=" O VAL A 286 " pdb=" OG SER A 289 " model vdw 2.235 3.040 nonbonded pdb=" NZ LYS A 212 " pdb=" OG1 THR B 121 " model vdw 2.236 3.120 ... (remaining 72355 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: 0.04 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 group one per residue 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: 5.720 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: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.920 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 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 : 0.005 0.094 8950 Z= 0.220 Angle : 0.891 11.645 12092 Z= 0.465 Chirality : 0.042 0.221 1440 Planarity : 0.006 0.091 1532 Dihedral : 15.830 89.538 3326 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.11 % Favored : 94.71 % Rotamer: Outliers : 0.31 % Allowed : 18.08 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1134 helix: 1.11 (0.19), residues: 716 sheet: 0.21 (0.83), residues: 32 loop : -0.99 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 17 HIS 0.007 0.001 HIS A 427 PHE 0.015 0.002 PHE A 429 TYR 0.017 0.001 TYR A 439 ARG 0.005 0.001 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.15212 ( 560) hydrogen bonds : angle 6.09752 ( 1662) covalent geometry : bond 0.00469 ( 8950) covalent geometry : angle 0.89057 (12092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9171 (tmm) cc_final: 0.8666 (tmm) REVERT: A 64 LEU cc_start: 0.9506 (tp) cc_final: 0.9291 (tp) REVERT: A 200 MET cc_start: 0.9338 (tpp) cc_final: 0.8863 (mmm) REVERT: A 244 MET cc_start: 0.8915 (tpp) cc_final: 0.8652 (tpp) REVERT: A 402 MET cc_start: 0.8535 (tmm) cc_final: 0.7866 (tmm) REVERT: A 460 MET cc_start: 0.8593 (tpp) cc_final: 0.8198 (mmm) REVERT: B 295 MET cc_start: 0.9353 (mmp) cc_final: 0.9123 (mmm) REVERT: B 402 MET cc_start: 0.8956 (tmm) cc_final: 0.7362 (tmm) outliers start: 3 outliers final: 0 residues processed: 82 average time/residue: 0.2272 time to fit residues: 25.9887 Evaluate side-chains 73 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.0040 chunk 45 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 GLN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.044027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.035317 restraints weight = 67874.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.036354 restraints weight = 38261.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.037069 restraints weight = 26104.256| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 8950 Z= 0.129 Angle : 0.596 10.104 12092 Z= 0.307 Chirality : 0.040 0.142 1440 Planarity : 0.005 0.087 1532 Dihedral : 4.257 22.033 1238 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.23 % Favored : 95.59 % Rotamer: Outliers : 1.34 % Allowed : 19.21 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1134 helix: 1.62 (0.19), residues: 734 sheet: 0.68 (0.89), residues: 32 loop : -0.99 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 91 HIS 0.005 0.001 HIS B 427 PHE 0.017 0.001 PHE B 429 TYR 0.011 0.001 TYR A 351 ARG 0.006 0.000 ARG B 569 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 560) hydrogen bonds : angle 4.59727 ( 1662) covalent geometry : bond 0.00268 ( 8950) covalent geometry : angle 0.59628 (12092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9100 (tmm) cc_final: 0.8617 (tmm) REVERT: A 45 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9054 (tp) REVERT: A 64 LEU cc_start: 0.9520 (tp) cc_final: 0.9205 (tp) REVERT: A 98 MET cc_start: 0.8870 (tpp) cc_final: 0.8320 (tpp) REVERT: A 196 MET cc_start: 0.9172 (tmm) cc_final: 0.7817 (tmm) REVERT: A 200 MET cc_start: 0.9335 (tpp) cc_final: 0.8955 (mmm) REVERT: A 210 MET cc_start: 0.8624 (tpp) cc_final: 0.8049 (tpp) REVERT: A 252 ASP cc_start: 0.9505 (m-30) cc_final: 0.9243 (t0) REVERT: A 402 MET cc_start: 0.8391 (tmm) cc_final: 0.7911 (tmm) REVERT: A 460 MET cc_start: 0.8676 (tpp) cc_final: 0.8432 (mmm) REVERT: B 210 MET cc_start: 0.8930 (mmm) cc_final: 0.8683 (tpp) REVERT: B 295 MET cc_start: 0.9302 (mmp) cc_final: 0.9027 (mmm) REVERT: B 402 MET cc_start: 0.8984 (tmm) cc_final: 0.7758 (tmm) REVERT: B 456 MET cc_start: 0.9305 (ttp) cc_final: 0.8566 (tpp) outliers start: 13 outliers final: 5 residues processed: 82 average time/residue: 0.2042 time to fit residues: 24.2636 Evaluate side-chains 75 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 534 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 46 optimal weight: 0.0470 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 52 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.044569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.035707 restraints weight = 69016.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.036712 restraints weight = 39904.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.037400 restraints weight = 27741.984| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 8950 Z= 0.115 Angle : 0.556 9.840 12092 Z= 0.286 Chirality : 0.039 0.139 1440 Planarity : 0.004 0.086 1532 Dihedral : 4.105 20.590 1238 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.79 % Favored : 96.03 % Rotamer: Outliers : 1.96 % Allowed : 19.52 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1134 helix: 1.71 (0.19), residues: 736 sheet: 3.80 (1.07), residues: 12 loop : -0.98 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 17 HIS 0.006 0.001 HIS A 568 PHE 0.013 0.001 PHE B 230 TYR 0.008 0.001 TYR A 572 ARG 0.005 0.000 ARG B 14 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 560) hydrogen bonds : angle 4.30716 ( 1662) covalent geometry : bond 0.00239 ( 8950) covalent geometry : angle 0.55583 (12092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9052 (tmm) cc_final: 0.8580 (tmm) REVERT: A 45 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9007 (tp) REVERT: A 98 MET cc_start: 0.8881 (tpp) cc_final: 0.8233 (tpp) REVERT: A 196 MET cc_start: 0.8905 (tmm) cc_final: 0.8052 (tmm) REVERT: A 200 MET cc_start: 0.9308 (tpp) cc_final: 0.8976 (mmm) REVERT: A 210 MET cc_start: 0.8490 (tpp) cc_final: 0.8216 (tpp) REVERT: A 252 ASP cc_start: 0.9466 (m-30) cc_final: 0.9258 (t70) REVERT: A 257 LEU cc_start: 0.9746 (tt) cc_final: 0.9486 (pp) REVERT: B 44 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8526 (tmm) REVERT: B 402 MET cc_start: 0.9080 (tmm) cc_final: 0.7592 (tmm) REVERT: B 456 MET cc_start: 0.9302 (ttp) cc_final: 0.8407 (tpp) REVERT: B 491 ILE cc_start: 0.9537 (OUTLIER) cc_final: 0.9302 (tt) outliers start: 19 outliers final: 6 residues processed: 91 average time/residue: 0.1856 time to fit residues: 24.9485 Evaluate side-chains 77 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 534 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.043245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.034513 restraints weight = 70245.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.035525 restraints weight = 40052.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.036237 restraints weight = 27396.805| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8950 Z= 0.148 Angle : 0.572 8.508 12092 Z= 0.295 Chirality : 0.040 0.177 1440 Planarity : 0.004 0.082 1532 Dihedral : 4.077 20.034 1238 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.97 % Favored : 95.86 % Rotamer: Outliers : 3.10 % Allowed : 19.01 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1134 helix: 1.89 (0.19), residues: 730 sheet: 1.19 (0.96), residues: 32 loop : -0.89 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 17 HIS 0.006 0.001 HIS A 568 PHE 0.015 0.001 PHE B 230 TYR 0.011 0.001 TYR B 268 ARG 0.005 0.000 ARG B 14 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 560) hydrogen bonds : angle 4.22417 ( 1662) covalent geometry : bond 0.00309 ( 8950) covalent geometry : angle 0.57175 (12092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9126 (tmm) cc_final: 0.8607 (tmm) REVERT: A 88 CYS cc_start: 0.9346 (OUTLIER) cc_final: 0.8775 (t) REVERT: A 98 MET cc_start: 0.8915 (tpp) cc_final: 0.8273 (tpp) REVERT: A 359 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9249 (tt) REVERT: A 402 MET cc_start: 0.8791 (ttm) cc_final: 0.8392 (tmm) REVERT: A 460 MET cc_start: 0.8721 (mmm) cc_final: 0.8421 (mmm) REVERT: B 88 CYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8812 (t) REVERT: B 236 ARG cc_start: 0.8940 (mmp80) cc_final: 0.8643 (tpp80) REVERT: B 402 MET cc_start: 0.9072 (tmm) cc_final: 0.7639 (tmm) REVERT: B 456 MET cc_start: 0.9390 (ttp) cc_final: 0.8713 (tpp) REVERT: B 491 ILE cc_start: 0.9573 (OUTLIER) cc_final: 0.9350 (tt) outliers start: 30 outliers final: 13 residues processed: 99 average time/residue: 0.2001 time to fit residues: 28.2742 Evaluate side-chains 87 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 534 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.042593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.033813 restraints weight = 70673.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.034807 restraints weight = 40708.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.035501 restraints weight = 28078.993| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 8950 Z= 0.178 Angle : 0.625 12.610 12092 Z= 0.315 Chirality : 0.040 0.158 1440 Planarity : 0.005 0.081 1532 Dihedral : 4.219 21.107 1238 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.06 % Favored : 95.77 % Rotamer: Outliers : 3.00 % Allowed : 21.28 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1134 helix: 1.82 (0.19), residues: 730 sheet: 1.17 (0.96), residues: 32 loop : -0.90 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 17 HIS 0.005 0.001 HIS A 568 PHE 0.016 0.002 PHE B 230 TYR 0.013 0.001 TYR B 268 ARG 0.005 0.000 ARG B 360 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 560) hydrogen bonds : angle 4.23169 ( 1662) covalent geometry : bond 0.00371 ( 8950) covalent geometry : angle 0.62486 (12092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9079 (tmm) cc_final: 0.8565 (tmm) REVERT: A 88 CYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8736 (t) REVERT: A 98 MET cc_start: 0.8877 (tpp) cc_final: 0.8240 (tpp) REVERT: A 210 MET cc_start: 0.8552 (tpp) cc_final: 0.8130 (tpp) REVERT: A 359 LEU cc_start: 0.9612 (tp) cc_final: 0.9236 (tt) REVERT: A 460 MET cc_start: 0.8714 (mmm) cc_final: 0.8405 (mmm) REVERT: B 44 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8648 (tmm) REVERT: B 291 MET cc_start: 0.9177 (tpp) cc_final: 0.8788 (tmm) REVERT: B 402 MET cc_start: 0.9112 (tmm) cc_final: 0.8584 (tmm) outliers start: 29 outliers final: 18 residues processed: 100 average time/residue: 0.2098 time to fit residues: 30.2183 Evaluate side-chains 90 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 534 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 86 optimal weight: 9.9990 chunk 51 optimal weight: 0.3980 chunk 55 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.043463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.034746 restraints weight = 69220.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.035750 restraints weight = 39736.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.036468 restraints weight = 27215.496| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 8950 Z= 0.117 Angle : 0.609 10.686 12092 Z= 0.299 Chirality : 0.039 0.143 1440 Planarity : 0.004 0.079 1532 Dihedral : 4.123 20.972 1238 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.62 % Favored : 96.21 % Rotamer: Outliers : 2.89 % Allowed : 21.90 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1134 helix: 1.85 (0.19), residues: 730 sheet: 1.46 (1.00), residues: 32 loop : -0.97 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 17 HIS 0.005 0.001 HIS A 568 PHE 0.012 0.001 PHE B 230 TYR 0.009 0.001 TYR A 351 ARG 0.008 0.000 ARG B 236 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 560) hydrogen bonds : angle 4.13076 ( 1662) covalent geometry : bond 0.00253 ( 8950) covalent geometry : angle 0.60941 (12092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9090 (tmm) cc_final: 0.8592 (tmm) REVERT: A 88 CYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8708 (t) REVERT: A 98 MET cc_start: 0.8900 (tpp) cc_final: 0.8237 (tpp) REVERT: A 210 MET cc_start: 0.8567 (tpp) cc_final: 0.8087 (tpp) REVERT: A 252 ASP cc_start: 0.9462 (m-30) cc_final: 0.9231 (t0) REVERT: A 295 MET cc_start: 0.8448 (ttt) cc_final: 0.8108 (tpp) REVERT: A 359 LEU cc_start: 0.9597 (tp) cc_final: 0.9242 (tt) REVERT: A 460 MET cc_start: 0.8780 (mmm) cc_final: 0.8458 (mmm) REVERT: B 88 CYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8749 (t) REVERT: B 210 MET cc_start: 0.8742 (tpp) cc_final: 0.8507 (tpp) REVERT: B 291 MET cc_start: 0.9217 (tpp) cc_final: 0.8962 (tmm) REVERT: B 402 MET cc_start: 0.9144 (tmm) cc_final: 0.8706 (tmm) REVERT: B 456 MET cc_start: 0.9296 (ttp) cc_final: 0.8884 (tmm) outliers start: 28 outliers final: 13 residues processed: 103 average time/residue: 0.2111 time to fit residues: 30.5806 Evaluate side-chains 87 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 534 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.043732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.034975 restraints weight = 70350.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.035987 restraints weight = 40175.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.036715 restraints weight = 27574.432| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 8950 Z= 0.117 Angle : 0.629 11.084 12092 Z= 0.306 Chirality : 0.040 0.206 1440 Planarity : 0.004 0.078 1532 Dihedral : 4.082 21.019 1238 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.79 % Favored : 96.03 % Rotamer: Outliers : 2.38 % Allowed : 22.83 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.26), residues: 1134 helix: 1.90 (0.19), residues: 730 sheet: 1.57 (1.01), residues: 32 loop : -0.95 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 17 HIS 0.005 0.001 HIS A 568 PHE 0.013 0.001 PHE B 230 TYR 0.008 0.001 TYR B 268 ARG 0.004 0.000 ARG B 236 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 560) hydrogen bonds : angle 4.09502 ( 1662) covalent geometry : bond 0.00255 ( 8950) covalent geometry : angle 0.62873 (12092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9090 (tmm) cc_final: 0.8783 (tmm) REVERT: A 88 CYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8712 (t) REVERT: A 98 MET cc_start: 0.8899 (tpp) cc_final: 0.8237 (tpp) REVERT: A 210 MET cc_start: 0.8514 (tpp) cc_final: 0.8050 (tpp) REVERT: A 252 ASP cc_start: 0.9466 (m-30) cc_final: 0.9219 (t0) REVERT: A 295 MET cc_start: 0.8451 (ttt) cc_final: 0.8094 (tpp) REVERT: A 359 LEU cc_start: 0.9582 (tp) cc_final: 0.9233 (tt) REVERT: A 460 MET cc_start: 0.8785 (mmm) cc_final: 0.8450 (mmm) REVERT: B 44 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8732 (tmm) REVERT: B 88 CYS cc_start: 0.9344 (OUTLIER) cc_final: 0.8802 (t) REVERT: B 291 MET cc_start: 0.9239 (tpp) cc_final: 0.8747 (tmm) REVERT: B 402 MET cc_start: 0.9124 (tmm) cc_final: 0.8715 (tmm) REVERT: B 456 MET cc_start: 0.9331 (ttp) cc_final: 0.8922 (tmm) outliers start: 23 outliers final: 15 residues processed: 95 average time/residue: 0.1751 time to fit residues: 24.9211 Evaluate side-chains 94 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 534 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 40 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 51 optimal weight: 0.0770 chunk 85 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 37 optimal weight: 0.0970 chunk 86 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.044542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.035539 restraints weight = 70764.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.036570 restraints weight = 41795.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.037299 restraints weight = 29208.865| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 8950 Z= 0.115 Angle : 0.638 12.276 12092 Z= 0.309 Chirality : 0.040 0.196 1440 Planarity : 0.004 0.077 1532 Dihedral : 4.030 20.673 1238 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.88 % Favored : 95.94 % Rotamer: Outliers : 1.96 % Allowed : 23.35 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1134 helix: 1.91 (0.19), residues: 730 sheet: 1.67 (1.03), residues: 32 loop : -1.01 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 17 HIS 0.005 0.001 HIS A 568 PHE 0.011 0.001 PHE B 230 TYR 0.007 0.001 TYR B 268 ARG 0.006 0.000 ARG B 441 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 560) hydrogen bonds : angle 4.06642 ( 1662) covalent geometry : bond 0.00249 ( 8950) covalent geometry : angle 0.63834 (12092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9063 (tmm) cc_final: 0.8753 (tmm) REVERT: A 88 CYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8687 (t) REVERT: A 98 MET cc_start: 0.8862 (tpp) cc_final: 0.8183 (tpp) REVERT: A 210 MET cc_start: 0.8496 (tpp) cc_final: 0.8048 (tpp) REVERT: A 252 ASP cc_start: 0.9426 (m-30) cc_final: 0.9177 (t0) REVERT: A 295 MET cc_start: 0.8435 (ttt) cc_final: 0.8109 (tpp) REVERT: A 359 LEU cc_start: 0.9576 (tp) cc_final: 0.9236 (tt) REVERT: A 418 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8524 (mm-40) REVERT: A 460 MET cc_start: 0.8788 (mmm) cc_final: 0.8439 (mmm) REVERT: B 44 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8694 (tmm) REVERT: B 88 CYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8742 (t) REVERT: B 291 MET cc_start: 0.9213 (tpp) cc_final: 0.8754 (tmm) REVERT: B 402 MET cc_start: 0.9122 (tmm) cc_final: 0.8717 (tmm) REVERT: B 456 MET cc_start: 0.9331 (ttp) cc_final: 0.8807 (tmm) outliers start: 19 outliers final: 13 residues processed: 97 average time/residue: 0.1706 time to fit residues: 25.0886 Evaluate side-chains 95 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 534 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.044341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.035432 restraints weight = 69909.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.036452 restraints weight = 41318.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.037148 restraints weight = 28904.221| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8950 Z= 0.118 Angle : 0.660 12.480 12092 Z= 0.316 Chirality : 0.040 0.204 1440 Planarity : 0.004 0.076 1532 Dihedral : 4.019 20.512 1238 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.06 % Favored : 95.77 % Rotamer: Outliers : 2.07 % Allowed : 23.45 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.26), residues: 1134 helix: 1.93 (0.19), residues: 730 sheet: 1.72 (1.05), residues: 32 loop : -1.01 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 17 HIS 0.005 0.001 HIS A 568 PHE 0.011 0.001 PHE B 230 TYR 0.008 0.001 TYR B 268 ARG 0.006 0.000 ARG B 441 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 560) hydrogen bonds : angle 4.07451 ( 1662) covalent geometry : bond 0.00260 ( 8950) covalent geometry : angle 0.66028 (12092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9065 (tmm) cc_final: 0.8760 (tmm) REVERT: A 64 LEU cc_start: 0.9529 (tp) cc_final: 0.9272 (tp) REVERT: A 88 CYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8731 (t) REVERT: A 98 MET cc_start: 0.8866 (tpp) cc_final: 0.8186 (tpp) REVERT: A 210 MET cc_start: 0.8494 (tpp) cc_final: 0.8077 (tpp) REVERT: A 252 ASP cc_start: 0.9435 (m-30) cc_final: 0.9179 (t0) REVERT: A 295 MET cc_start: 0.8416 (ttt) cc_final: 0.8085 (tpp) REVERT: A 359 LEU cc_start: 0.9578 (tp) cc_final: 0.9231 (tt) REVERT: A 456 MET cc_start: 0.9389 (ttp) cc_final: 0.8829 (tmm) REVERT: A 460 MET cc_start: 0.8794 (mmm) cc_final: 0.8445 (mmm) REVERT: B 88 CYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8737 (t) REVERT: B 291 MET cc_start: 0.9219 (tpp) cc_final: 0.8982 (tmm) REVERT: B 295 MET cc_start: 0.9143 (tpp) cc_final: 0.8706 (ttt) REVERT: B 402 MET cc_start: 0.9126 (tmm) cc_final: 0.8722 (tmm) outliers start: 20 outliers final: 14 residues processed: 98 average time/residue: 0.1763 time to fit residues: 25.8805 Evaluate side-chains 93 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 534 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.044237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.035407 restraints weight = 69732.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.036427 restraints weight = 40740.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.037148 restraints weight = 28330.471| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8950 Z= 0.118 Angle : 0.671 11.798 12092 Z= 0.317 Chirality : 0.040 0.187 1440 Planarity : 0.004 0.074 1532 Dihedral : 3.977 20.561 1238 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.97 % Favored : 95.86 % Rotamer: Outliers : 1.86 % Allowed : 23.45 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.26), residues: 1134 helix: 1.92 (0.19), residues: 732 sheet: 1.84 (1.06), residues: 32 loop : -0.99 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 17 HIS 0.005 0.001 HIS A 568 PHE 0.011 0.001 PHE B 230 TYR 0.009 0.001 TYR B 268 ARG 0.006 0.000 ARG B 441 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 560) hydrogen bonds : angle 4.07871 ( 1662) covalent geometry : bond 0.00261 ( 8950) covalent geometry : angle 0.67054 (12092) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9109 (tmm) cc_final: 0.8813 (tmm) REVERT: A 64 LEU cc_start: 0.9540 (tp) cc_final: 0.9280 (tp) REVERT: A 88 CYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8771 (t) REVERT: A 98 MET cc_start: 0.8895 (tpp) cc_final: 0.8212 (tpp) REVERT: A 210 MET cc_start: 0.8505 (tpp) cc_final: 0.8082 (tpp) REVERT: A 252 ASP cc_start: 0.9461 (m-30) cc_final: 0.9188 (t0) REVERT: A 295 MET cc_start: 0.8423 (ttt) cc_final: 0.8098 (tpp) REVERT: A 359 LEU cc_start: 0.9564 (tp) cc_final: 0.9223 (tt) REVERT: A 456 MET cc_start: 0.9420 (ttp) cc_final: 0.9163 (tmm) REVERT: A 460 MET cc_start: 0.8800 (mmm) cc_final: 0.8440 (mmm) REVERT: B 88 CYS cc_start: 0.9316 (OUTLIER) cc_final: 0.8726 (t) REVERT: B 291 MET cc_start: 0.9250 (tpp) cc_final: 0.9006 (tmm) REVERT: B 295 MET cc_start: 0.9168 (tpp) cc_final: 0.8710 (ttt) REVERT: B 402 MET cc_start: 0.9117 (tmm) cc_final: 0.8711 (tmm) REVERT: B 456 MET cc_start: 0.9405 (ttp) cc_final: 0.8994 (tmm) outliers start: 18 outliers final: 15 residues processed: 98 average time/residue: 0.1792 time to fit residues: 26.0924 Evaluate side-chains 96 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 534 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 0.6980 chunk 37 optimal weight: 0.0970 chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.044534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.035528 restraints weight = 70307.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.036558 restraints weight = 41748.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.037290 restraints weight = 29300.117| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8950 Z= 0.121 Angle : 0.671 11.460 12092 Z= 0.319 Chirality : 0.040 0.184 1440 Planarity : 0.004 0.073 1532 Dihedral : 3.970 20.408 1238 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.23 % Favored : 95.59 % Rotamer: Outliers : 1.76 % Allowed : 23.97 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.26), residues: 1134 helix: 1.92 (0.19), residues: 732 sheet: 1.98 (1.05), residues: 32 loop : -0.99 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 17 HIS 0.004 0.001 HIS A 568 PHE 0.011 0.001 PHE B 230 TYR 0.008 0.001 TYR B 268 ARG 0.006 0.000 ARG A 296 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 560) hydrogen bonds : angle 4.04212 ( 1662) covalent geometry : bond 0.00267 ( 8950) covalent geometry : angle 0.67067 (12092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2764.67 seconds wall clock time: 49 minutes 32.57 seconds (2972.57 seconds total)