Starting phenix.real_space_refine on Mon Jul 28 02:56:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ch1_30368/07_2025/7ch1_30368.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ch1_30368/07_2025/7ch1_30368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ch1_30368/07_2025/7ch1_30368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ch1_30368/07_2025/7ch1_30368.map" model { file = "/net/cci-nas-00/data/ceres_data/7ch1_30368/07_2025/7ch1_30368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ch1_30368/07_2025/7ch1_30368.cif" } resolution = 2.6 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= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians S 66 5.16 5 Cl 4 4.86 5 Na 2 4.78 5 C 6502 2.51 5 N 1576 2.21 5 O 1798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9948 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 4933 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 28, 'TRANS': 611} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Restraints were copied for chains: B Time building chain proxies: 9.60, per 1000 atoms: 0.97 Number of scatterers: 9948 At special positions: 0 Unit cell: (103.645, 118.919, 111.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 66 16.00 Na 2 11.00 O 1798 8.00 N 1576 7.00 C 6502 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: 2.35 Conformation dependent library (CDL) restraints added in 1.3 seconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2372 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 7 sheets defined 65.9% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 3.743A pdb=" N ASP A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 66 through 96 removed outlier: 6.185A pdb=" N ILE A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Proline residue: A 73 - end of helix removed outlier: 3.971A pdb=" N ILE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Proline residue: A 87 - end of helix removed outlier: 3.505A pdb=" N LEU A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 109 through 118 removed outlier: 4.126A pdb=" N THR A 113 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 142 removed outlier: 3.589A pdb=" N ASN A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 161 through 191 removed outlier: 3.543A pdb=" N HIS A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 219 Processing helix chain 'A' and resid 219 through 225 Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 248 through 251 removed outlier: 3.596A pdb=" N THR A 251 " --> pdb=" O LEU A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 251' Processing helix chain 'A' and resid 252 through 272 removed outlier: 3.544A pdb=" N VAL A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 299 removed outlier: 3.606A pdb=" N VAL A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 Processing helix chain 'A' and resid 326 through 332 removed outlier: 3.505A pdb=" N TRP A 330 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS A 331 " --> pdb=" O SER A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 360 removed outlier: 3.509A pdb=" N SER A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 381 removed outlier: 3.699A pdb=" N MET A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE A 381 " --> pdb=" O PHE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.751A pdb=" N SER A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 414 " --> pdb=" O CYS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 441 removed outlier: 3.812A pdb=" N ASN A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 447 Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.644A pdb=" N TYR A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 476 removed outlier: 3.701A pdb=" N ILE A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 473 " --> pdb=" O SER A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 497 Processing helix chain 'A' and resid 542 through 555 removed outlier: 3.713A pdb=" N ARG A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 566 Processing helix chain 'A' and resid 676 through 693 removed outlier: 3.949A pdb=" N ILE A 693 " --> pdb=" O THR A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 713 Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'A' and resid 729 through 741 Processing helix chain 'A' and resid 774 through 778 Processing helix chain 'B' and resid 16 through 24 removed outlier: 3.743A pdb=" N ASP B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 66 through 96 removed outlier: 6.185A pdb=" N ILE B 72 " --> pdb=" O LYS B 68 " (cutoff:3.500A) Proline residue: B 73 - end of helix removed outlier: 3.971A pdb=" N ILE B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 86 " --> pdb=" O GLY B 82 " (cutoff:3.500A) Proline residue: B 87 - end of helix removed outlier: 3.505A pdb=" N LEU B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 109 through 118 removed outlier: 4.126A pdb=" N THR B 113 " --> pdb=" O PHE B 109 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 142 removed outlier: 3.589A pdb=" N ASN B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 161 through 191 removed outlier: 3.543A pdb=" N HIS B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 219 Processing helix chain 'B' and resid 219 through 225 Processing helix chain 'B' and resid 235 through 247 Processing helix chain 'B' and resid 248 through 251 removed outlier: 3.596A pdb=" N THR B 251 " --> pdb=" O LEU B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 248 through 251' Processing helix chain 'B' and resid 252 through 272 removed outlier: 3.544A pdb=" N VAL B 269 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 299 removed outlier: 3.606A pdb=" N VAL B 290 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 307 Processing helix chain 'B' and resid 326 through 332 removed outlier: 3.505A pdb=" N TRP B 330 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS B 331 " --> pdb=" O SER B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 360 removed outlier: 3.509A pdb=" N SER B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 381 removed outlier: 3.699A pdb=" N MET B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE B 381 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 405 through 419 removed outlier: 3.751A pdb=" N SER B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 414 " --> pdb=" O CYS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 441 removed outlier: 3.812A pdb=" N ASN B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 447 Processing helix chain 'B' and resid 450 through 459 removed outlier: 3.644A pdb=" N TYR B 454 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG B 457 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 476 removed outlier: 3.701A pdb=" N ILE B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 497 Processing helix chain 'B' and resid 542 through 555 removed outlier: 3.713A pdb=" N ARG B 547 " --> pdb=" O SER B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 566 Processing helix chain 'B' and resid 676 through 693 removed outlier: 3.949A pdb=" N ILE B 693 " --> pdb=" O THR B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 713 Processing helix chain 'B' and resid 722 through 724 No H-bonds generated for 'chain 'B' and resid 722 through 724' Processing helix chain 'B' and resid 729 through 741 Processing helix chain 'B' and resid 774 through 778 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 126 Processing sheet with id=AA3, first strand: chain 'A' and resid 503 through 504 removed outlier: 6.431A pdb=" N LYS A 530 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP A 668 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE A 532 " --> pdb=" O ASP A 668 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N PHE A 727 " --> pdb=" O VAL A 697 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 699 " --> pdb=" O PHE A 727 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 514 through 515 Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 126 Processing sheet with id=AA6, first strand: chain 'B' and resid 503 through 504 removed outlier: 6.431A pdb=" N LYS B 530 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP B 668 " --> pdb=" O LYS B 530 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE B 532 " --> pdb=" O ASP B 668 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N PHE B 727 " --> pdb=" O VAL B 697 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 699 " --> pdb=" O PHE B 727 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 514 through 515 538 hydrogen bonds defined for protein. 1572 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: 2.72 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2970 1.34 - 1.46: 1798 1.46 - 1.57: 5220 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 10096 Sorted by residual: bond pdb=" C LEU A 478 " pdb=" N PRO A 479 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.25e-02 6.40e+03 1.97e+01 bond pdb=" C LEU B 478 " pdb=" N PRO B 479 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.25e-02 6.40e+03 1.97e+01 bond pdb=" N PRO B 479 " pdb=" CD PRO B 479 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.53e+01 bond pdb=" N PRO A 479 " pdb=" CD PRO A 479 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.53e+01 bond pdb=" C VAL A 86 " pdb=" N PRO A 87 " ideal model delta sigma weight residual 1.336 1.374 -0.038 1.20e-02 6.94e+03 1.02e+01 ... (remaining 10091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 13434 2.73 - 5.46: 238 5.46 - 8.19: 18 8.19 - 10.91: 2 10.91 - 13.64: 2 Bond angle restraints: 13694 Sorted by residual: angle pdb=" C LEU B 478 " pdb=" N PRO B 479 " pdb=" CA PRO B 479 " ideal model delta sigma weight residual 119.56 114.18 5.38 1.01e+00 9.80e-01 2.83e+01 angle pdb=" C LEU A 478 " pdb=" N PRO A 479 " pdb=" CA PRO A 479 " ideal model delta sigma weight residual 119.56 114.18 5.38 1.01e+00 9.80e-01 2.83e+01 angle pdb=" N PHE B 475 " pdb=" CA PHE B 475 " pdb=" C PHE B 475 " ideal model delta sigma weight residual 112.68 118.33 -5.65 1.33e+00 5.65e-01 1.81e+01 angle pdb=" N PHE A 475 " pdb=" CA PHE A 475 " pdb=" C PHE A 475 " ideal model delta sigma weight residual 112.68 118.33 -5.65 1.33e+00 5.65e-01 1.81e+01 angle pdb=" C SER A 459 " pdb=" N LYS A 460 " pdb=" CA LYS A 460 " ideal model delta sigma weight residual 121.54 129.06 -7.52 1.91e+00 2.74e-01 1.55e+01 ... (remaining 13689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5414 17.85 - 35.70: 376 35.70 - 53.55: 86 53.55 - 71.40: 66 71.40 - 89.26: 10 Dihedral angle restraints: 5952 sinusoidal: 2258 harmonic: 3694 Sorted by residual: dihedral pdb=" CA PHE A 282 " pdb=" C PHE A 282 " pdb=" N PRO A 283 " pdb=" CA PRO A 283 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA PHE B 282 " pdb=" C PHE B 282 " pdb=" N PRO B 283 " pdb=" CA PRO B 283 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ARG B 281 " pdb=" C ARG B 281 " pdb=" N PHE B 282 " pdb=" CA PHE B 282 " ideal model delta harmonic sigma weight residual -180.00 -153.07 -26.93 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 5949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1384 0.073 - 0.145: 210 0.145 - 0.218: 16 0.218 - 0.291: 0 0.291 - 0.363: 2 Chirality restraints: 1612 Sorted by residual: chirality pdb=" CB VAL A 292 " pdb=" CA VAL A 292 " pdb=" CG1 VAL A 292 " pdb=" CG2 VAL A 292 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CB VAL B 292 " pdb=" CA VAL B 292 " pdb=" CG1 VAL B 292 " pdb=" CG2 VAL B 292 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CB ILE B 284 " pdb=" CA ILE B 284 " pdb=" CG1 ILE B 284 " pdb=" CG2 ILE B 284 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1609 not shown) Planarity restraints: 1688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 248 " 0.045 5.00e-02 4.00e+02 6.68e-02 7.15e+00 pdb=" N PRO B 249 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 249 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 249 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 248 " -0.045 5.00e-02 4.00e+02 6.68e-02 7.15e+00 pdb=" N PRO A 249 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 249 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 249 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 303 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO B 304 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 304 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 304 " -0.036 5.00e-02 4.00e+02 ... (remaining 1685 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1634 2.75 - 3.29: 8868 3.29 - 3.83: 16143 3.83 - 4.36: 20846 4.36 - 4.90: 34252 Nonbonded interactions: 81743 Sorted by model distance: nonbonded pdb=" OE1 GLN B 85 " pdb="NA NA B 803 " model vdw 2.218 2.470 nonbonded pdb=" OE1 GLN A 85 " pdb="NA NA A 803 " model vdw 2.218 2.470 nonbonded pdb=" O HOH B 933 " pdb=" O HOH B 934 " model vdw 2.246 3.040 nonbonded pdb=" O HOH A 933 " pdb=" O HOH A 934 " model vdw 2.246 3.040 nonbonded pdb=" O HOH B 921 " pdb=" O HOH B 938 " model vdw 2.250 3.040 ... (remaining 81738 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: 0.05 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: 2.180 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.790 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.007 0.066 10096 Z= 0.312 Angle : 0.868 13.642 13694 Z= 0.495 Chirality : 0.056 0.363 1612 Planarity : 0.007 0.067 1688 Dihedral : 15.519 89.256 3580 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.29 % Favored : 95.56 % Rotamer: Outliers : 6.10 % Allowed : 3.88 % Favored : 90.02 % 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: -5.35 (0.16), residues: 1260 helix: -4.18 (0.07), residues: 774 sheet: 0.66 (0.67), residues: 56 loop : -2.42 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 61 HIS 0.004 0.001 HIS A 385 PHE 0.018 0.002 PHE B 499 TYR 0.014 0.002 TYR B 539 ARG 0.002 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.30287 ( 538) hydrogen bonds : angle 9.38533 ( 1572) covalent geometry : bond 0.00715 (10096) covalent geometry : angle 0.86782 (13694) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 156 time to evaluate : 1.013 Fit side-chains REVERT: A 317 ARG cc_start: 0.8297 (mtp85) cc_final: 0.8060 (mtp85) REVERT: A 333 MET cc_start: 0.8621 (mtt) cc_final: 0.8107 (mtt) REVERT: A 527 GLN cc_start: 0.8262 (tp-100) cc_final: 0.8038 (tp40) REVERT: A 669 MET cc_start: 0.8581 (mtp) cc_final: 0.8246 (mtp) REVERT: B 317 ARG cc_start: 0.8297 (mtp85) cc_final: 0.8059 (mtp85) REVERT: B 333 MET cc_start: 0.8623 (mtt) cc_final: 0.8108 (mtt) REVERT: B 527 GLN cc_start: 0.8264 (tp-100) cc_final: 0.8036 (tp40) REVERT: B 669 MET cc_start: 0.8586 (mtp) cc_final: 0.8250 (mtp) outliers start: 66 outliers final: 6 residues processed: 194 average time/residue: 1.0552 time to fit residues: 222.3897 Evaluate side-chains 98 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 720 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 0.0970 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 116 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 191 GLN A 376 ASN A 385 HIS A 405 GLN A 507 GLN A 559 GLN B 102 ASN B 191 GLN B 376 ASN B 385 HIS B 405 GLN B 507 GLN B 559 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.080715 restraints weight = 13295.357| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.87 r_work: 0.2773 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10096 Z= 0.132 Angle : 0.579 6.053 13694 Z= 0.314 Chirality : 0.043 0.132 1612 Planarity : 0.006 0.047 1688 Dihedral : 5.911 41.876 1356 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.85 % Allowed : 8.50 % Favored : 89.65 % 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: -1.80 (0.21), residues: 1260 helix: -0.95 (0.16), residues: 778 sheet: 1.27 (0.66), residues: 54 loop : -1.77 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 61 HIS 0.003 0.001 HIS B 385 PHE 0.017 0.001 PHE A 24 TYR 0.012 0.001 TYR A 159 ARG 0.003 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.05247 ( 538) hydrogen bonds : angle 4.45967 ( 1572) covalent geometry : bond 0.00286 (10096) covalent geometry : angle 0.57921 (13694) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 1.174 Fit side-chains REVERT: A 287 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: A 527 GLN cc_start: 0.8736 (tp-100) cc_final: 0.8460 (tp40) REVERT: B 287 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: B 527 GLN cc_start: 0.8746 (tp-100) cc_final: 0.8465 (tp40) outliers start: 20 outliers final: 10 residues processed: 116 average time/residue: 1.2514 time to fit residues: 156.4083 Evaluate side-chains 98 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 720 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 11 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN A 663 HIS B 501 ASN B 663 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.098206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.076194 restraints weight = 13574.586| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.84 r_work: 0.2710 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10096 Z= 0.184 Angle : 0.596 6.063 13694 Z= 0.321 Chirality : 0.045 0.148 1612 Planarity : 0.005 0.053 1688 Dihedral : 5.282 29.586 1352 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.85 % Allowed : 10.17 % Favored : 87.99 % 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: -0.21 (0.23), residues: 1260 helix: 0.53 (0.18), residues: 794 sheet: 1.14 (0.67), residues: 56 loop : -1.59 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 61 HIS 0.005 0.001 HIS A 385 PHE 0.016 0.001 PHE A 499 TYR 0.011 0.002 TYR A 514 ARG 0.004 0.001 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.05681 ( 538) hydrogen bonds : angle 4.09769 ( 1572) covalent geometry : bond 0.00445 (10096) covalent geometry : angle 0.59596 (13694) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 1.078 Fit side-chains REVERT: A 168 GLU cc_start: 0.8438 (tp30) cc_final: 0.8117 (tp30) REVERT: A 316 GLN cc_start: 0.7970 (mt0) cc_final: 0.7558 (mp10) REVERT: A 527 GLN cc_start: 0.8826 (tp-100) cc_final: 0.8545 (tp40) REVERT: B 168 GLU cc_start: 0.8450 (tp30) cc_final: 0.8125 (tp30) REVERT: B 316 GLN cc_start: 0.7974 (mt0) cc_final: 0.7560 (mp10) REVERT: B 527 GLN cc_start: 0.8839 (tp-100) cc_final: 0.8558 (tp40) outliers start: 20 outliers final: 14 residues processed: 112 average time/residue: 1.2727 time to fit residues: 153.3092 Evaluate side-chains 100 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 673 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 3 optimal weight: 0.0470 chunk 77 optimal weight: 6.9990 chunk 20 optimal weight: 0.2980 chunk 58 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.3213 r_free = 0.3213 target = 0.101138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.079033 restraints weight = 13474.094| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.85 r_work: 0.2757 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10096 Z= 0.113 Angle : 0.515 5.911 13694 Z= 0.275 Chirality : 0.042 0.145 1612 Planarity : 0.004 0.048 1688 Dihedral : 4.822 20.757 1350 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.48 % Allowed : 10.54 % Favored : 87.99 % 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: 0.79 (0.24), residues: 1260 helix: 1.44 (0.19), residues: 768 sheet: 1.73 (0.67), residues: 54 loop : -1.30 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 61 HIS 0.004 0.001 HIS A 385 PHE 0.012 0.001 PHE B 24 TYR 0.012 0.001 TYR B 159 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 538) hydrogen bonds : angle 3.85556 ( 1572) covalent geometry : bond 0.00251 (10096) covalent geometry : angle 0.51451 (13694) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.107 Fit side-chains REVERT: A 168 GLU cc_start: 0.8417 (tp30) cc_final: 0.8088 (tp30) REVERT: A 287 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: A 316 GLN cc_start: 0.7949 (mt0) cc_final: 0.7523 (mp10) REVERT: A 527 GLN cc_start: 0.8802 (tp-100) cc_final: 0.8509 (tp40) REVERT: B 168 GLU cc_start: 0.8417 (tp30) cc_final: 0.8089 (tp30) REVERT: B 287 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: B 316 GLN cc_start: 0.7953 (mt0) cc_final: 0.7526 (mp10) REVERT: B 527 GLN cc_start: 0.8811 (tp-100) cc_final: 0.8518 (tp40) outliers start: 16 outliers final: 10 residues processed: 108 average time/residue: 1.1252 time to fit residues: 131.8416 Evaluate side-chains 102 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 661 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 121 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 68 optimal weight: 0.0370 chunk 118 optimal weight: 0.0670 chunk 113 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.101660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.079565 restraints weight = 13507.227| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.84 r_work: 0.2771 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10096 Z= 0.108 Angle : 0.495 6.287 13694 Z= 0.263 Chirality : 0.041 0.137 1612 Planarity : 0.004 0.047 1688 Dihedral : 4.538 20.219 1348 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.29 % Allowed : 11.09 % Favored : 87.62 % 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: 1.35 (0.24), residues: 1260 helix: 1.92 (0.19), residues: 764 sheet: 1.90 (0.68), residues: 54 loop : -1.12 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 61 HIS 0.004 0.001 HIS A 385 PHE 0.011 0.001 PHE A 24 TYR 0.011 0.001 TYR A 159 ARG 0.002 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 538) hydrogen bonds : angle 3.73273 ( 1572) covalent geometry : bond 0.00238 (10096) covalent geometry : angle 0.49503 (13694) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.167 Fit side-chains REVERT: A 168 GLU cc_start: 0.8413 (tp30) cc_final: 0.8125 (tp30) REVERT: A 280 ILE cc_start: 0.4833 (OUTLIER) cc_final: 0.4526 (pt) REVERT: A 316 GLN cc_start: 0.7953 (mt0) cc_final: 0.7549 (mp10) REVERT: A 527 GLN cc_start: 0.8746 (tp-100) cc_final: 0.8455 (tp40) REVERT: B 168 GLU cc_start: 0.8412 (tp30) cc_final: 0.8124 (tp30) REVERT: B 280 ILE cc_start: 0.4838 (OUTLIER) cc_final: 0.4532 (pt) REVERT: B 316 GLN cc_start: 0.7956 (mt0) cc_final: 0.7547 (mp10) REVERT: B 527 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8468 (tp40) outliers start: 14 outliers final: 8 residues processed: 112 average time/residue: 1.5575 time to fit residues: 187.9525 Evaluate side-chains 102 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 661 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 0.0040 chunk 82 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 39 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 1 optimal weight: 0.0980 chunk 91 optimal weight: 0.0970 chunk 41 optimal weight: 0.0570 chunk 70 optimal weight: 0.8980 overall best weight: 0.0708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS B 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.108161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.086237 restraints weight = 13556.871| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.84 r_work: 0.2887 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10096 Z= 0.091 Angle : 0.467 7.161 13694 Z= 0.243 Chirality : 0.040 0.138 1612 Planarity : 0.003 0.043 1688 Dihedral : 4.063 19.711 1348 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.92 % Allowed : 12.01 % Favored : 87.06 % 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: 1.80 (0.25), residues: 1260 helix: 2.31 (0.19), residues: 780 sheet: 2.12 (0.71), residues: 48 loop : -1.10 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 61 HIS 0.002 0.000 HIS B 278 PHE 0.010 0.001 PHE B 674 TYR 0.012 0.001 TYR B 454 ARG 0.002 0.000 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.02848 ( 538) hydrogen bonds : angle 3.58531 ( 1572) covalent geometry : bond 0.00188 (10096) covalent geometry : angle 0.46740 (13694) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 1.032 Fit side-chains TARDY: cannot create tardy model for: "SER A 404 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER B 404 " (corrupted residue). Skipping it. REVERT: A 168 GLU cc_start: 0.8307 (tp30) cc_final: 0.7983 (tp30) REVERT: A 280 ILE cc_start: 0.4539 (OUTLIER) cc_final: 0.4252 (pt) REVERT: A 287 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: A 316 GLN cc_start: 0.7975 (mt0) cc_final: 0.7547 (mp10) REVERT: A 501 ASN cc_start: 0.7081 (OUTLIER) cc_final: 0.6775 (m-40) REVERT: A 527 GLN cc_start: 0.8668 (tp-100) cc_final: 0.8398 (tp40) REVERT: A 659 PHE cc_start: 0.7724 (m-80) cc_final: 0.7368 (m-80) REVERT: B 168 GLU cc_start: 0.8313 (tp30) cc_final: 0.7992 (tp30) REVERT: B 280 ILE cc_start: 0.4545 (OUTLIER) cc_final: 0.4256 (pt) REVERT: B 287 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: B 316 GLN cc_start: 0.7989 (mt0) cc_final: 0.7547 (mp10) REVERT: B 501 ASN cc_start: 0.7089 (OUTLIER) cc_final: 0.6784 (m-40) REVERT: B 527 GLN cc_start: 0.8670 (tp-100) cc_final: 0.8403 (tp40) REVERT: B 659 PHE cc_start: 0.7716 (m-80) cc_final: 0.7358 (m-80) outliers start: 10 outliers final: 0 residues processed: 118 average time/residue: 1.3116 time to fit residues: 167.6043 Evaluate side-chains 108 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 501 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 16 optimal weight: 0.0060 chunk 30 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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 = 0.3219 r_free = 0.3219 target = 0.101304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.079173 restraints weight = 13652.144| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.85 r_work: 0.2725 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10096 Z= 0.131 Angle : 0.512 7.124 13694 Z= 0.270 Chirality : 0.043 0.132 1612 Planarity : 0.004 0.044 1688 Dihedral : 4.393 19.655 1348 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.29 % Allowed : 12.20 % Favored : 86.51 % 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: 1.83 (0.25), residues: 1260 helix: 2.26 (0.19), residues: 782 sheet: 1.64 (0.70), residues: 56 loop : -0.92 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 61 HIS 0.005 0.001 HIS B 385 PHE 0.012 0.001 PHE B 499 TYR 0.008 0.001 TYR A 345 ARG 0.002 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 538) hydrogen bonds : angle 3.65160 ( 1572) covalent geometry : bond 0.00308 (10096) covalent geometry : angle 0.51188 (13694) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 1.069 Fit side-chains REVERT: A 168 GLU cc_start: 0.8431 (tp30) cc_final: 0.8110 (tp30) REVERT: A 280 ILE cc_start: 0.4408 (OUTLIER) cc_final: 0.4126 (pt) REVERT: A 316 GLN cc_start: 0.7980 (mt0) cc_final: 0.7551 (mp10) REVERT: A 501 ASN cc_start: 0.7304 (OUTLIER) cc_final: 0.7010 (m-40) REVERT: A 527 GLN cc_start: 0.8663 (tp-100) cc_final: 0.8371 (tp40) REVERT: B 168 GLU cc_start: 0.8435 (tp30) cc_final: 0.8115 (tp30) REVERT: B 280 ILE cc_start: 0.4410 (OUTLIER) cc_final: 0.4126 (pt) REVERT: B 316 GLN cc_start: 0.7984 (mt0) cc_final: 0.7555 (mp10) REVERT: B 501 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.7011 (m-40) REVERT: B 527 GLN cc_start: 0.8677 (tp-100) cc_final: 0.8381 (tp40) outliers start: 14 outliers final: 8 residues processed: 111 average time/residue: 1.1830 time to fit residues: 142.0395 Evaluate side-chains 105 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 501 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 66 optimal weight: 0.0010 chunk 120 optimal weight: 0.7980 chunk 50 optimal weight: 0.0770 chunk 4 optimal weight: 0.0060 chunk 65 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 124 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 overall best weight: 0.2160 ------------------------------------------------------------------------------- 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 = 0.3280 r_free = 0.3280 target = 0.105765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.083493 restraints weight = 13600.595| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.86 r_work: 0.2827 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10096 Z= 0.090 Angle : 0.469 8.033 13694 Z= 0.244 Chirality : 0.040 0.132 1612 Planarity : 0.003 0.041 1688 Dihedral : 4.077 19.954 1348 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.29 % Allowed : 12.66 % Favored : 86.04 % 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: 2.11 (0.25), residues: 1260 helix: 2.59 (0.19), residues: 774 sheet: 1.81 (0.73), residues: 50 loop : -0.97 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 61 HIS 0.003 0.000 HIS B 385 PHE 0.010 0.001 PHE B 674 TYR 0.011 0.001 TYR B 454 ARG 0.001 0.000 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.03196 ( 538) hydrogen bonds : angle 3.56457 ( 1572) covalent geometry : bond 0.00189 (10096) covalent geometry : angle 0.46913 (13694) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 1.100 Fit side-chains TARDY: cannot create tardy model for: "SER A 404 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER B 404 " (corrupted residue). Skipping it. REVERT: A 48 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8543 (mm) REVERT: A 168 GLU cc_start: 0.8375 (tp30) cc_final: 0.8045 (tp30) REVERT: A 316 GLN cc_start: 0.7955 (mt0) cc_final: 0.7554 (mp10) REVERT: A 501 ASN cc_start: 0.7189 (OUTLIER) cc_final: 0.6891 (m-40) REVERT: A 509 MET cc_start: 0.7177 (pmm) cc_final: 0.6762 (mpt) REVERT: A 527 GLN cc_start: 0.8628 (tp-100) cc_final: 0.8351 (tp40) REVERT: A 659 PHE cc_start: 0.7750 (m-80) cc_final: 0.7373 (m-80) REVERT: B 48 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8542 (mm) REVERT: B 168 GLU cc_start: 0.8373 (tp30) cc_final: 0.8045 (tp30) REVERT: B 316 GLN cc_start: 0.7971 (mt0) cc_final: 0.7556 (mp10) REVERT: B 501 ASN cc_start: 0.7189 (OUTLIER) cc_final: 0.6888 (m-40) REVERT: B 509 MET cc_start: 0.7171 (pmm) cc_final: 0.6758 (mpt) REVERT: B 527 GLN cc_start: 0.8630 (tp-100) cc_final: 0.8354 (tp40) REVERT: B 659 PHE cc_start: 0.7751 (m-80) cc_final: 0.7372 (m-80) outliers start: 14 outliers final: 6 residues processed: 117 average time/residue: 1.1780 time to fit residues: 149.0885 Evaluate side-chains 109 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 501 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 86 optimal weight: 0.0010 overall best weight: 0.8188 ------------------------------------------------------------------------------- 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 = 0.3195 r_free = 0.3195 target = 0.100250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.077103 restraints weight = 13269.428| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.91 r_work: 0.2703 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10096 Z= 0.134 Angle : 0.519 7.151 13694 Z= 0.274 Chirality : 0.043 0.131 1612 Planarity : 0.004 0.040 1688 Dihedral : 4.394 20.120 1348 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.29 % Allowed : 12.85 % Favored : 85.86 % 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: 2.02 (0.24), residues: 1260 helix: 2.40 (0.18), residues: 782 sheet: 1.58 (0.70), residues: 56 loop : -0.80 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 61 HIS 0.005 0.001 HIS B 385 PHE 0.013 0.001 PHE A 499 TYR 0.010 0.001 TYR B 159 ARG 0.003 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 538) hydrogen bonds : angle 3.65337 ( 1572) covalent geometry : bond 0.00317 (10096) covalent geometry : angle 0.51944 (13694) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 1.017 Fit side-chains REVERT: A 168 GLU cc_start: 0.8480 (tp30) cc_final: 0.8157 (tp30) REVERT: A 316 GLN cc_start: 0.8006 (mt0) cc_final: 0.7509 (mp10) REVERT: A 501 ASN cc_start: 0.7290 (OUTLIER) cc_final: 0.6866 (m110) REVERT: A 527 GLN cc_start: 0.8638 (tp-100) cc_final: 0.8281 (tp40) REVERT: B 168 GLU cc_start: 0.8474 (tp30) cc_final: 0.8149 (tp30) REVERT: B 316 GLN cc_start: 0.8012 (mt0) cc_final: 0.7512 (mp10) REVERT: B 501 ASN cc_start: 0.7286 (OUTLIER) cc_final: 0.6865 (m110) REVERT: B 527 GLN cc_start: 0.8643 (tp-100) cc_final: 0.8286 (tp40) outliers start: 14 outliers final: 8 residues processed: 111 average time/residue: 1.2031 time to fit residues: 144.1174 Evaluate side-chains 105 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 501 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 60 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 0.0470 chunk 107 optimal weight: 0.7980 chunk 103 optimal weight: 0.0000 chunk 75 optimal weight: 0.6980 overall best weight: 0.3882 ------------------------------------------------------------------------------- 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 = 0.3235 r_free = 0.3235 target = 0.102930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.079655 restraints weight = 13211.407| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.94 r_work: 0.2748 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10096 Z= 0.100 Angle : 0.489 9.374 13694 Z= 0.254 Chirality : 0.041 0.130 1612 Planarity : 0.003 0.038 1688 Dihedral : 4.186 20.555 1348 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.74 % Allowed : 13.22 % Favored : 86.04 % 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: 2.22 (0.25), residues: 1260 helix: 2.62 (0.18), residues: 778 sheet: 1.86 (0.73), residues: 50 loop : -0.82 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 61 HIS 0.003 0.000 HIS A 385 PHE 0.011 0.001 PHE A 265 TYR 0.011 0.001 TYR B 159 ARG 0.001 0.000 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 538) hydrogen bonds : angle 3.60046 ( 1572) covalent geometry : bond 0.00218 (10096) covalent geometry : angle 0.48863 (13694) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 1.123 Fit side-chains TARDY: cannot create tardy model for: "SER A 404 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER B 404 " (corrupted residue). Skipping it. REVERT: A 168 GLU cc_start: 0.8449 (tp30) cc_final: 0.8166 (tp30) REVERT: A 316 GLN cc_start: 0.7980 (mt0) cc_final: 0.7494 (mp10) REVERT: A 501 ASN cc_start: 0.7277 (OUTLIER) cc_final: 0.6969 (m-40) REVERT: A 509 MET cc_start: 0.7234 (pmm) cc_final: 0.6777 (mpt) REVERT: A 527 GLN cc_start: 0.8625 (tp-100) cc_final: 0.8300 (tp40) REVERT: A 659 PHE cc_start: 0.7725 (m-80) cc_final: 0.7335 (m-80) REVERT: B 168 GLU cc_start: 0.8441 (tp30) cc_final: 0.8158 (tp30) REVERT: B 316 GLN cc_start: 0.7987 (mt0) cc_final: 0.7492 (mp10) REVERT: B 501 ASN cc_start: 0.7272 (OUTLIER) cc_final: 0.6965 (m-40) REVERT: B 509 MET cc_start: 0.7238 (pmm) cc_final: 0.6772 (mpt) REVERT: B 527 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8302 (tp40) REVERT: B 659 PHE cc_start: 0.7732 (m-80) cc_final: 0.7339 (m-80) outliers start: 8 outliers final: 6 residues processed: 109 average time/residue: 1.2587 time to fit residues: 147.8158 Evaluate side-chains 109 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 501 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 112 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 74 optimal weight: 0.0570 chunk 98 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.3218 r_free = 0.3218 target = 0.101511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.079268 restraints weight = 13532.455| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.85 r_work: 0.2766 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10096 Z= 0.119 Angle : 0.512 8.891 13694 Z= 0.268 Chirality : 0.042 0.131 1612 Planarity : 0.004 0.038 1688 Dihedral : 4.306 20.528 1348 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.11 % Allowed : 13.03 % Favored : 85.86 % 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: 2.17 (0.25), residues: 1260 helix: 2.54 (0.18), residues: 780 sheet: 1.60 (0.70), residues: 56 loop : -0.75 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 61 HIS 0.005 0.001 HIS A 385 PHE 0.013 0.001 PHE A 265 TYR 0.011 0.001 TYR B 159 ARG 0.002 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 538) hydrogen bonds : angle 3.62431 ( 1572) covalent geometry : bond 0.00274 (10096) covalent geometry : angle 0.51181 (13694) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7548.06 seconds wall clock time: 132 minutes 58.89 seconds (7978.89 seconds total)