Starting phenix.real_space_refine on Wed Mar 4 01:46:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ch1_30368/03_2026/7ch1_30368.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ch1_30368/03_2026/7ch1_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ch1_30368/03_2026/7ch1_30368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ch1_30368/03_2026/7ch1_30368.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ch1_30368/03_2026/7ch1_30368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ch1_30368/03_2026/7ch1_30368.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 4.13, per 1000 atoms: 0.42 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: 0.77 Conformation dependent library (CDL) restraints added in 522.1 milliseconds 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: 0.34 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: 1.70 Time building geometry restraints manager: 1.09 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: 0.02 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: 3.100 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.570 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.980 ------------------------------------------------------------------------------- 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 : 3.34 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.35 (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 ARG 0.002 0.000 ARG A 205 TYR 0.014 0.002 TYR B 539 PHE 0.018 0.002 PHE B 499 TRP 0.011 0.002 TRP B 61 HIS 0.004 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00715 (10096) covalent geometry : angle 0.86782 (13694) hydrogen bonds : bond 0.30287 ( 538) hydrogen bonds : angle 9.38533 ( 1572) *********************** 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 : 0.404 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: 0.4928 time to fit residues: 103.1823 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 : 0.391 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 chunk 55 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 A 663 HIS B 102 ASN B 191 GLN B 376 ASN B 385 HIS B 405 GLN B 507 GLN B 559 GLN B 663 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.080443 restraints weight = 13328.608| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.88 r_work: 0.2768 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2347 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= 0.134 Angle : 0.576 6.165 13694 Z= 0.312 Chirality : 0.043 0.133 1612 Planarity : 0.006 0.048 1688 Dihedral : 5.884 40.754 1356 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.39 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.21), residues: 1260 helix: -1.08 (0.16), residues: 778 sheet: 1.25 (0.66), residues: 54 loop : -1.75 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 457 TYR 0.012 0.001 TYR A 159 PHE 0.017 0.001 PHE A 24 TRP 0.010 0.001 TRP A 61 HIS 0.003 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00286 (10096) covalent geometry : angle 0.57632 (13694) hydrogen bonds : bond 0.05245 ( 538) hydrogen bonds : angle 4.49455 ( 1572) *********************** 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 122 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.366 Fit side-chains REVERT: A 287 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7532 (tt0) REVERT: A 527 GLN cc_start: 0.8747 (tp-100) cc_final: 0.8461 (tp40) REVERT: B 287 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: B 527 GLN cc_start: 0.8751 (tp-100) cc_final: 0.8460 (tp40) outliers start: 20 outliers final: 10 residues processed: 118 average time/residue: 0.5771 time to fit residues: 72.8467 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 : 0.285 ------------------------------------------------------------------------------- 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 109 optimal weight: 3.9990 chunk 10 optimal weight: 0.0010 chunk 64 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN B 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.076980 restraints weight = 13565.848| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.83 r_work: 0.2710 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10096 Z= 0.166 Angle : 0.579 6.138 13694 Z= 0.311 Chirality : 0.044 0.149 1612 Planarity : 0.005 0.054 1688 Dihedral : 5.179 26.717 1352 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.03 % Allowed : 9.80 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.23), residues: 1260 helix: 0.58 (0.18), residues: 782 sheet: 1.19 (0.67), residues: 56 loop : -1.55 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 205 TYR 0.011 0.001 TYR A 8 PHE 0.015 0.001 PHE B 24 TRP 0.009 0.001 TRP A 61 HIS 0.005 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00396 (10096) covalent geometry : angle 0.57856 (13694) hydrogen bonds : bond 0.05475 ( 538) hydrogen bonds : angle 4.05307 ( 1572) *********************** 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 118 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.317 Fit side-chains REVERT: A 168 GLU cc_start: 0.8432 (tp30) cc_final: 0.8109 (tp30) REVERT: A 275 ARG cc_start: 0.7503 (ptm160) cc_final: 0.7212 (ptm-80) REVERT: A 527 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8553 (tp40) REVERT: B 168 GLU cc_start: 0.8444 (tp30) cc_final: 0.8117 (tp30) REVERT: B 275 ARG cc_start: 0.7512 (ptm160) cc_final: 0.7220 (ptm-80) REVERT: B 527 GLN cc_start: 0.8835 (tp-100) cc_final: 0.8560 (tp40) outliers start: 22 outliers final: 14 residues processed: 114 average time/residue: 0.5934 time to fit residues: 72.5555 Evaluate side-chains 104 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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: 0.0870 chunk 49 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 101 optimal weight: 0.0170 chunk 11 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.101500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.079607 restraints weight = 13741.918| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.84 r_work: 0.2768 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10096 Z= 0.110 Angle : 0.512 6.421 13694 Z= 0.273 Chirality : 0.042 0.144 1612 Planarity : 0.004 0.047 1688 Dihedral : 4.739 20.744 1350 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.24), residues: 1260 helix: 1.46 (0.19), residues: 766 sheet: 1.73 (0.67), residues: 54 loop : -1.34 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 457 TYR 0.010 0.001 TYR B 454 PHE 0.012 0.001 PHE B 24 TRP 0.010 0.001 TRP A 61 HIS 0.004 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00245 (10096) covalent geometry : angle 0.51206 (13694) hydrogen bonds : bond 0.04064 ( 538) hydrogen bonds : angle 3.83023 ( 1572) *********************** 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 112 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.365 Fit side-chains REVERT: A 168 GLU cc_start: 0.8411 (tp30) cc_final: 0.8129 (tp30) REVERT: A 287 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: A 527 GLN cc_start: 0.8800 (tp-100) cc_final: 0.8513 (tp40) REVERT: B 168 GLU cc_start: 0.8416 (tp30) cc_final: 0.8132 (tp30) REVERT: B 287 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: B 527 GLN cc_start: 0.8810 (tp-100) cc_final: 0.8523 (tp40) outliers start: 16 outliers final: 10 residues processed: 110 average time/residue: 0.5593 time to fit residues: 66.1870 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 : 0.430 ------------------------------------------------------------------------------- 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 36 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3175 r_free = 0.3175 target = 0.098782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.075722 restraints weight = 13387.229| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 1.91 r_work: 0.2682 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3310 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= 0.137 Angle : 0.528 6.142 13694 Z= 0.282 Chirality : 0.043 0.142 1612 Planarity : 0.004 0.048 1688 Dihedral : 4.730 20.120 1348 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.48 % Allowed : 11.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.24), residues: 1260 helix: 1.73 (0.19), residues: 770 sheet: 1.52 (0.69), residues: 56 loop : -1.16 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 205 TYR 0.009 0.001 TYR A 514 PHE 0.013 0.001 PHE B 499 TRP 0.009 0.001 TRP A 61 HIS 0.005 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00321 (10096) covalent geometry : angle 0.52795 (13694) hydrogen bonds : bond 0.04605 ( 538) hydrogen bonds : angle 3.81499 ( 1572) *********************** 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 108 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.398 Fit side-chains REVERT: A 168 GLU cc_start: 0.8497 (tp30) cc_final: 0.8221 (tp30) REVERT: A 316 GLN cc_start: 0.7464 (mm110) cc_final: 0.7141 (mp10) REVERT: A 527 GLN cc_start: 0.8765 (tp-100) cc_final: 0.8452 (tp40) REVERT: B 168 GLU cc_start: 0.8493 (tp30) cc_final: 0.8215 (tp30) REVERT: B 316 GLN cc_start: 0.7459 (mm110) cc_final: 0.7143 (mp10) REVERT: B 527 GLN cc_start: 0.8768 (tp-100) cc_final: 0.8452 (tp40) outliers start: 16 outliers final: 12 residues processed: 106 average time/residue: 0.5719 time to fit residues: 65.2548 Evaluate side-chains 104 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 26 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3128 r_free = 0.3128 target = 0.095725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.072699 restraints weight = 13413.323| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 1.91 r_work: 0.2635 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10096 Z= 0.217 Angle : 0.599 6.293 13694 Z= 0.321 Chirality : 0.047 0.164 1612 Planarity : 0.005 0.049 1688 Dihedral : 5.047 19.560 1348 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.03 % Allowed : 11.28 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.24), residues: 1260 helix: 1.49 (0.18), residues: 796 sheet: 1.48 (0.70), residues: 56 loop : -1.24 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 205 TYR 0.014 0.002 TYR B 514 PHE 0.020 0.002 PHE A 499 TRP 0.008 0.002 TRP B 61 HIS 0.006 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00532 (10096) covalent geometry : angle 0.59859 (13694) hydrogen bonds : bond 0.05582 ( 538) hydrogen bonds : angle 3.97380 ( 1572) *********************** 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 106 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.250 Fit side-chains REVERT: A 168 GLU cc_start: 0.8504 (tp30) cc_final: 0.8261 (tp30) REVERT: A 287 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7903 (mt-10) REVERT: A 316 GLN cc_start: 0.7475 (mm110) cc_final: 0.7163 (mp10) REVERT: A 527 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8371 (tp40) REVERT: B 168 GLU cc_start: 0.8494 (tp30) cc_final: 0.8249 (tp30) REVERT: B 287 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7897 (mt-10) REVERT: B 316 GLN cc_start: 0.7464 (mm110) cc_final: 0.7166 (mp10) REVERT: B 527 GLN cc_start: 0.8753 (tp-100) cc_final: 0.8367 (tp40) outliers start: 22 outliers final: 12 residues processed: 102 average time/residue: 0.5900 time to fit residues: 64.6235 Evaluate side-chains 98 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 417 ILE Chi-restraints excluded: chain A residue 661 THR 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 417 ILE Chi-restraints excluded: chain B residue 661 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 123 optimal weight: 0.3980 chunk 112 optimal weight: 0.0980 chunk 120 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 92 optimal weight: 0.0270 chunk 113 optimal weight: 0.3980 overall best weight: 0.3038 ------------------------------------------------------------------------------- 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 = 0.3237 r_free = 0.3237 target = 0.102756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.080688 restraints weight = 13506.162| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.84 r_work: 0.2780 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3557 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= 0.098 Angle : 0.488 7.497 13694 Z= 0.257 Chirality : 0.041 0.142 1612 Planarity : 0.004 0.043 1688 Dihedral : 4.454 19.968 1348 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.85 % Allowed : 12.01 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.24), residues: 1260 helix: 2.22 (0.19), residues: 762 sheet: 1.83 (0.71), residues: 54 loop : -1.10 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.012 0.001 TYR B 454 PHE 0.011 0.001 PHE B 24 TRP 0.012 0.001 TRP A 61 HIS 0.003 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00206 (10096) covalent geometry : angle 0.48775 (13694) hydrogen bonds : bond 0.03540 ( 538) hydrogen bonds : angle 3.70968 ( 1572) *********************** 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 120 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.354 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: 0.8380 (tp30) cc_final: 0.8094 (tp30) REVERT: A 280 ILE cc_start: 0.4636 (OUTLIER) cc_final: 0.4319 (pt) REVERT: A 316 GLN cc_start: 0.7510 (mm110) cc_final: 0.7269 (mp10) REVERT: A 501 ASN cc_start: 0.7362 (OUTLIER) cc_final: 0.7077 (m-40) REVERT: A 527 GLN cc_start: 0.8703 (tp-100) cc_final: 0.8352 (tp40) REVERT: B 168 GLU cc_start: 0.8386 (tp30) cc_final: 0.8100 (tp30) REVERT: B 280 ILE cc_start: 0.4637 (OUTLIER) cc_final: 0.4320 (pt) REVERT: B 316 GLN cc_start: 0.7508 (mm110) cc_final: 0.7275 (mp10) REVERT: B 501 ASN cc_start: 0.7364 (OUTLIER) cc_final: 0.7081 (m-40) REVERT: B 527 GLN cc_start: 0.8704 (tp-100) cc_final: 0.8352 (tp40) outliers start: 20 outliers final: 6 residues processed: 118 average time/residue: 0.5711 time to fit residues: 72.5616 Evaluate side-chains 104 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 501 ASN 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 9 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 25 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.099705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.077699 restraints weight = 13604.103| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.84 r_work: 0.2735 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3506 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= 0.139 Angle : 0.532 7.927 13694 Z= 0.281 Chirality : 0.043 0.138 1612 Planarity : 0.004 0.043 1688 Dihedral : 4.614 19.877 1348 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.66 % Allowed : 12.01 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.24), residues: 1260 helix: 2.20 (0.19), residues: 768 sheet: 1.52 (0.71), residues: 56 loop : -0.97 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 205 TYR 0.009 0.001 TYR B 8 PHE 0.013 0.001 PHE B 499 TRP 0.008 0.001 TRP A 61 HIS 0.005 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00329 (10096) covalent geometry : angle 0.53198 (13694) hydrogen bonds : bond 0.04484 ( 538) hydrogen bonds : angle 3.74217 ( 1572) *********************** 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 110 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.370 Fit side-chains REVERT: A 168 GLU cc_start: 0.8423 (tp30) cc_final: 0.8135 (tp30) REVERT: A 280 ILE cc_start: 0.4514 (OUTLIER) cc_final: 0.4240 (pt) REVERT: A 316 GLN cc_start: 0.7534 (mm110) cc_final: 0.7304 (mp10) REVERT: A 501 ASN cc_start: 0.7289 (OUTLIER) cc_final: 0.6983 (m-40) REVERT: A 527 GLN cc_start: 0.8736 (tp-100) cc_final: 0.8379 (tp40) REVERT: B 168 GLU cc_start: 0.8426 (tp30) cc_final: 0.8140 (tp30) REVERT: B 280 ILE cc_start: 0.4510 (OUTLIER) cc_final: 0.4233 (pt) REVERT: B 316 GLN cc_start: 0.7530 (mm110) cc_final: 0.7305 (mp10) REVERT: B 501 ASN cc_start: 0.7288 (OUTLIER) cc_final: 0.6984 (m-40) REVERT: B 527 GLN cc_start: 0.8744 (tp-100) cc_final: 0.8388 (tp40) outliers start: 18 outliers final: 12 residues processed: 106 average time/residue: 0.5777 time to fit residues: 65.7783 Evaluate side-chains 106 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 333 MET Chi-restraints excluded: chain A residue 417 ILE 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 333 MET Chi-restraints excluded: chain B residue 417 ILE 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 90 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 118 optimal weight: 0.0000 chunk 40 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 42 optimal weight: 0.0270 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 0.5042 ------------------------------------------------------------------------------- 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 = 0.3221 r_free = 0.3221 target = 0.101716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.079640 restraints weight = 13493.741| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.85 r_work: 0.2770 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3618 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= 0.108 Angle : 0.506 9.134 13694 Z= 0.265 Chirality : 0.042 0.134 1612 Planarity : 0.004 0.041 1688 Dihedral : 4.428 20.282 1348 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.64 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.24), residues: 1260 helix: 2.44 (0.19), residues: 762 sheet: 1.43 (0.71), residues: 56 loop : -0.94 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 457 TYR 0.011 0.001 TYR A 159 PHE 0.011 0.001 PHE B 24 TRP 0.011 0.001 TRP B 61 HIS 0.004 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00243 (10096) covalent geometry : angle 0.50618 (13694) hydrogen bonds : bond 0.03871 ( 538) hydrogen bonds : angle 3.67575 ( 1572) *********************** 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 110 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.303 Fit side-chains REVERT: A 168 GLU cc_start: 0.8398 (tp30) cc_final: 0.8104 (tp30) REVERT: A 316 GLN cc_start: 0.7526 (mm110) cc_final: 0.7282 (mp10) REVERT: A 501 ASN cc_start: 0.7198 (OUTLIER) cc_final: 0.6923 (m-40) REVERT: A 509 MET cc_start: 0.7281 (pmm) cc_final: 0.6979 (mpt) REVERT: A 527 GLN cc_start: 0.8648 (tp-100) cc_final: 0.8427 (tm-30) REVERT: B 168 GLU cc_start: 0.8396 (tp30) cc_final: 0.8103 (tp30) REVERT: B 316 GLN cc_start: 0.7525 (mm110) cc_final: 0.7283 (mp10) REVERT: B 501 ASN cc_start: 0.7198 (OUTLIER) cc_final: 0.6924 (m-40) REVERT: B 509 MET cc_start: 0.7290 (pmm) cc_final: 0.6986 (mpt) REVERT: B 527 GLN cc_start: 0.8661 (tp-100) cc_final: 0.8439 (tm-30) outliers start: 14 outliers final: 10 residues processed: 108 average time/residue: 0.5949 time to fit residues: 68.8020 Evaluate side-chains 108 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 287 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 333 MET 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 287 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 MET 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 7 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3164 r_free = 0.3164 target = 0.097814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.075764 restraints weight = 13530.160| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 1.84 r_work: 0.2702 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10096 Z= 0.186 Angle : 0.578 8.240 13694 Z= 0.306 Chirality : 0.045 0.146 1612 Planarity : 0.004 0.044 1688 Dihedral : 4.800 20.461 1348 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.11 % Allowed : 12.75 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.24), residues: 1260 helix: 2.08 (0.18), residues: 778 sheet: 1.46 (0.70), residues: 56 loop : -1.00 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 205 TYR 0.012 0.002 TYR A 514 PHE 0.017 0.001 PHE A 499 TRP 0.007 0.001 TRP B 61 HIS 0.005 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00453 (10096) covalent geometry : angle 0.57802 (13694) hydrogen bonds : bond 0.05177 ( 538) hydrogen bonds : angle 3.83834 ( 1572) ********************** 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 104 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.403 Fit side-chains REVERT: A 168 GLU cc_start: 0.8442 (tp30) cc_final: 0.8153 (tp30) REVERT: A 287 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7889 (mt-10) REVERT: A 316 GLN cc_start: 0.7539 (mm110) cc_final: 0.7322 (mp10) REVERT: A 527 GLN cc_start: 0.8736 (tp-100) cc_final: 0.8514 (tm-30) REVERT: B 168 GLU cc_start: 0.8456 (tp30) cc_final: 0.8169 (tp30) REVERT: B 287 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: B 316 GLN cc_start: 0.7526 (mm110) cc_final: 0.7319 (mp10) REVERT: B 527 GLN cc_start: 0.8745 (tp-100) cc_final: 0.8521 (tm-30) outliers start: 12 outliers final: 6 residues processed: 100 average time/residue: 0.6266 time to fit residues: 66.8742 Evaluate side-chains 100 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 287 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 12 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3193 r_free = 0.3193 target = 0.099772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.077728 restraints weight = 13590.140| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.85 r_work: 0.2737 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10096 Z= 0.131 Angle : 0.529 8.357 13694 Z= 0.279 Chirality : 0.043 0.136 1612 Planarity : 0.004 0.040 1688 Dihedral : 4.613 21.019 1348 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.92 % Allowed : 13.12 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.24), residues: 1260 helix: 2.26 (0.18), residues: 770 sheet: 1.41 (0.71), residues: 56 loop : -0.83 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 457 TYR 0.012 0.001 TYR A 159 PHE 0.013 0.001 PHE A 265 TRP 0.009 0.001 TRP B 61 HIS 0.005 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00306 (10096) covalent geometry : angle 0.52890 (13694) hydrogen bonds : bond 0.04377 ( 538) hydrogen bonds : angle 3.75566 ( 1572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3173.11 seconds wall clock time: 54 minutes 45.72 seconds (3285.72 seconds total)