Starting phenix.real_space_refine on Fri Feb 14 07:45:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ch1_30368/02_2025/7ch1_30368.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ch1_30368/02_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_30368/02_2025/7ch1_30368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ch1_30368/02_2025/7ch1_30368.map" model { file = "/net/cci-nas-00/data/ceres_data/7ch1_30368/02_2025/7ch1_30368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ch1_30368/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 9.77, per 1000 atoms: 0.98 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 1.2 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: 1.03 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: 2.85 Time building geometry restraints manager: 2.77 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: 1.750 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.750 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.040 ------------------------------------------------------------------------------- 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= 0.456 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 *********************** 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 : 1.120 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: 1.0729 time to fit residues: 225.8656 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 : 1.236 ------------------------------------------------------------------------------- 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 = 0.103265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.080719 restraints weight = 13294.678| |-----------------------------------------------------------------------------| 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: 0.8582 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= 0.181 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 *********************** 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 : 1.229 Fit side-chains REVERT: A 287 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: A 527 GLN cc_start: 0.8737 (tp-100) cc_final: 0.8460 (tp40) REVERT: B 287 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7514 (tt0) REVERT: B 527 GLN cc_start: 0.8745 (tp-100) cc_final: 0.8465 (tp40) outliers start: 20 outliers final: 10 residues processed: 116 average time/residue: 1.3797 time to fit residues: 171.6429 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 : 1.162 ------------------------------------------------------------------------------- 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: 0.0070 chunk 69 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 HIS B 501 ASN B 663 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.076859 restraints weight = 13571.628| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 1.84 r_work: 0.2721 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2980 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= 0.255 Angle : 0.580 6.027 13694 Z= 0.312 Chirality : 0.044 0.140 1612 Planarity : 0.005 0.054 1688 Dihedral : 5.201 28.092 1352 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.85 % Allowed : 10.35 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.18 (0.23), residues: 1260 helix: 0.58 (0.18), residues: 782 sheet: 1.15 (0.67), residues: 56 loop : -1.56 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 61 HIS 0.006 0.001 HIS A 385 PHE 0.015 0.001 PHE B 24 TYR 0.010 0.001 TYR A 8 ARG 0.002 0.000 ARG B 457 *********************** 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 116 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 1.224 Fit side-chains REVERT: A 168 GLU cc_start: 0.8428 (tp30) cc_final: 0.8109 (tp30) REVERT: A 316 GLN cc_start: 0.7970 (mt0) cc_final: 0.7559 (mp10) REVERT: A 527 GLN cc_start: 0.8822 (tp-100) cc_final: 0.8550 (tp40) REVERT: B 168 GLU cc_start: 0.8437 (tp30) cc_final: 0.8115 (tp30) REVERT: B 316 GLN cc_start: 0.7970 (mt0) cc_final: 0.7564 (mp10) REVERT: B 527 GLN cc_start: 0.8835 (tp-100) cc_final: 0.8560 (tp40) outliers start: 20 outliers final: 14 residues processed: 114 average time/residue: 1.3055 time to fit residues: 160.0300 Evaluate side-chains 102 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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: 0.7980 chunk 77 optimal weight: 6.9990 chunk 20 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.100524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.078502 restraints weight = 13507.395| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.84 r_work: 0.2747 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3204 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= 0.181 Angle : 0.525 6.257 13694 Z= 0.281 Chirality : 0.042 0.148 1612 Planarity : 0.004 0.048 1688 Dihedral : 4.867 21.447 1350 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.57 % Allowed : 10.44 % 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: 0.73 (0.24), residues: 1260 helix: 1.39 (0.19), residues: 768 sheet: 1.69 (0.67), residues: 54 loop : -1.32 (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 B 385 PHE 0.013 0.001 PHE B 24 TYR 0.011 0.001 TYR B 159 ARG 0.002 0.000 ARG B 457 *********************** 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 111 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 1.056 Fit side-chains REVERT: A 168 GLU cc_start: 0.8429 (tp30) cc_final: 0.8131 (tp30) REVERT: A 287 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: A 316 GLN cc_start: 0.7949 (mt0) cc_final: 0.7529 (mp10) REVERT: A 501 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.7200 (m110) REVERT: A 527 GLN cc_start: 0.8804 (tp-100) cc_final: 0.8527 (tp40) REVERT: B 168 GLU cc_start: 0.8427 (tp30) cc_final: 0.8130 (tp30) REVERT: B 287 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: B 316 GLN cc_start: 0.7959 (mt0) cc_final: 0.7537 (mp10) REVERT: B 527 GLN cc_start: 0.8815 (tp-100) cc_final: 0.8536 (tp40) outliers start: 17 outliers final: 10 residues processed: 109 average time/residue: 1.2083 time to fit residues: 143.1818 Evaluate side-chains 101 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 501 ASN 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: 0.8980 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 118 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3200 r_free = 0.3200 target = 0.100150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.078032 restraints weight = 13526.066| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.84 r_work: 0.2743 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3331 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= 0.187 Angle : 0.518 6.353 13694 Z= 0.277 Chirality : 0.042 0.140 1612 Planarity : 0.004 0.048 1688 Dihedral : 4.693 20.218 1348 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.57 % Allowed : 11.37 % 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: 1.20 (0.24), residues: 1260 helix: 1.76 (0.19), residues: 770 sheet: 1.87 (0.68), residues: 54 loop : -1.15 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 61 HIS 0.005 0.001 HIS B 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 *********************** 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 113 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.174 Fit side-chains REVERT: A 168 GLU cc_start: 0.8424 (tp30) cc_final: 0.8147 (tp30) REVERT: A 280 ILE cc_start: 0.4902 (OUTLIER) cc_final: 0.4609 (pt) REVERT: A 316 GLN cc_start: 0.7952 (mt0) cc_final: 0.7539 (mp10) REVERT: A 501 ASN cc_start: 0.7520 (OUTLIER) cc_final: 0.7244 (m110) REVERT: A 527 GLN cc_start: 0.8768 (tp-100) cc_final: 0.8459 (tp40) REVERT: B 168 GLU cc_start: 0.8424 (tp30) cc_final: 0.8147 (tp30) REVERT: B 280 ILE cc_start: 0.4903 (OUTLIER) cc_final: 0.4611 (pt) REVERT: B 316 GLN cc_start: 0.7961 (mt0) cc_final: 0.7541 (mp10) REVERT: B 527 GLN cc_start: 0.8768 (tp-100) cc_final: 0.8458 (tp40) outliers start: 17 outliers final: 10 residues processed: 111 average time/residue: 1.2716 time to fit residues: 152.1122 Evaluate side-chains 103 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 501 ASN 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 86 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 1 optimal weight: 0.2980 chunk 91 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.100055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.077016 restraints weight = 13318.736| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.91 r_work: 0.2701 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3407 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= 0.178 Angle : 0.513 6.921 13694 Z= 0.272 Chirality : 0.042 0.145 1612 Planarity : 0.004 0.045 1688 Dihedral : 4.596 19.605 1348 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.03 % Allowed : 10.91 % 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: 1.47 (0.24), residues: 1260 helix: 2.01 (0.19), residues: 768 sheet: 1.90 (0.69), residues: 54 loop : -1.08 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 61 HIS 0.004 0.001 HIS B 385 PHE 0.012 0.001 PHE B 24 TYR 0.010 0.001 TYR B 454 ARG 0.002 0.000 ARG B 457 *********************** 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 110 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.908 Fit side-chains REVERT: A 48 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8514 (mm) REVERT: A 147 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8108 (mtpp) REVERT: A 168 GLU cc_start: 0.8475 (tp30) cc_final: 0.8182 (tp30) REVERT: A 280 ILE cc_start: 0.4857 (OUTLIER) cc_final: 0.4561 (pt) REVERT: A 316 GLN cc_start: 0.7990 (mt0) cc_final: 0.7515 (mp10) REVERT: A 501 ASN cc_start: 0.7459 (OUTLIER) cc_final: 0.7220 (m110) REVERT: A 527 GLN cc_start: 0.8710 (tp-100) cc_final: 0.8389 (tp40) REVERT: B 48 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8512 (mm) REVERT: B 147 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8116 (mtpp) REVERT: B 168 GLU cc_start: 0.8465 (tp30) cc_final: 0.8173 (tp30) REVERT: B 280 ILE cc_start: 0.4859 (OUTLIER) cc_final: 0.4562 (pt) REVERT: B 316 GLN cc_start: 0.7999 (mt0) cc_final: 0.7522 (mp10) REVERT: B 501 ASN cc_start: 0.7518 (OUTLIER) cc_final: 0.7224 (m-40) REVERT: B 527 GLN cc_start: 0.8696 (tp-100) cc_final: 0.8343 (tp40) outliers start: 22 outliers final: 12 residues processed: 106 average time/residue: 1.3489 time to fit residues: 153.6850 Evaluate side-chains 106 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 147 LYS 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 A residue 661 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 147 LYS 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 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 23 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 24 optimal weight: 0.0060 chunk 87 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 16 optimal weight: 0.0070 chunk 30 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- 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 = 0.3226 r_free = 0.3226 target = 0.101967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.079818 restraints weight = 13621.899| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.85 r_work: 0.2774 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3508 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= 0.152 Angle : 0.497 7.294 13694 Z= 0.262 Chirality : 0.041 0.136 1612 Planarity : 0.004 0.044 1688 Dihedral : 4.430 20.058 1348 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.03 % Allowed : 10.91 % 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: 1.75 (0.24), residues: 1260 helix: 2.27 (0.19), residues: 764 sheet: 1.87 (0.68), residues: 54 loop : -0.98 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 61 HIS 0.004 0.001 HIS A 385 PHE 0.011 0.001 PHE B 24 TYR 0.010 0.001 TYR B 454 ARG 0.002 0.000 ARG B 457 *********************** 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 119 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 1.169 Fit side-chains REVERT: A 48 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8556 (mm) REVERT: A 168 GLU cc_start: 0.8406 (tp30) cc_final: 0.8098 (tp30) REVERT: A 280 ILE cc_start: 0.4489 (OUTLIER) cc_final: 0.4197 (pt) REVERT: A 316 GLN cc_start: 0.7942 (mt0) cc_final: 0.7518 (mp10) REVERT: A 501 ASN cc_start: 0.7425 (OUTLIER) cc_final: 0.7168 (m110) REVERT: A 527 GLN cc_start: 0.8706 (tp-100) cc_final: 0.8372 (tp40) REVERT: B 48 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8556 (mm) REVERT: B 168 GLU cc_start: 0.8406 (tp30) cc_final: 0.8100 (tp30) REVERT: B 280 ILE cc_start: 0.4490 (OUTLIER) cc_final: 0.4196 (pt) REVERT: B 316 GLN cc_start: 0.7952 (mt0) cc_final: 0.7524 (mp10) REVERT: B 501 ASN cc_start: 0.7392 (OUTLIER) cc_final: 0.7104 (m-40) REVERT: B 527 GLN cc_start: 0.8712 (tp-100) cc_final: 0.8378 (tp40) outliers start: 22 outliers final: 8 residues processed: 115 average time/residue: 1.2302 time to fit residues: 153.0539 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 : 1.152 ------------------------------------------------------------------------------- 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 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 501 ASN Chi-restraints excluded: chain B residue 48 ILE 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 501 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3198 r_free = 0.3198 target = 0.099977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.077786 restraints weight = 13676.543| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.86 r_work: 0.2738 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3478 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= 0.205 Angle : 0.524 7.840 13694 Z= 0.278 Chirality : 0.043 0.140 1612 Planarity : 0.004 0.043 1688 Dihedral : 4.572 19.910 1348 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.22 % Allowed : 11.55 % Favored : 86.23 % 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: 1.71 (0.24), residues: 1260 helix: 2.20 (0.18), residues: 770 sheet: 1.55 (0.70), residues: 56 loop : -0.93 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 61 HIS 0.005 0.001 HIS B 385 PHE 0.014 0.001 PHE B 499 TYR 0.009 0.001 TYR A 514 ARG 0.002 0.000 ARG B 205 *********************** 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 118 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 1.159 Fit side-chains REVERT: A 147 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8181 (mtpp) REVERT: A 168 GLU cc_start: 0.8437 (tp30) cc_final: 0.8131 (tp30) REVERT: A 280 ILE cc_start: 0.4404 (OUTLIER) cc_final: 0.4123 (pt) REVERT: A 501 ASN cc_start: 0.7412 (OUTLIER) cc_final: 0.7188 (m110) REVERT: A 527 GLN cc_start: 0.8703 (tp-100) cc_final: 0.8361 (tp40) REVERT: B 168 GLU cc_start: 0.8436 (tp30) cc_final: 0.8130 (tp30) REVERT: B 280 ILE cc_start: 0.4400 (OUTLIER) cc_final: 0.4117 (pt) REVERT: B 501 ASN cc_start: 0.7450 (OUTLIER) cc_final: 0.7182 (m-40) REVERT: B 527 GLN cc_start: 0.8713 (tp-100) cc_final: 0.8369 (tp40) outliers start: 24 outliers final: 15 residues processed: 114 average time/residue: 1.2987 time to fit residues: 159.4720 Evaluate side-chains 110 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LYS 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 349 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 147 LYS 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 349 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 661 THR 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: 0.7980 chunk 83 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 12 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3199 r_free = 0.3199 target = 0.100313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.077269 restraints weight = 13276.725| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 1.92 r_work: 0.2705 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3533 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= 0.172 Angle : 0.514 9.015 13694 Z= 0.270 Chirality : 0.042 0.133 1612 Planarity : 0.004 0.041 1688 Dihedral : 4.471 20.300 1348 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.94 % Allowed : 11.65 % Favored : 86.41 % 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: 1.87 (0.24), residues: 1260 helix: 2.35 (0.18), residues: 768 sheet: 1.84 (0.70), residues: 54 loop : -0.92 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 61 HIS 0.004 0.001 HIS B 385 PHE 0.012 0.001 PHE B 24 TYR 0.010 0.001 TYR B 454 ARG 0.001 0.000 ARG B 457 *********************** 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 116 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.094 Fit side-chains REVERT: A 168 GLU cc_start: 0.8475 (tp30) cc_final: 0.8161 (tp30) REVERT: A 501 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.7211 (m110) REVERT: A 509 MET cc_start: 0.7362 (pmm) cc_final: 0.7004 (mpt) REVERT: A 527 GLN cc_start: 0.8682 (tp-100) cc_final: 0.8325 (tp40) REVERT: B 168 GLU cc_start: 0.8466 (tp30) cc_final: 0.8153 (tp30) REVERT: B 501 ASN cc_start: 0.7299 (OUTLIER) cc_final: 0.6926 (m110) REVERT: B 509 MET cc_start: 0.7366 (pmm) cc_final: 0.7004 (mpt) REVERT: B 527 GLN cc_start: 0.8659 (tp-100) cc_final: 0.8301 (tp40) outliers start: 21 outliers final: 15 residues processed: 112 average time/residue: 1.2877 time to fit residues: 155.3447 Evaluate side-chains 108 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 349 LEU Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 147 LYS 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 349 LEU Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 661 THR 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: 0.1980 chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 41 optimal weight: 0.0670 chunk 107 optimal weight: 0.0050 chunk 103 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 overall best weight: 0.2932 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.104316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.082185 restraints weight = 13509.817| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.85 r_work: 0.2815 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3715 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= 0.130 Angle : 0.480 8.711 13694 Z= 0.250 Chirality : 0.041 0.131 1612 Planarity : 0.004 0.038 1688 Dihedral : 4.176 20.811 1348 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.29 % Allowed : 12.57 % 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 (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: 2.13 (0.25), residues: 1260 helix: 2.60 (0.19), residues: 774 sheet: 2.09 (0.73), residues: 48 loop : -0.95 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 61 HIS 0.003 0.000 HIS B 385 PHE 0.011 0.001 PHE A 265 TYR 0.011 0.001 TYR A 454 ARG 0.001 0.000 ARG B 547 ********************** 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 118 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.060 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: 0.8376 (tp30) cc_final: 0.8102 (tp30) REVERT: A 316 GLN cc_start: 0.7939 (mt0) cc_final: 0.7509 (mp10) REVERT: A 501 ASN cc_start: 0.7342 (OUTLIER) cc_final: 0.7058 (m110) REVERT: A 509 MET cc_start: 0.7223 (pmm) cc_final: 0.6935 (mpt) REVERT: A 527 GLN cc_start: 0.8623 (tp-100) cc_final: 0.8300 (tp40) REVERT: A 659 PHE cc_start: 0.7748 (m-80) cc_final: 0.7363 (m-80) REVERT: B 168 GLU cc_start: 0.8364 (tp30) cc_final: 0.8090 (tp30) REVERT: B 316 GLN cc_start: 0.7953 (mt0) cc_final: 0.7514 (mp10) REVERT: B 501 ASN cc_start: 0.7203 (OUTLIER) cc_final: 0.6899 (m-40) REVERT: B 509 MET cc_start: 0.7229 (pmm) cc_final: 0.6933 (mpt) REVERT: B 527 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8301 (tp40) REVERT: B 659 PHE cc_start: 0.7744 (m-80) cc_final: 0.7356 (m-80) outliers start: 14 outliers final: 6 residues processed: 116 average time/residue: 1.2593 time to fit residues: 157.8603 Evaluate side-chains 108 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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: 0.7980 chunk 103 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 74 optimal weight: 0.3980 chunk 98 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3199 r_free = 0.3199 target = 0.100357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.077283 restraints weight = 13223.854| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 1.92 r_work: 0.2706 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 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 : 0.003 0.030 10096 Z= 0.190 Angle : 0.518 8.061 13694 Z= 0.272 Chirality : 0.042 0.130 1612 Planarity : 0.004 0.038 1688 Dihedral : 4.380 21.019 1348 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.11 % Allowed : 13.12 % Favored : 85.77 % 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: 2.06 (0.25), residues: 1260 helix: 2.47 (0.18), residues: 780 sheet: 1.51 (0.71), residues: 56 loop : -0.84 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 61 HIS 0.004 0.001 HIS A 385 PHE 0.014 0.001 PHE A 265 TYR 0.009 0.001 TYR B 454 ARG 0.002 0.000 ARG A 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6940.73 seconds wall clock time: 123 minutes 39.78 seconds (7419.78 seconds total)