Starting phenix.real_space_refine on Thu Feb 5 12:36:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mzc_24089/02_2026/7mzc_24089.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mzc_24089/02_2026/7mzc_24089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mzc_24089/02_2026/7mzc_24089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mzc_24089/02_2026/7mzc_24089.map" model { file = "/net/cci-nas-00/data/ceres_data/7mzc_24089/02_2026/7mzc_24089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mzc_24089/02_2026/7mzc_24089.cif" } resolution = 3.03 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= 0.002 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: 5 Type Number sf(0) Gaussians S 100 5.16 5 Na 2 4.78 5 C 11384 2.51 5 N 2780 2.21 5 O 3068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17334 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4287 Classifications: {'peptide': 528} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 513} Chain: "D" Number of atoms: 4287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4287 Classifications: {'peptide': 528} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 513} Chain: "B" Number of atoms: 4287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4287 Classifications: {'peptide': 528} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 513} Chain: "C" Number of atoms: 4287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4287 Classifications: {'peptide': 528} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 513} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {' NA': 2, '6EU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.11, per 1000 atoms: 0.24 Number of scatterers: 17334 At special positions: 0 Unit cell: (125.934, 125.934, 108.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 Na 2 11.00 O 3068 8.00 N 2780 7.00 C 11384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.04 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: 1.66 Conformation dependent library (CDL) restraints added in 747.9 milliseconds 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4000 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 4 sheets defined 67.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.504A pdb=" N ILE A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.634A pdb=" N ALA A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 411 through 414 Processing helix chain 'A' and resid 415 through 454 removed outlier: 5.235A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.769A pdb=" N VAL A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.805A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 561 through 575 removed outlier: 4.306A pdb=" N TYR A 565 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 599 Processing helix chain 'A' and resid 629 through 642 removed outlier: 3.860A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 672 through 712 removed outlier: 3.874A pdb=" N ASN A 676 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.538A pdb=" N ALA D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 324 through 328 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.760A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 411 through 414 Processing helix chain 'D' and resid 415 through 454 removed outlier: 5.239A pdb=" N LYS D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE D 433 " --> pdb=" O PHE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 504 through 509 removed outlier: 3.809A pdb=" N VAL D 508 " --> pdb=" O LYS D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.823A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 557 Processing helix chain 'D' and resid 562 through 575 removed outlier: 3.632A pdb=" N ALA D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 599 Processing helix chain 'D' and resid 629 through 642 removed outlier: 4.005A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 672 through 712 removed outlier: 3.854A pdb=" N ASN D 676 " --> pdb=" O ILE D 672 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN D 695 " --> pdb=" O GLN D 691 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.615A pdb=" N ALA B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'B' and resid 415 through 429 Processing helix chain 'B' and resid 429 through 454 removed outlier: 4.067A pdb=" N ILE B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 504 through 509 removed outlier: 3.750A pdb=" N VAL B 508 " --> pdb=" O LYS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.811A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 Processing helix chain 'B' and resid 561 through 575 removed outlier: 4.277A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 599 Processing helix chain 'B' and resid 629 through 642 removed outlier: 3.872A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 672 through 712 removed outlier: 3.868A pdb=" N ASN B 676 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN B 695 " --> pdb=" O GLN B 691 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 211 removed outlier: 3.575A pdb=" N ILE C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.617A pdb=" N ALA C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 411 through 414 Processing helix chain 'C' and resid 415 through 454 removed outlier: 5.225A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 504 through 509 removed outlier: 3.949A pdb=" N VAL C 508 " --> pdb=" O LYS C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.824A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 Processing helix chain 'C' and resid 559 through 575 removed outlier: 3.821A pdb=" N ILE C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 599 Processing helix chain 'C' and resid 629 through 642 removed outlier: 4.015A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 671 Processing helix chain 'C' and resid 672 through 712 removed outlier: 3.855A pdb=" N ASN C 676 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN C 695 " --> pdb=" O GLN C 691 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 373 removed outlier: 7.046A pdb=" N SER A 379 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA A 373 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 368 through 373 removed outlier: 7.167A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ALA D 373 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 373 removed outlier: 6.951A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA B 373 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 368 through 373 removed outlier: 5.619A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) 1023 hydrogen bonds defined for protein. 2937 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: 2.84 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2685 1.31 - 1.44: 5067 1.44 - 1.57: 9836 1.57 - 1.70: 16 1.70 - 1.83: 164 Bond restraints: 17768 Sorted by residual: bond pdb=" CAM 6EU B 901 " pdb=" OAC 6EU B 901 " ideal model delta sigma weight residual 1.422 1.182 0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" CAM 6EU A 901 " pdb=" OAC 6EU A 901 " ideal model delta sigma weight residual 1.422 1.183 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" CAM 6EU D 901 " pdb=" OAC 6EU D 901 " ideal model delta sigma weight residual 1.422 1.184 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" CAM 6EU C 901 " pdb=" OAC 6EU C 901 " ideal model delta sigma weight residual 1.422 1.184 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" CAV 6EU B 901 " pdb=" CBB 6EU B 901 " ideal model delta sigma weight residual 1.330 1.523 -0.193 2.00e-02 2.50e+03 9.34e+01 ... (remaining 17763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 23694 2.70 - 5.41: 355 5.41 - 8.11: 18 8.11 - 10.82: 33 10.82 - 13.52: 12 Bond angle restraints: 24112 Sorted by residual: angle pdb=" N ASP C 654 " pdb=" CA ASP C 654 " pdb=" C ASP C 654 " ideal model delta sigma weight residual 109.85 100.05 9.80 1.58e+00 4.01e-01 3.85e+01 angle pdb=" N ILE D 387 " pdb=" CA ILE D 387 " pdb=" C ILE D 387 " ideal model delta sigma weight residual 111.48 106.34 5.14 9.40e-01 1.13e+00 2.99e+01 angle pdb=" N SER C 722 " pdb=" CA SER C 722 " pdb=" CB SER C 722 " ideal model delta sigma weight residual 114.17 108.89 5.28 1.14e+00 7.69e-01 2.14e+01 angle pdb=" C SER B 711 " pdb=" N PHE B 712 " pdb=" CA PHE B 712 " ideal model delta sigma weight residual 121.54 130.33 -8.79 1.91e+00 2.74e-01 2.12e+01 angle pdb=" N SER B 722 " pdb=" CA SER B 722 " pdb=" CB SER B 722 " ideal model delta sigma weight residual 114.17 109.02 5.15 1.14e+00 7.69e-01 2.04e+01 ... (remaining 24107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 10097 17.78 - 35.55: 482 35.55 - 53.33: 89 53.33 - 71.11: 34 71.11 - 88.88: 17 Dihedral angle restraints: 10719 sinusoidal: 4499 harmonic: 6220 Sorted by residual: dihedral pdb=" CA PHE A 429 " pdb=" C PHE A 429 " pdb=" N VAL A 430 " pdb=" CA VAL A 430 " ideal model delta harmonic sigma weight residual 180.00 -153.73 -26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA PHE B 429 " pdb=" C PHE B 429 " pdb=" N VAL B 430 " pdb=" CA VAL B 430 " ideal model delta harmonic sigma weight residual -180.00 -154.04 -25.96 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA PHE C 429 " pdb=" C PHE C 429 " pdb=" N VAL C 430 " pdb=" CA VAL C 430 " ideal model delta harmonic sigma weight residual -180.00 -154.30 -25.70 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 10716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2649 0.105 - 0.209: 51 0.209 - 0.313: 4 0.313 - 0.418: 0 0.418 - 0.522: 12 Chirality restraints: 2716 Sorted by residual: chirality pdb=" CAJ 6EU A 901 " pdb=" CAK 6EU A 901 " pdb=" CAN 6EU A 901 " pdb=" CAO 6EU A 901 " both_signs ideal model delta sigma weight residual False 2.66 2.13 0.52 2.00e-01 2.50e+01 6.82e+00 chirality pdb=" CAJ 6EU B 901 " pdb=" CAK 6EU B 901 " pdb=" CAN 6EU B 901 " pdb=" CAO 6EU B 901 " both_signs ideal model delta sigma weight residual False 2.66 2.14 0.51 2.00e-01 2.50e+01 6.57e+00 chirality pdb=" CAJ 6EU D 901 " pdb=" CAK 6EU D 901 " pdb=" CAN 6EU D 901 " pdb=" CAO 6EU D 901 " both_signs ideal model delta sigma weight residual False 2.66 2.14 0.51 2.00e-01 2.50e+01 6.55e+00 ... (remaining 2713 not shown) Planarity restraints: 2968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM 6EU D 901 " -0.110 2.00e-02 2.50e+03 1.91e-01 3.64e+02 pdb=" CAV 6EU D 901 " 0.331 2.00e-02 2.50e+03 pdb=" CBB 6EU D 901 " -0.111 2.00e-02 2.50e+03 pdb=" CBD 6EU D 901 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU C 901 " -0.109 2.00e-02 2.50e+03 1.91e-01 3.63e+02 pdb=" CAV 6EU C 901 " 0.330 2.00e-02 2.50e+03 pdb=" CBB 6EU C 901 " -0.111 2.00e-02 2.50e+03 pdb=" CBD 6EU C 901 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU B 901 " 0.109 2.00e-02 2.50e+03 1.90e-01 3.59e+02 pdb=" CAV 6EU B 901 " -0.328 2.00e-02 2.50e+03 pdb=" CBB 6EU B 901 " 0.110 2.00e-02 2.50e+03 pdb=" CBD 6EU B 901 " 0.110 2.00e-02 2.50e+03 ... (remaining 2965 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 143 2.60 - 3.18: 15763 3.18 - 3.75: 26736 3.75 - 4.33: 37832 4.33 - 4.90: 62370 Nonbonded interactions: 142844 Sorted by model distance: nonbonded pdb=" OG1 THR D 731 " pdb=" OD1 ASP D 733 " model vdw 2.028 3.040 nonbonded pdb=" OG1 THR C 731 " pdb=" OD1 ASP C 733 " model vdw 2.049 3.040 nonbonded pdb=" OG1 THR A 731 " pdb=" OD1 ASP A 733 " model vdw 2.062 3.040 nonbonded pdb=" OG1 THR B 731 " pdb=" OD1 ASP B 733 " model vdw 2.077 3.040 nonbonded pdb=" O GLY B 643 " pdb="NA NA A 902 " model vdw 2.334 2.470 ... (remaining 142839 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 202 through 901) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 3.170 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.800 Find NCS groups from input model: 0.260 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 : 0.012 0.240 17769 Z= 0.555 Angle : 0.905 13.521 24114 Z= 0.456 Chirality : 0.053 0.522 2716 Planarity : 0.008 0.191 2968 Dihedral : 12.070 88.883 6716 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.28 % Favored : 94.58 % Rotamer: Outliers : 1.12 % Allowed : 1.61 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.39 (0.18), residues: 2104 helix: 1.22 (0.14), residues: 1360 sheet: -1.03 (0.53), residues: 76 loop : -1.58 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 739 TYR 0.020 0.002 TYR D 627 PHE 0.029 0.002 PHE D 649 TRP 0.008 0.002 TRP A 549 HIS 0.003 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.01153 (17768) covalent geometry : angle 0.90488 (24112) SS BOND : bond 0.01036 ( 1) SS BOND : angle 2.67927 ( 2) hydrogen bonds : bond 0.11892 ( 1023) hydrogen bonds : angle 5.02245 ( 2937) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 714 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLN cc_start: 0.8014 (tp40) cc_final: 0.7772 (tp40) REVERT: A 315 LEU cc_start: 0.9019 (mt) cc_final: 0.8708 (mp) REVERT: A 368 LYS cc_start: 0.8170 (tttt) cc_final: 0.7876 (tttm) REVERT: A 369 PHE cc_start: 0.8744 (m-80) cc_final: 0.8447 (m-80) REVERT: A 385 SER cc_start: 0.8888 (t) cc_final: 0.8482 (m) REVERT: A 401 TYR cc_start: 0.8427 (m-80) cc_final: 0.8168 (m-10) REVERT: A 428 ARG cc_start: 0.7883 (mtt-85) cc_final: 0.7594 (mtt90) REVERT: A 435 TYR cc_start: 0.9056 (m-80) cc_final: 0.8828 (m-10) REVERT: A 438 PHE cc_start: 0.9224 (t80) cc_final: 0.8800 (t80) REVERT: A 465 LEU cc_start: 0.8864 (tp) cc_final: 0.8495 (tt) REVERT: A 478 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8186 (mt-10) REVERT: A 513 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8600 (mm-30) REVERT: A 561 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8208 (pm20) REVERT: A 737 ASP cc_start: 0.7391 (p0) cc_final: 0.7138 (p0) REVERT: A 745 ASP cc_start: 0.7609 (m-30) cc_final: 0.7249 (t0) REVERT: D 273 GLN cc_start: 0.7983 (tp40) cc_final: 0.7740 (tp40) REVERT: D 310 ASN cc_start: 0.8910 (t0) cc_final: 0.8519 (t0) REVERT: D 311 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8353 (mm-30) REVERT: D 315 LEU cc_start: 0.9058 (mt) cc_final: 0.8702 (mp) REVERT: D 368 LYS cc_start: 0.8277 (tttt) cc_final: 0.7630 (tttm) REVERT: D 378 HIS cc_start: 0.7865 (p-80) cc_final: 0.6918 (p-80) REVERT: D 385 SER cc_start: 0.8754 (t) cc_final: 0.8309 (m) REVERT: D 401 TYR cc_start: 0.8449 (m-80) cc_final: 0.8222 (m-10) REVERT: D 428 ARG cc_start: 0.7917 (mtt-85) cc_final: 0.7627 (mtt90) REVERT: D 438 PHE cc_start: 0.9242 (t80) cc_final: 0.8826 (t80) REVERT: D 465 LEU cc_start: 0.8878 (tp) cc_final: 0.8468 (tt) REVERT: D 561 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8203 (pm20) REVERT: B 266 PHE cc_start: 0.8745 (t80) cc_final: 0.8513 (t80) REVERT: B 310 ASN cc_start: 0.8882 (t0) cc_final: 0.8432 (t0) REVERT: B 311 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8426 (mm-30) REVERT: B 315 LEU cc_start: 0.9058 (mt) cc_final: 0.8739 (mp) REVERT: B 378 HIS cc_start: 0.7790 (p-80) cc_final: 0.6522 (p-80) REVERT: B 385 SER cc_start: 0.8970 (t) cc_final: 0.8551 (m) REVERT: B 401 TYR cc_start: 0.8470 (m-80) cc_final: 0.8131 (m-10) REVERT: B 423 GLN cc_start: 0.8530 (tp40) cc_final: 0.8030 (tp-100) REVERT: B 428 ARG cc_start: 0.7977 (mtt-85) cc_final: 0.7670 (mtt90) REVERT: B 435 TYR cc_start: 0.9063 (m-80) cc_final: 0.8849 (m-10) REVERT: B 438 PHE cc_start: 0.9232 (t80) cc_final: 0.8819 (t80) REVERT: B 465 LEU cc_start: 0.8865 (tp) cc_final: 0.7973 (tp) REVERT: B 513 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8638 (mm-30) REVERT: B 561 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8236 (pm20) REVERT: B 698 LYS cc_start: 0.9134 (mttm) cc_final: 0.8606 (mtmm) REVERT: B 733 ASP cc_start: 0.7498 (p0) cc_final: 0.7226 (p0) REVERT: B 737 ASP cc_start: 0.7081 (p0) cc_final: 0.6784 (p0) REVERT: B 745 ASP cc_start: 0.7781 (m-30) cc_final: 0.7317 (t0) REVERT: C 266 PHE cc_start: 0.8818 (t80) cc_final: 0.8612 (t80) REVERT: C 273 GLN cc_start: 0.7994 (tp40) cc_final: 0.7743 (tp40) REVERT: C 310 ASN cc_start: 0.8893 (t0) cc_final: 0.8587 (t0) REVERT: C 315 LEU cc_start: 0.8984 (mt) cc_final: 0.8761 (mp) REVERT: C 369 PHE cc_start: 0.8636 (m-80) cc_final: 0.8286 (m-80) REVERT: C 378 HIS cc_start: 0.7760 (p-80) cc_final: 0.6829 (p-80) REVERT: C 385 SER cc_start: 0.9104 (t) cc_final: 0.8874 (t) REVERT: C 397 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7857 (mt-10) REVERT: C 401 TYR cc_start: 0.8481 (m-80) cc_final: 0.8206 (m-10) REVERT: C 409 ARG cc_start: 0.8316 (ptm-80) cc_final: 0.7932 (ttp-170) REVERT: C 428 ARG cc_start: 0.7884 (mtt-85) cc_final: 0.7615 (mtt90) REVERT: C 438 PHE cc_start: 0.9237 (t80) cc_final: 0.8823 (t80) REVERT: C 465 LEU cc_start: 0.8862 (tp) cc_final: 0.8458 (tt) REVERT: C 478 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8193 (mt-10) REVERT: C 504 LYS cc_start: 0.8865 (mttt) cc_final: 0.8616 (mptt) REVERT: C 506 LEU cc_start: 0.9002 (tp) cc_final: 0.8772 (tp) REVERT: C 513 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8411 (mm-30) REVERT: C 561 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8231 (pm20) REVERT: C 733 ASP cc_start: 0.7553 (p0) cc_final: 0.7350 (p0) REVERT: C 737 ASP cc_start: 0.7409 (p0) cc_final: 0.7201 (p0) REVERT: C 745 ASP cc_start: 0.7695 (m-30) cc_final: 0.7227 (t0) outliers start: 21 outliers final: 2 residues processed: 719 average time/residue: 0.1513 time to fit residues: 155.1413 Evaluate side-chains 465 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 459 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain C residue 561 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 393 ASN A 652 ASN D 310 ASN D 652 ASN B 310 ASN B 354 GLN B 358 HIS B 652 ASN B 676 ASN B 727 GLN C 652 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.149014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.095191 restraints weight = 25405.877| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.47 r_work: 0.2899 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17769 Z= 0.143 Angle : 0.567 8.558 24114 Z= 0.305 Chirality : 0.040 0.136 2716 Planarity : 0.004 0.070 2968 Dihedral : 8.401 79.407 2714 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.56 % Favored : 94.39 % Rotamer: Outliers : 1.23 % Allowed : 10.71 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.12 (0.19), residues: 2104 helix: 1.85 (0.14), residues: 1336 sheet: -0.15 (0.58), residues: 76 loop : -1.43 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 363 TYR 0.016 0.002 TYR D 401 PHE 0.031 0.002 PHE A 304 TRP 0.009 0.001 TRP C 697 HIS 0.006 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00307 (17768) covalent geometry : angle 0.56526 (24112) SS BOND : bond 0.01766 ( 1) SS BOND : angle 4.80255 ( 2) hydrogen bonds : bond 0.04887 ( 1023) hydrogen bonds : angle 3.95770 ( 2937) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 543 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 LEU cc_start: 0.9263 (mt) cc_final: 0.8998 (mt) REVERT: A 351 TYR cc_start: 0.8913 (t80) cc_final: 0.8710 (t80) REVERT: A 361 GLU cc_start: 0.7584 (tp30) cc_final: 0.7373 (tp30) REVERT: A 368 LYS cc_start: 0.8414 (tttt) cc_final: 0.8064 (tttm) REVERT: A 369 PHE cc_start: 0.8647 (m-80) cc_final: 0.8344 (m-10) REVERT: A 383 ASP cc_start: 0.8257 (t0) cc_final: 0.7818 (t0) REVERT: A 385 SER cc_start: 0.9041 (t) cc_final: 0.8463 (m) REVERT: A 394 SER cc_start: 0.9157 (m) cc_final: 0.8809 (p) REVERT: A 401 TYR cc_start: 0.8772 (m-80) cc_final: 0.8343 (m-10) REVERT: A 423 GLN cc_start: 0.8805 (tp40) cc_final: 0.8576 (tp-100) REVERT: A 428 ARG cc_start: 0.8755 (mtt-85) cc_final: 0.8460 (mtt90) REVERT: A 435 TYR cc_start: 0.9304 (m-80) cc_final: 0.9084 (m-10) REVERT: A 438 PHE cc_start: 0.9307 (t80) cc_final: 0.8838 (t80) REVERT: A 472 TYR cc_start: 0.8957 (m-80) cc_final: 0.8746 (m-10) REVERT: A 561 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8262 (pm20) REVERT: A 575 ARG cc_start: 0.7760 (mmt180) cc_final: 0.7550 (mmm160) REVERT: D 325 LEU cc_start: 0.9210 (mt) cc_final: 0.8883 (mt) REVERT: D 361 GLU cc_start: 0.7395 (tp30) cc_final: 0.7158 (tp30) REVERT: D 385 SER cc_start: 0.8868 (t) cc_final: 0.8349 (m) REVERT: D 394 SER cc_start: 0.9009 (m) cc_final: 0.8490 (p) REVERT: D 423 GLN cc_start: 0.8806 (tp40) cc_final: 0.8577 (tp-100) REVERT: D 428 ARG cc_start: 0.8736 (mtt-85) cc_final: 0.8481 (mtt90) REVERT: D 438 PHE cc_start: 0.9323 (t80) cc_final: 0.9008 (t80) REVERT: D 561 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8269 (pm20) REVERT: D 743 ARG cc_start: 0.8805 (ttm-80) cc_final: 0.8472 (ttm-80) REVERT: B 311 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8653 (mm-30) REVERT: B 351 TYR cc_start: 0.8993 (t80) cc_final: 0.8697 (t80) REVERT: B 372 TRP cc_start: 0.8392 (p-90) cc_final: 0.8075 (p-90) REVERT: B 383 ASP cc_start: 0.8112 (t0) cc_final: 0.7576 (t0) REVERT: B 385 SER cc_start: 0.9090 (t) cc_final: 0.8519 (m) REVERT: B 394 SER cc_start: 0.9074 (m) cc_final: 0.8849 (p) REVERT: B 397 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8122 (mt-10) REVERT: B 401 TYR cc_start: 0.8793 (m-80) cc_final: 0.8576 (m-10) REVERT: B 423 GLN cc_start: 0.8786 (tp40) cc_final: 0.8376 (tp40) REVERT: B 427 ASP cc_start: 0.9003 (m-30) cc_final: 0.8754 (m-30) REVERT: B 428 ARG cc_start: 0.8669 (mtt-85) cc_final: 0.8435 (mtt90) REVERT: B 438 PHE cc_start: 0.9316 (t80) cc_final: 0.8858 (t80) REVERT: B 472 TYR cc_start: 0.8955 (m-10) cc_final: 0.8753 (m-10) REVERT: B 561 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8252 (pm20) REVERT: B 575 ARG cc_start: 0.7730 (mmt180) cc_final: 0.7455 (mmm160) REVERT: B 698 LYS cc_start: 0.9180 (mttm) cc_final: 0.8626 (mtmm) REVERT: B 743 ARG cc_start: 0.8530 (ttm-80) cc_final: 0.8155 (ttm-80) REVERT: C 383 ASP cc_start: 0.8230 (t0) cc_final: 0.7663 (t0) REVERT: C 385 SER cc_start: 0.9159 (t) cc_final: 0.8486 (m) REVERT: C 427 ASP cc_start: 0.8998 (m-30) cc_final: 0.8739 (m-30) REVERT: C 428 ARG cc_start: 0.8714 (mtt-85) cc_final: 0.8426 (mtt90) REVERT: C 438 PHE cc_start: 0.9334 (t80) cc_final: 0.8886 (t80) REVERT: C 504 LYS cc_start: 0.9069 (mttt) cc_final: 0.8631 (mptt) REVERT: C 513 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8942 (mm-30) REVERT: C 561 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8312 (pm20) outliers start: 23 outliers final: 12 residues processed: 552 average time/residue: 0.1358 time to fit residues: 112.5704 Evaluate side-chains 486 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 470 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 561 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 80 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 205 optimal weight: 10.0000 chunk 143 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.143896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.090236 restraints weight = 25704.117| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.44 r_work: 0.2844 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 17769 Z= 0.264 Angle : 0.625 8.494 24114 Z= 0.331 Chirality : 0.043 0.135 2716 Planarity : 0.004 0.050 2968 Dihedral : 8.354 89.870 2711 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.36 % Allowed : 13.38 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.03 (0.18), residues: 2104 helix: 1.82 (0.14), residues: 1316 sheet: -0.13 (0.58), residues: 76 loop : -1.46 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 499 TYR 0.018 0.002 TYR A 627 PHE 0.023 0.002 PHE A 304 TRP 0.015 0.001 TRP D 372 HIS 0.004 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00620 (17768) covalent geometry : angle 0.62277 (24112) SS BOND : bond 0.01691 ( 1) SS BOND : angle 6.28836 ( 2) hydrogen bonds : bond 0.05216 ( 1023) hydrogen bonds : angle 4.02027 ( 2937) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 450 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8255 (tpt) cc_final: 0.7748 (tpt) REVERT: A 351 TYR cc_start: 0.9023 (t80) cc_final: 0.8712 (t80) REVERT: A 361 GLU cc_start: 0.7568 (tp30) cc_final: 0.7300 (tp30) REVERT: A 374 TYR cc_start: 0.8016 (t80) cc_final: 0.7674 (t80) REVERT: A 394 SER cc_start: 0.9123 (m) cc_final: 0.8774 (p) REVERT: A 401 TYR cc_start: 0.8850 (m-80) cc_final: 0.8414 (m-10) REVERT: A 438 PHE cc_start: 0.9356 (t80) cc_final: 0.8940 (t80) REVERT: A 472 TYR cc_start: 0.8947 (m-80) cc_final: 0.8701 (m-10) REVERT: A 561 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8175 (pm20) REVERT: A 564 ILE cc_start: 0.8533 (mt) cc_final: 0.8248 (mt) REVERT: A 575 ARG cc_start: 0.7833 (mmt180) cc_final: 0.7612 (mmm160) REVERT: A 743 ARG cc_start: 0.8795 (ttm-80) cc_final: 0.8540 (ttm-80) REVERT: D 291 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8879 (mt) REVERT: D 361 GLU cc_start: 0.7508 (tp30) cc_final: 0.7244 (tp30) REVERT: D 423 GLN cc_start: 0.8841 (tp40) cc_final: 0.8597 (tp-100) REVERT: D 438 PHE cc_start: 0.9361 (t80) cc_final: 0.9059 (t80) REVERT: D 561 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8227 (pm20) REVERT: D 564 ILE cc_start: 0.8400 (mt) cc_final: 0.8193 (mm) REVERT: D 743 ARG cc_start: 0.8845 (ttm-80) cc_final: 0.8580 (ttm-80) REVERT: D 746 GLU cc_start: 0.7353 (tm-30) cc_final: 0.7145 (tm-30) REVERT: B 351 TYR cc_start: 0.9087 (t80) cc_final: 0.8741 (t80) REVERT: B 372 TRP cc_start: 0.8454 (p-90) cc_final: 0.8135 (p-90) REVERT: B 385 SER cc_start: 0.9237 (t) cc_final: 0.8804 (m) REVERT: B 394 SER cc_start: 0.9128 (m) cc_final: 0.8769 (p) REVERT: B 397 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8011 (mt-10) REVERT: B 401 TYR cc_start: 0.8828 (m-80) cc_final: 0.8614 (m-10) REVERT: B 423 GLN cc_start: 0.8835 (tp40) cc_final: 0.8435 (tp40) REVERT: B 427 ASP cc_start: 0.8992 (m-30) cc_final: 0.8731 (m-30) REVERT: B 428 ARG cc_start: 0.8802 (mtt-85) cc_final: 0.8573 (mtt90) REVERT: B 561 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8207 (pm20) REVERT: B 564 ILE cc_start: 0.8477 (mt) cc_final: 0.8253 (mm) REVERT: C 385 SER cc_start: 0.9220 (t) cc_final: 0.8940 (m) REVERT: C 392 LYS cc_start: 0.8285 (mttt) cc_final: 0.7529 (mtpp) REVERT: C 424 ASP cc_start: 0.9178 (t70) cc_final: 0.8904 (t70) REVERT: C 428 ARG cc_start: 0.8764 (mtt-85) cc_final: 0.8474 (mtt90) REVERT: C 438 PHE cc_start: 0.9386 (t80) cc_final: 0.8975 (t80) REVERT: C 472 TYR cc_start: 0.8935 (m-80) cc_final: 0.8657 (m-10) REVERT: C 499 ARG cc_start: 0.8574 (mmp-170) cc_final: 0.8348 (mmt90) REVERT: C 504 LYS cc_start: 0.9047 (mttt) cc_final: 0.8547 (mptt) REVERT: C 513 GLU cc_start: 0.9339 (mm-30) cc_final: 0.9018 (mm-30) REVERT: C 561 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.8265 (pm20) REVERT: C 564 ILE cc_start: 0.8511 (mt) cc_final: 0.8245 (mm) REVERT: C 743 ARG cc_start: 0.8763 (ttm-80) cc_final: 0.8442 (ttm-80) outliers start: 44 outliers final: 29 residues processed: 472 average time/residue: 0.1290 time to fit residues: 91.5769 Evaluate side-chains 463 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 429 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 648 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 13 optimal weight: 0.9980 chunk 195 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 178 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 206 optimal weight: 0.0030 chunk 183 optimal weight: 1.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 408 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 ASN B 727 GLN C 410 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.147768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.094670 restraints weight = 25635.443| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.47 r_work: 0.2906 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17769 Z= 0.121 Angle : 0.537 8.333 24114 Z= 0.287 Chirality : 0.039 0.143 2716 Planarity : 0.004 0.049 2968 Dihedral : 7.733 86.964 2711 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.82 % Allowed : 14.19 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.31 (0.19), residues: 2104 helix: 2.09 (0.14), residues: 1316 sheet: 0.11 (0.61), residues: 76 loop : -1.48 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 409 TYR 0.013 0.001 TYR B 511 PHE 0.024 0.001 PHE A 369 TRP 0.017 0.001 TRP D 372 HIS 0.004 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00249 (17768) covalent geometry : angle 0.53666 (24112) SS BOND : bond 0.00633 ( 1) SS BOND : angle 2.10843 ( 2) hydrogen bonds : bond 0.04174 ( 1023) hydrogen bonds : angle 3.79201 ( 2937) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 483 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8334 (tpt) cc_final: 0.7812 (tpt) REVERT: A 351 TYR cc_start: 0.8875 (t80) cc_final: 0.8507 (t80) REVERT: A 361 GLU cc_start: 0.7602 (tp30) cc_final: 0.7353 (tp30) REVERT: A 374 TYR cc_start: 0.7912 (t80) cc_final: 0.7625 (t80) REVERT: A 394 SER cc_start: 0.9028 (m) cc_final: 0.8791 (p) REVERT: A 401 TYR cc_start: 0.8801 (m-80) cc_final: 0.8220 (m-10) REVERT: A 409 ARG cc_start: 0.8771 (ttt180) cc_final: 0.8534 (ttt180) REVERT: A 423 GLN cc_start: 0.8785 (tp40) cc_final: 0.8475 (tp40) REVERT: A 427 ASP cc_start: 0.8902 (m-30) cc_final: 0.8689 (m-30) REVERT: A 438 PHE cc_start: 0.9314 (t80) cc_final: 0.9004 (t80) REVERT: A 472 TYR cc_start: 0.8951 (m-80) cc_final: 0.8662 (m-10) REVERT: A 561 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8123 (pm20) REVERT: A 564 ILE cc_start: 0.8432 (mt) cc_final: 0.8224 (mm) REVERT: A 575 ARG cc_start: 0.7701 (mmt180) cc_final: 0.7413 (mmm160) REVERT: A 743 ARG cc_start: 0.8767 (ttm-80) cc_final: 0.8433 (ttm-80) REVERT: D 291 LEU cc_start: 0.9157 (mt) cc_final: 0.8861 (mt) REVERT: D 310 ASN cc_start: 0.8514 (t0) cc_final: 0.8282 (t0) REVERT: D 351 TYR cc_start: 0.8980 (t80) cc_final: 0.8724 (t80) REVERT: D 361 GLU cc_start: 0.7515 (tp30) cc_final: 0.7267 (tp30) REVERT: D 423 GLN cc_start: 0.8855 (tp40) cc_final: 0.8616 (tp40) REVERT: D 438 PHE cc_start: 0.9322 (t80) cc_final: 0.9016 (t80) REVERT: D 561 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8155 (pm20) REVERT: D 564 ILE cc_start: 0.8317 (mt) cc_final: 0.8114 (mm) REVERT: D 733 ASP cc_start: 0.7461 (p0) cc_final: 0.7210 (p0) REVERT: D 743 ARG cc_start: 0.8814 (ttm-80) cc_final: 0.8513 (ttm-80) REVERT: B 351 TYR cc_start: 0.8958 (t80) cc_final: 0.8575 (t80) REVERT: B 369 PHE cc_start: 0.7342 (t80) cc_final: 0.6779 (t80) REVERT: B 383 ASP cc_start: 0.8074 (t0) cc_final: 0.7479 (t0) REVERT: B 385 SER cc_start: 0.9191 (t) cc_final: 0.8622 (m) REVERT: B 401 TYR cc_start: 0.8786 (m-80) cc_final: 0.8491 (m-10) REVERT: B 423 GLN cc_start: 0.8830 (tp40) cc_final: 0.8178 (tp-100) REVERT: B 424 ASP cc_start: 0.9157 (t70) cc_final: 0.8918 (t70) REVERT: B 427 ASP cc_start: 0.8926 (m-30) cc_final: 0.8373 (m-30) REVERT: B 428 ARG cc_start: 0.8718 (mtt-85) cc_final: 0.8454 (mtt90) REVERT: B 438 PHE cc_start: 0.9314 (t80) cc_final: 0.9009 (t80) REVERT: B 561 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8136 (pm20) REVERT: B 564 ILE cc_start: 0.8379 (mt) cc_final: 0.8099 (mt) REVERT: B 575 ARG cc_start: 0.7638 (mmt180) cc_final: 0.7389 (mmm160) REVERT: B 743 ARG cc_start: 0.8767 (ttm-80) cc_final: 0.8362 (ttm-80) REVERT: C 351 TYR cc_start: 0.8903 (t80) cc_final: 0.8519 (t80) REVERT: C 385 SER cc_start: 0.9029 (t) cc_final: 0.8712 (m) REVERT: C 438 PHE cc_start: 0.9347 (t80) cc_final: 0.9053 (t80) REVERT: C 472 TYR cc_start: 0.8928 (m-80) cc_final: 0.8611 (m-10) REVERT: C 504 LYS cc_start: 0.8990 (mttt) cc_final: 0.8461 (mptt) REVERT: C 561 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8240 (pm20) REVERT: C 564 ILE cc_start: 0.8430 (mt) cc_final: 0.8122 (mm) REVERT: C 743 ARG cc_start: 0.8711 (ttm-80) cc_final: 0.8338 (ttm-80) outliers start: 34 outliers final: 24 residues processed: 503 average time/residue: 0.1251 time to fit residues: 95.2493 Evaluate side-chains 461 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 433 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 722 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 573 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 177 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 108 optimal weight: 0.0050 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.144406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.091248 restraints weight = 25655.396| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.45 r_work: 0.2850 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17769 Z= 0.205 Angle : 0.577 8.336 24114 Z= 0.308 Chirality : 0.041 0.138 2716 Planarity : 0.004 0.049 2968 Dihedral : 7.638 85.310 2711 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.62 % Allowed : 15.31 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.17 (0.19), residues: 2104 helix: 1.98 (0.14), residues: 1316 sheet: 0.02 (0.62), residues: 76 loop : -1.54 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 499 TYR 0.013 0.002 TYR C 309 PHE 0.020 0.002 PHE A 304 TRP 0.019 0.001 TRP D 372 HIS 0.004 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00478 (17768) covalent geometry : angle 0.57693 (24112) SS BOND : bond 0.00093 ( 1) SS BOND : angle 1.34685 ( 2) hydrogen bonds : bond 0.04658 ( 1023) hydrogen bonds : angle 3.90642 ( 2937) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 432 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8325 (tpt) cc_final: 0.7804 (tpt) REVERT: A 351 TYR cc_start: 0.8962 (t80) cc_final: 0.8624 (t80) REVERT: A 361 GLU cc_start: 0.7614 (tp30) cc_final: 0.7361 (tp30) REVERT: A 394 SER cc_start: 0.9073 (m) cc_final: 0.8816 (p) REVERT: A 401 TYR cc_start: 0.8777 (m-80) cc_final: 0.8405 (m-10) REVERT: A 438 PHE cc_start: 0.9338 (t80) cc_final: 0.8898 (t80) REVERT: A 472 TYR cc_start: 0.8936 (m-80) cc_final: 0.8682 (m-10) REVERT: A 561 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8158 (pm20) REVERT: A 564 ILE cc_start: 0.8635 (mt) cc_final: 0.8383 (mm) REVERT: A 575 ARG cc_start: 0.7754 (mmt180) cc_final: 0.7413 (mmm160) REVERT: A 743 ARG cc_start: 0.8821 (ttm-80) cc_final: 0.8489 (ttm-80) REVERT: D 291 LEU cc_start: 0.9167 (mt) cc_final: 0.8849 (mt) REVERT: D 361 GLU cc_start: 0.7522 (tp30) cc_final: 0.7250 (tp30) REVERT: D 384 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8557 (mp) REVERT: D 423 GLN cc_start: 0.8872 (tp40) cc_final: 0.8660 (tp40) REVERT: D 438 PHE cc_start: 0.9343 (t80) cc_final: 0.9046 (t80) REVERT: D 561 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8126 (pm20) REVERT: D 564 ILE cc_start: 0.8488 (mt) cc_final: 0.8266 (mm) REVERT: D 743 ARG cc_start: 0.8863 (ttm-80) cc_final: 0.8626 (ttm-80) REVERT: B 308 MET cc_start: 0.9218 (tpp) cc_final: 0.8945 (tpp) REVERT: B 351 TYR cc_start: 0.9043 (t80) cc_final: 0.8712 (t80) REVERT: B 385 SER cc_start: 0.9205 (t) cc_final: 0.8877 (t) REVERT: B 401 TYR cc_start: 0.8803 (m-80) cc_final: 0.8529 (m-10) REVERT: B 423 GLN cc_start: 0.8828 (tp40) cc_final: 0.8154 (tp-100) REVERT: B 427 ASP cc_start: 0.8920 (m-30) cc_final: 0.8393 (m-30) REVERT: B 428 ARG cc_start: 0.8743 (mtt-85) cc_final: 0.8518 (mtt90) REVERT: B 561 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8165 (pm20) REVERT: B 564 ILE cc_start: 0.8569 (mt) cc_final: 0.8309 (mm) REVERT: B 575 ARG cc_start: 0.7767 (mmt180) cc_final: 0.7361 (mmm160) REVERT: B 743 ARG cc_start: 0.8863 (ttm-80) cc_final: 0.8489 (ttm-80) REVERT: C 392 LYS cc_start: 0.8000 (mttt) cc_final: 0.7768 (mtpp) REVERT: C 438 PHE cc_start: 0.9362 (t80) cc_final: 0.8935 (t80) REVERT: C 472 TYR cc_start: 0.8920 (m-80) cc_final: 0.8655 (m-10) REVERT: C 504 LYS cc_start: 0.9036 (mttt) cc_final: 0.8506 (mptt) REVERT: C 743 ARG cc_start: 0.8730 (ttm-80) cc_final: 0.8377 (ttm-80) outliers start: 49 outliers final: 33 residues processed: 466 average time/residue: 0.1274 time to fit residues: 89.5140 Evaluate side-chains 437 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 400 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 722 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain C residue 697 TRP Chi-restraints excluded: chain C residue 722 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 193 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 78 optimal weight: 0.0770 chunk 117 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.092386 restraints weight = 25547.913| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.46 r_work: 0.2868 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17769 Z= 0.163 Angle : 0.563 10.821 24114 Z= 0.300 Chirality : 0.040 0.153 2716 Planarity : 0.004 0.049 2968 Dihedral : 7.150 80.936 2705 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.30 % Allowed : 15.74 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.16 (0.19), residues: 2104 helix: 1.98 (0.14), residues: 1316 sheet: 0.07 (0.64), residues: 76 loop : -1.55 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 499 TYR 0.019 0.001 TYR B 309 PHE 0.019 0.001 PHE A 304 TRP 0.021 0.001 TRP D 372 HIS 0.004 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00372 (17768) covalent geometry : angle 0.56207 (24112) SS BOND : bond 0.00568 ( 1) SS BOND : angle 2.66670 ( 2) hydrogen bonds : bond 0.04437 ( 1023) hydrogen bonds : angle 3.90161 ( 2937) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 425 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8362 (tpt) cc_final: 0.7870 (tpt) REVERT: A 361 GLU cc_start: 0.7647 (tp30) cc_final: 0.7401 (tp30) REVERT: A 381 LEU cc_start: 0.8267 (mm) cc_final: 0.8046 (mm) REVERT: A 394 SER cc_start: 0.9055 (m) cc_final: 0.8830 (p) REVERT: A 401 TYR cc_start: 0.8817 (m-80) cc_final: 0.8379 (m-10) REVERT: A 438 PHE cc_start: 0.9319 (t80) cc_final: 0.9027 (t80) REVERT: A 472 TYR cc_start: 0.8968 (m-80) cc_final: 0.8706 (m-10) REVERT: A 575 ARG cc_start: 0.7695 (mmt180) cc_final: 0.7362 (mmm160) REVERT: A 743 ARG cc_start: 0.8816 (ttm-80) cc_final: 0.8488 (ttm-80) REVERT: D 291 LEU cc_start: 0.9165 (mt) cc_final: 0.8809 (mp) REVERT: D 308 MET cc_start: 0.9175 (tpp) cc_final: 0.8767 (tpp) REVERT: D 361 GLU cc_start: 0.7563 (tp30) cc_final: 0.7330 (tp30) REVERT: D 384 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8573 (mp) REVERT: D 423 GLN cc_start: 0.8867 (tp40) cc_final: 0.8625 (tp40) REVERT: D 438 PHE cc_start: 0.9328 (t80) cc_final: 0.9032 (t80) REVERT: D 491 ARG cc_start: 0.9100 (mmm-85) cc_final: 0.8509 (mmm-85) REVERT: D 561 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8144 (pm20) REVERT: D 564 ILE cc_start: 0.8493 (mt) cc_final: 0.8267 (mm) REVERT: D 743 ARG cc_start: 0.8858 (ttm-80) cc_final: 0.8620 (ttm-80) REVERT: D 746 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7184 (tm-30) REVERT: B 308 MET cc_start: 0.9220 (tpp) cc_final: 0.8943 (tpp) REVERT: B 351 TYR cc_start: 0.8994 (t80) cc_final: 0.8630 (t80) REVERT: B 401 TYR cc_start: 0.8788 (m-80) cc_final: 0.8484 (m-10) REVERT: B 424 ASP cc_start: 0.9151 (t70) cc_final: 0.8937 (t70) REVERT: B 427 ASP cc_start: 0.8904 (m-30) cc_final: 0.8623 (m-30) REVERT: B 428 ARG cc_start: 0.8705 (mtt-85) cc_final: 0.8470 (mtt90) REVERT: B 564 ILE cc_start: 0.8583 (mt) cc_final: 0.8326 (mm) REVERT: B 575 ARG cc_start: 0.7747 (mmt180) cc_final: 0.7336 (mmm160) REVERT: B 743 ARG cc_start: 0.8859 (ttm-80) cc_final: 0.8461 (ttm-80) REVERT: C 392 LYS cc_start: 0.8069 (mttt) cc_final: 0.7840 (mtpp) REVERT: C 427 ASP cc_start: 0.9036 (m-30) cc_final: 0.8770 (m-30) REVERT: C 472 TYR cc_start: 0.8914 (m-80) cc_final: 0.8599 (m-10) REVERT: C 504 LYS cc_start: 0.9043 (mttt) cc_final: 0.8491 (mptt) REVERT: C 560 GLN cc_start: 0.9165 (tt0) cc_final: 0.8648 (tp40) REVERT: C 743 ARG cc_start: 0.8715 (ttm-80) cc_final: 0.8362 (ttm-80) outliers start: 43 outliers final: 32 residues processed: 450 average time/residue: 0.1298 time to fit residues: 88.3218 Evaluate side-chains 448 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 414 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain D residue 722 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain C residue 697 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 9 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 112 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN D 206 HIS D 419 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.148023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.095294 restraints weight = 25482.199| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.46 r_work: 0.2903 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17769 Z= 0.123 Angle : 0.545 12.416 24114 Z= 0.290 Chirality : 0.040 0.192 2716 Planarity : 0.004 0.049 2968 Dihedral : 6.229 69.893 2699 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.19 % Allowed : 16.17 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.29 (0.19), residues: 2104 helix: 2.10 (0.14), residues: 1312 sheet: 0.13 (0.66), residues: 76 loop : -1.53 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 499 TYR 0.021 0.001 TYR B 309 PHE 0.022 0.001 PHE A 304 TRP 0.023 0.001 TRP D 372 HIS 0.003 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00265 (17768) covalent geometry : angle 0.54496 (24112) SS BOND : bond 0.00415 ( 1) SS BOND : angle 2.01715 ( 2) hydrogen bonds : bond 0.04036 ( 1023) hydrogen bonds : angle 3.82387 ( 2937) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 439 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8212 (tp30) cc_final: 0.7882 (pp20) REVERT: A 214 MET cc_start: 0.8324 (tpt) cc_final: 0.7882 (tpt) REVERT: A 310 ASN cc_start: 0.8439 (t0) cc_final: 0.8167 (t0) REVERT: A 351 TYR cc_start: 0.8846 (t80) cc_final: 0.8487 (t80) REVERT: A 361 GLU cc_start: 0.7647 (tp30) cc_final: 0.7405 (tp30) REVERT: A 372 TRP cc_start: 0.8418 (p-90) cc_final: 0.8183 (p-90) REVERT: A 385 SER cc_start: 0.8931 (t) cc_final: 0.8635 (m) REVERT: A 401 TYR cc_start: 0.8806 (m-80) cc_final: 0.8290 (m-10) REVERT: A 438 PHE cc_start: 0.9292 (t80) cc_final: 0.9018 (t80) REVERT: A 472 TYR cc_start: 0.8951 (m-80) cc_final: 0.8647 (m-10) REVERT: D 291 LEU cc_start: 0.9111 (mt) cc_final: 0.8795 (mp) REVERT: D 361 GLU cc_start: 0.7615 (tp30) cc_final: 0.7382 (tp30) REVERT: D 384 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8577 (mp) REVERT: D 423 GLN cc_start: 0.8889 (tp40) cc_final: 0.8671 (tp40) REVERT: D 438 PHE cc_start: 0.9298 (t80) cc_final: 0.9026 (t80) REVERT: D 491 ARG cc_start: 0.9080 (mmm-85) cc_final: 0.8860 (mmm-85) REVERT: D 564 ILE cc_start: 0.8468 (mt) cc_final: 0.8243 (mm) REVERT: D 743 ARG cc_start: 0.8830 (ttm-80) cc_final: 0.8532 (ttm-80) REVERT: D 746 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7221 (tm-30) REVERT: B 308 MET cc_start: 0.9209 (tpp) cc_final: 0.8910 (tpp) REVERT: B 351 TYR cc_start: 0.8926 (t80) cc_final: 0.8498 (t80) REVERT: B 383 ASP cc_start: 0.8112 (t0) cc_final: 0.7571 (t0) REVERT: B 385 SER cc_start: 0.9134 (t) cc_final: 0.8589 (m) REVERT: B 401 TYR cc_start: 0.8782 (m-80) cc_final: 0.8456 (m-10) REVERT: B 424 ASP cc_start: 0.9133 (t70) cc_final: 0.8660 (t70) REVERT: B 428 ARG cc_start: 0.8728 (mtt-85) cc_final: 0.8409 (mtt90) REVERT: B 438 PHE cc_start: 0.9306 (t80) cc_final: 0.9034 (t80) REVERT: B 564 ILE cc_start: 0.8565 (mt) cc_final: 0.8308 (mm) REVERT: B 575 ARG cc_start: 0.7750 (mmt180) cc_final: 0.7291 (mmm160) REVERT: C 351 TYR cc_start: 0.8873 (t80) cc_final: 0.8571 (t80) REVERT: C 392 LYS cc_start: 0.8144 (mttt) cc_final: 0.7901 (mtpp) REVERT: C 423 GLN cc_start: 0.8988 (tp40) cc_final: 0.8580 (tp40) REVERT: C 427 ASP cc_start: 0.9002 (m-30) cc_final: 0.8616 (m-30) REVERT: C 438 PHE cc_start: 0.9323 (t80) cc_final: 0.8893 (t80) REVERT: C 472 TYR cc_start: 0.8922 (m-80) cc_final: 0.8612 (m-10) REVERT: C 504 LYS cc_start: 0.9041 (mttt) cc_final: 0.8485 (mptt) REVERT: C 560 GLN cc_start: 0.9181 (tt0) cc_final: 0.8878 (tp40) REVERT: C 694 LYS cc_start: 0.8328 (tptp) cc_final: 0.8008 (ttpt) REVERT: C 743 ARG cc_start: 0.8693 (ttm-80) cc_final: 0.8346 (ttm-80) outliers start: 41 outliers final: 23 residues processed: 460 average time/residue: 0.1332 time to fit residues: 92.5590 Evaluate side-chains 444 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 420 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 565 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 202 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 189 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.093160 restraints weight = 25554.392| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.44 r_work: 0.2851 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17769 Z= 0.175 Angle : 0.582 13.801 24114 Z= 0.310 Chirality : 0.041 0.169 2716 Planarity : 0.004 0.049 2968 Dihedral : 6.100 47.087 2696 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.03 % Allowed : 16.97 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.16 (0.19), residues: 2104 helix: 1.97 (0.14), residues: 1316 sheet: -0.07 (0.66), residues: 76 loop : -1.53 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 499 TYR 0.016 0.001 TYR A 309 PHE 0.030 0.001 PHE C 369 TRP 0.025 0.001 TRP D 372 HIS 0.003 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00407 (17768) covalent geometry : angle 0.58188 (24112) SS BOND : bond 0.00272 ( 1) SS BOND : angle 1.76117 ( 2) hydrogen bonds : bond 0.04419 ( 1023) hydrogen bonds : angle 3.89469 ( 2937) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 417 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8243 (tp30) cc_final: 0.7907 (pp20) REVERT: A 214 MET cc_start: 0.8329 (tpt) cc_final: 0.7877 (tpt) REVERT: A 351 TYR cc_start: 0.8891 (t80) cc_final: 0.8566 (t80) REVERT: A 361 GLU cc_start: 0.7646 (tp30) cc_final: 0.7400 (tp30) REVERT: A 372 TRP cc_start: 0.8416 (p-90) cc_final: 0.8187 (p-90) REVERT: A 401 TYR cc_start: 0.8780 (m-80) cc_final: 0.8397 (m-10) REVERT: A 438 PHE cc_start: 0.9322 (t80) cc_final: 0.9038 (t80) REVERT: A 472 TYR cc_start: 0.8964 (m-80) cc_final: 0.8693 (m-10) REVERT: A 743 ARG cc_start: 0.8879 (ttm-80) cc_final: 0.8534 (ttm-80) REVERT: D 291 LEU cc_start: 0.9120 (mt) cc_final: 0.8808 (mp) REVERT: D 361 GLU cc_start: 0.7627 (tp30) cc_final: 0.7387 (tp30) REVERT: D 384 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8564 (mp) REVERT: D 423 GLN cc_start: 0.8912 (tp40) cc_final: 0.8674 (tp40) REVERT: D 438 PHE cc_start: 0.9323 (t80) cc_final: 0.8871 (t80) REVERT: D 564 ILE cc_start: 0.8576 (mt) cc_final: 0.8356 (mm) REVERT: D 746 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7291 (tm-30) REVERT: B 308 MET cc_start: 0.9204 (tpp) cc_final: 0.8946 (tpp) REVERT: B 351 TYR cc_start: 0.8979 (t80) cc_final: 0.8616 (t80) REVERT: B 401 TYR cc_start: 0.8810 (m-80) cc_final: 0.8405 (m-10) REVERT: B 424 ASP cc_start: 0.9134 (t70) cc_final: 0.8891 (t70) REVERT: B 428 ARG cc_start: 0.8770 (mtt-85) cc_final: 0.8538 (mtt90) REVERT: B 575 ARG cc_start: 0.7783 (mmt180) cc_final: 0.7313 (mmm160) REVERT: C 351 TYR cc_start: 0.8929 (t80) cc_final: 0.8601 (t80) REVERT: C 392 LYS cc_start: 0.8226 (mttt) cc_final: 0.7994 (mtpp) REVERT: C 427 ASP cc_start: 0.9032 (m-30) cc_final: 0.8739 (m-30) REVERT: C 472 TYR cc_start: 0.8941 (m-80) cc_final: 0.8620 (m-10) REVERT: C 504 LYS cc_start: 0.9081 (mttt) cc_final: 0.8518 (mptt) REVERT: C 560 GLN cc_start: 0.9178 (tt0) cc_final: 0.8640 (tp40) REVERT: C 561 GLN cc_start: 0.9242 (mp10) cc_final: 0.8197 (pm20) outliers start: 38 outliers final: 33 residues processed: 438 average time/residue: 0.1372 time to fit residues: 90.2929 Evaluate side-chains 434 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 400 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain C residue 697 TRP Chi-restraints excluded: chain C residue 722 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 183 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.148310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.095784 restraints weight = 25439.349| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.44 r_work: 0.2885 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17769 Z= 0.126 Angle : 0.579 14.420 24114 Z= 0.306 Chirality : 0.040 0.162 2716 Planarity : 0.004 0.049 2968 Dihedral : 5.724 43.097 2696 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.71 % Allowed : 17.61 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.23 (0.19), residues: 2104 helix: 2.05 (0.14), residues: 1316 sheet: -0.13 (0.67), residues: 76 loop : -1.52 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 499 TYR 0.011 0.001 TYR C 511 PHE 0.025 0.001 PHE A 304 TRP 0.026 0.001 TRP D 372 HIS 0.003 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00277 (17768) covalent geometry : angle 0.57880 (24112) SS BOND : bond 0.00323 ( 1) SS BOND : angle 1.56621 ( 2) hydrogen bonds : bond 0.04080 ( 1023) hydrogen bonds : angle 3.81627 ( 2937) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 430 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8288 (tp30) cc_final: 0.7933 (pp20) REVERT: A 214 MET cc_start: 0.8360 (tpt) cc_final: 0.7923 (tpt) REVERT: A 361 GLU cc_start: 0.7625 (tp30) cc_final: 0.7396 (tp30) REVERT: A 372 TRP cc_start: 0.8464 (p-90) cc_final: 0.8247 (p-90) REVERT: A 401 TYR cc_start: 0.8786 (m-80) cc_final: 0.8292 (m-10) REVERT: A 409 ARG cc_start: 0.8724 (ttt180) cc_final: 0.7930 (ttt180) REVERT: A 438 PHE cc_start: 0.9280 (t80) cc_final: 0.9004 (t80) REVERT: A 472 TYR cc_start: 0.8950 (m-80) cc_final: 0.8642 (m-10) REVERT: A 743 ARG cc_start: 0.8838 (ttm-80) cc_final: 0.8469 (ttm-80) REVERT: D 291 LEU cc_start: 0.9064 (mt) cc_final: 0.8746 (mp) REVERT: D 308 MET cc_start: 0.9127 (tpp) cc_final: 0.8894 (tpp) REVERT: D 361 GLU cc_start: 0.7632 (tp30) cc_final: 0.7398 (tp30) REVERT: D 384 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8531 (mp) REVERT: D 423 GLN cc_start: 0.8899 (tp40) cc_final: 0.8679 (tp40) REVERT: D 438 PHE cc_start: 0.9292 (t80) cc_final: 0.8808 (t80) REVERT: D 499 ARG cc_start: 0.8586 (tpp80) cc_final: 0.7940 (mmt-90) REVERT: D 564 ILE cc_start: 0.8547 (mt) cc_final: 0.8323 (mm) REVERT: D 746 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7208 (tm-30) REVERT: B 308 MET cc_start: 0.9185 (tpp) cc_final: 0.8897 (tpp) REVERT: B 351 TYR cc_start: 0.8903 (t80) cc_final: 0.8615 (t80) REVERT: B 383 ASP cc_start: 0.8218 (t0) cc_final: 0.7981 (t0) REVERT: B 401 TYR cc_start: 0.8799 (m-80) cc_final: 0.8391 (m-10) REVERT: B 424 ASP cc_start: 0.9088 (t70) cc_final: 0.8816 (t70) REVERT: B 428 ARG cc_start: 0.8721 (mtt-85) cc_final: 0.8504 (mtt90) REVERT: B 575 ARG cc_start: 0.7779 (mmt180) cc_final: 0.7307 (mmm160) REVERT: C 351 TYR cc_start: 0.8848 (t80) cc_final: 0.8569 (t80) REVERT: C 392 LYS cc_start: 0.8210 (mttt) cc_final: 0.7974 (mtpp) REVERT: C 427 ASP cc_start: 0.9031 (m-30) cc_final: 0.8667 (m-30) REVERT: C 438 PHE cc_start: 0.9318 (t80) cc_final: 0.8846 (t80) REVERT: C 472 TYR cc_start: 0.8922 (m-80) cc_final: 0.8610 (m-10) REVERT: C 491 ARG cc_start: 0.9078 (mmm-85) cc_final: 0.8462 (mmm-85) REVERT: C 504 LYS cc_start: 0.9054 (mttt) cc_final: 0.8499 (mptt) REVERT: C 560 GLN cc_start: 0.9166 (tt0) cc_final: 0.8663 (tp40) REVERT: C 561 GLN cc_start: 0.9219 (mp10) cc_final: 0.8140 (pm20) outliers start: 32 outliers final: 24 residues processed: 445 average time/residue: 0.1301 time to fit residues: 86.8904 Evaluate side-chains 441 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 416 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 565 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 74 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 195 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 181 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.148845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.096087 restraints weight = 25357.069| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.45 r_work: 0.2916 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17769 Z= 0.129 Angle : 0.580 13.827 24114 Z= 0.305 Chirality : 0.040 0.186 2716 Planarity : 0.004 0.049 2968 Dihedral : 5.405 37.937 2696 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.55 % Allowed : 18.09 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.24 (0.19), residues: 2104 helix: 2.06 (0.14), residues: 1316 sheet: -0.18 (0.66), residues: 76 loop : -1.51 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 499 TYR 0.010 0.001 TYR C 511 PHE 0.022 0.001 PHE A 304 TRP 0.025 0.001 TRP D 372 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00288 (17768) covalent geometry : angle 0.57951 (24112) SS BOND : bond 0.00273 ( 1) SS BOND : angle 1.47223 ( 2) hydrogen bonds : bond 0.04025 ( 1023) hydrogen bonds : angle 3.80976 ( 2937) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 429 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8247 (tp30) cc_final: 0.7922 (pp20) REVERT: A 214 MET cc_start: 0.8371 (tpt) cc_final: 0.7921 (tpt) REVERT: A 351 TYR cc_start: 0.8814 (t80) cc_final: 0.8442 (t80) REVERT: A 361 GLU cc_start: 0.7574 (tp30) cc_final: 0.7342 (tp30) REVERT: A 369 PHE cc_start: 0.8316 (m-80) cc_final: 0.8097 (m-10) REVERT: A 372 TRP cc_start: 0.8492 (p-90) cc_final: 0.8268 (p-90) REVERT: A 401 TYR cc_start: 0.8789 (m-80) cc_final: 0.8192 (m-10) REVERT: A 438 PHE cc_start: 0.9288 (t80) cc_final: 0.8822 (t80) REVERT: A 472 TYR cc_start: 0.8950 (m-80) cc_final: 0.8647 (m-10) REVERT: D 291 LEU cc_start: 0.9052 (mt) cc_final: 0.8747 (mp) REVERT: D 308 MET cc_start: 0.9124 (tpp) cc_final: 0.8873 (tpp) REVERT: D 361 GLU cc_start: 0.7598 (tp30) cc_final: 0.7372 (tp30) REVERT: D 384 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8532 (mp) REVERT: D 385 SER cc_start: 0.8993 (t) cc_final: 0.8648 (m) REVERT: D 423 GLN cc_start: 0.8897 (tp40) cc_final: 0.8638 (tp40) REVERT: D 438 PHE cc_start: 0.9294 (t80) cc_final: 0.8828 (t80) REVERT: D 491 ARG cc_start: 0.9110 (mmm-85) cc_final: 0.8529 (mmm-85) REVERT: D 564 ILE cc_start: 0.8523 (mt) cc_final: 0.8309 (mm) REVERT: D 743 ARG cc_start: 0.8820 (ttm-80) cc_final: 0.8584 (ttm-80) REVERT: D 746 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7222 (tm-30) REVERT: B 308 MET cc_start: 0.9164 (tpp) cc_final: 0.8876 (tpp) REVERT: B 351 TYR cc_start: 0.8918 (t80) cc_final: 0.8674 (t80) REVERT: B 401 TYR cc_start: 0.8766 (m-80) cc_final: 0.8424 (m-10) REVERT: B 424 ASP cc_start: 0.9060 (t70) cc_final: 0.8671 (t70) REVERT: B 428 ARG cc_start: 0.8666 (mtt-85) cc_final: 0.8432 (mtt90) REVERT: B 438 PHE cc_start: 0.9298 (t80) cc_final: 0.9039 (t80) REVERT: B 575 ARG cc_start: 0.7736 (mmt180) cc_final: 0.7296 (mmm160) REVERT: C 351 TYR cc_start: 0.8848 (t80) cc_final: 0.8588 (t80) REVERT: C 392 LYS cc_start: 0.8181 (mttt) cc_final: 0.7956 (mtpp) REVERT: C 427 ASP cc_start: 0.8996 (m-30) cc_final: 0.8724 (m-30) REVERT: C 438 PHE cc_start: 0.9316 (t80) cc_final: 0.8855 (t80) REVERT: C 472 TYR cc_start: 0.8942 (m-80) cc_final: 0.8631 (m-10) REVERT: C 491 ARG cc_start: 0.9076 (mmm-85) cc_final: 0.8453 (mmm-85) REVERT: C 504 LYS cc_start: 0.9038 (mttt) cc_final: 0.8510 (mptt) REVERT: C 560 GLN cc_start: 0.9125 (tt0) cc_final: 0.8893 (tp40) REVERT: C 694 LYS cc_start: 0.8207 (tptp) cc_final: 0.7931 (ttpt) outliers start: 29 outliers final: 25 residues processed: 440 average time/residue: 0.1386 time to fit residues: 91.5693 Evaluate side-chains 444 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 418 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 648 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 168 optimal weight: 0.0870 chunk 51 optimal weight: 0.0000 chunk 172 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 overall best weight: 1.2168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN A 498 GLN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.147737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.095538 restraints weight = 25438.106| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.42 r_work: 0.2907 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17769 Z= 0.145 Angle : 0.599 16.164 24114 Z= 0.311 Chirality : 0.041 0.193 2716 Planarity : 0.004 0.049 2968 Dihedral : 5.379 36.628 2696 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.45 % Allowed : 18.42 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.18 (0.19), residues: 2104 helix: 2.01 (0.14), residues: 1316 sheet: -0.18 (0.67), residues: 76 loop : -1.55 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 499 TYR 0.025 0.001 TYR A 309 PHE 0.032 0.001 PHE C 369 TRP 0.027 0.001 TRP D 372 HIS 0.003 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00333 (17768) covalent geometry : angle 0.59852 (24112) SS BOND : bond 0.00272 ( 1) SS BOND : angle 1.51114 ( 2) hydrogen bonds : bond 0.04142 ( 1023) hydrogen bonds : angle 3.85911 ( 2937) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5497.27 seconds wall clock time: 94 minutes 32.87 seconds (5672.87 seconds total)