Starting phenix.real_space_refine on Wed Mar 4 03:49:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kcl_22812/03_2026/7kcl_22812.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kcl_22812/03_2026/7kcl_22812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kcl_22812/03_2026/7kcl_22812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kcl_22812/03_2026/7kcl_22812.map" model { file = "/net/cci-nas-00/data/ceres_data/7kcl_22812/03_2026/7kcl_22812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kcl_22812/03_2026/7kcl_22812.cif" } resolution = 3.14 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 522 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 6 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 6358 2.51 5 N 1742 2.21 5 O 1903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10057 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4890 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 18, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 4915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4915 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 18, 'TRANS': 595} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 186 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.17, per 1000 atoms: 0.22 Number of scatterers: 10057 At special positions: 0 Unit cell: (92.796, 91.982, 132.682, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 44 16.00 P 6 15.00 Mg 2 11.99 O 1903 8.00 N 1742 7.00 C 6358 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 413.0 milliseconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2384 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 12 sheets defined 47.3% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 93 through 103 Processing helix chain 'A' and resid 110 through 135 removed outlier: 4.461A pdb=" N ARG A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 173 Processing helix chain 'A' and resid 178 through 186 removed outlier: 3.749A pdb=" N ALA A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.812A pdb=" N PHE A 264 " --> pdb=" O CYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 307 through 320 Processing helix chain 'A' and resid 382 through 386 removed outlier: 4.255A pdb=" N PHE A 386 " --> pdb=" O TRP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 433 Processing helix chain 'A' and resid 433 through 455 removed outlier: 6.299A pdb=" N LEU A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 466 Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.550A pdb=" N ARG A 489 " --> pdb=" O GLU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 511 through 517 Processing helix chain 'A' and resid 518 through 520 No H-bonds generated for 'chain 'A' and resid 518 through 520' Processing helix chain 'A' and resid 531 through 540 Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'A' and resid 575 through 590 removed outlier: 3.509A pdb=" N TRP A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 628 removed outlier: 3.638A pdb=" N HIS A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 653 Processing helix chain 'A' and resid 653 through 659 removed outlier: 3.703A pdb=" N ALA A 659 " --> pdb=" O ASN A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 680 Processing helix chain 'A' and resid 686 through 701 removed outlier: 3.794A pdb=" N VAL A 690 " --> pdb=" O PRO A 686 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY A 691 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 Processing helix chain 'B' and resid 110 through 131 removed outlier: 4.278A pdb=" N ARG B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 178 through 186 removed outlier: 3.902A pdb=" N ALA B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.533A pdb=" N VAL B 306 " --> pdb=" O PRO B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 Processing helix chain 'B' and resid 351 through 356 removed outlier: 3.600A pdb=" N VAL B 355 " --> pdb=" O SER B 351 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 356' Processing helix chain 'B' and resid 381 through 387 removed outlier: 4.399A pdb=" N PHE B 386 " --> pdb=" O TRP B 383 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 387 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 433 Processing helix chain 'B' and resid 433 through 455 removed outlier: 6.812A pdb=" N LEU B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 466 Processing helix chain 'B' and resid 482 through 488 Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 511 through 518 Processing helix chain 'B' and resid 531 through 540 Processing helix chain 'B' and resid 550 through 557 Processing helix chain 'B' and resid 575 through 590 Processing helix chain 'B' and resid 614 through 625 removed outlier: 3.504A pdb=" N HIS B 620 " --> pdb=" O GLY B 616 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 639 removed outlier: 3.964A pdb=" N LEU B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 removed outlier: 3.886A pdb=" N ASN B 655 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 681 removed outlier: 3.512A pdb=" N GLN B 666 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 701 removed outlier: 4.586A pdb=" N ARG B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 removed outlier: 4.058A pdb=" N VAL C 140 " --> pdb=" O LYS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 157 removed outlier: 3.755A pdb=" N GLN C 149 " --> pdb=" O ASN C 145 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR C 150 " --> pdb=" O PHE C 146 " (cutoff:3.500A) Proline residue: C 155 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.899A pdb=" N ARG B 214 " --> pdb=" O HIS B 256 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 143 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 7.219A pdb=" N GLN A 91 " --> pdb=" O ILE B 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 291 removed outlier: 6.331A pdb=" N ILE A 143 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 291 removed outlier: 6.331A pdb=" N ILE A 143 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 333 removed outlier: 6.448A pdb=" N VAL A 345 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR A 328 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE A 343 " --> pdb=" O THR A 328 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N HIS A 330 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER A 341 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS A 332 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A 339 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 471 through 472 removed outlier: 3.941A pdb=" N GLU A 471 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N LEU A 525 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR A 498 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N CYS A 527 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU A 500 " --> pdb=" O CYS A 527 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 499 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 596 through 599 Processing sheet with id=AB1, first strand: chain 'B' and resid 325 through 333 Processing sheet with id=AB2, first strand: chain 'B' and resid 524 through 527 removed outlier: 8.769A pdb=" N LEU B 525 " --> pdb=" O ASN B 496 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR B 498 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N CYS B 527 " --> pdb=" O TYR B 498 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU B 500 " --> pdb=" O CYS B 527 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR B 499 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 596 through 599 removed outlier: 6.385A pdb=" N ASN B 596 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE B 644 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS B 598 " --> pdb=" O ILE B 644 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3313 1.34 - 1.46: 2175 1.46 - 1.58: 4658 1.58 - 1.70: 8 1.70 - 1.81: 80 Bond restraints: 10234 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" O5' ANP A 801 " pdb=" PA ANP A 801 " ideal model delta sigma weight residual 1.655 1.577 0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 10229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 13746 3.26 - 6.52: 55 6.52 - 9.78: 8 9.78 - 13.04: 2 13.04 - 16.30: 2 Bond angle restraints: 13813 Sorted by residual: angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 110.65 16.30 3.00e+00 1.11e-01 2.95e+01 angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 110.80 16.15 3.00e+00 1.11e-01 2.90e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 108.92 11.16 3.00e+00 1.11e-01 1.38e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 109.00 11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " pdb=" O2G ANP A 801 " ideal model delta sigma weight residual 101.05 109.79 -8.74 3.00e+00 1.11e-01 8.48e+00 ... (remaining 13808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5587 17.96 - 35.92: 547 35.92 - 53.87: 114 53.87 - 71.83: 31 71.83 - 89.79: 17 Dihedral angle restraints: 6296 sinusoidal: 2627 harmonic: 3669 Sorted by residual: dihedral pdb=" CB GLU A 216 " pdb=" CG GLU A 216 " pdb=" CD GLU A 216 " pdb=" OE1 GLU A 216 " ideal model delta sinusoidal sigma weight residual 0.00 89.79 -89.79 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG A 415 " pdb=" CD ARG A 415 " pdb=" NE ARG A 415 " pdb=" CZ ARG A 415 " ideal model delta sinusoidal sigma weight residual 90.00 134.20 -44.20 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CB GLU A 578 " pdb=" CG GLU A 578 " pdb=" CD GLU A 578 " pdb=" OE1 GLU A 578 " ideal model delta sinusoidal sigma weight residual 0.00 -87.66 87.66 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 6293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1304 0.055 - 0.109: 227 0.109 - 0.164: 23 0.164 - 0.219: 1 0.219 - 0.274: 2 Chirality restraints: 1557 Sorted by residual: chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE B 156 " pdb=" CA ILE B 156 " pdb=" CG1 ILE B 156 " pdb=" CG2 ILE B 156 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1554 not shown) Planarity restraints: 1752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 639 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO B 640 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 640 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 640 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 123 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C ALA A 123 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA A 123 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 124 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 121 " 0.006 2.00e-02 2.50e+03 1.28e-02 1.63e+00 pdb=" C SER A 121 " -0.022 2.00e-02 2.50e+03 pdb=" O SER A 121 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP A 122 " 0.007 2.00e-02 2.50e+03 ... (remaining 1749 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.63: 158 2.63 - 3.26: 10413 3.26 - 3.89: 20514 3.89 - 4.51: 28111 4.51 - 5.14: 43557 Nonbonded interactions: 102753 Sorted by model distance: nonbonded pdb=" O3G ANP B 801 " pdb="MG MG B 802 " model vdw 2.009 2.170 nonbonded pdb=" O3G ANP A 801 " pdb="MG MG A 802 " model vdw 2.011 2.170 nonbonded pdb=" OD1 ASN B 119 " pdb="MG MG B 802 " model vdw 2.029 2.170 nonbonded pdb=" OD1 ASN A 119 " pdb="MG MG A 802 " model vdw 2.061 2.170 nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 2.089 2.170 ... (remaining 102748 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 70 through 355 or resid 361 through 626 or resid 631 throu \ gh 803)) selection = (chain 'B' and (resid 70 through 355 or resid 361 through 625 or resid 631 or re \ sid 636 through 803)) } 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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.630 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 : 0.004 0.144 10234 Z= 0.194 Angle : 0.621 16.305 13813 Z= 0.306 Chirality : 0.042 0.274 1557 Planarity : 0.003 0.053 1752 Dihedral : 15.769 89.789 3912 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.24), residues: 1231 helix: 0.53 (0.23), residues: 531 sheet: 0.60 (0.41), residues: 175 loop : -0.82 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 692 TYR 0.010 0.001 TYR A 317 PHE 0.019 0.001 PHE C 146 TRP 0.009 0.001 TRP A 231 HIS 0.004 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00394 (10234) covalent geometry : angle 0.62119 (13813) hydrogen bonds : bond 0.12679 ( 470) hydrogen bonds : angle 6.11222 ( 1389) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.267 Fit side-chains REVERT: A 643 GLU cc_start: 0.7549 (mp0) cc_final: 0.7133 (mp0) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1005 time to fit residues: 21.1973 Evaluate side-chains 128 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 279 ASN A 506 HIS B 72 HIS B 256 HIS B 288 ASN B 406 GLN B 510 HIS B 648 HIS B 655 ASN B 671 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.132457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.103878 restraints weight = 14297.596| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.46 r_work: 0.3127 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10234 Z= 0.238 Angle : 0.604 8.367 13813 Z= 0.311 Chirality : 0.045 0.209 1557 Planarity : 0.004 0.043 1752 Dihedral : 5.776 56.325 1427 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.64 % Allowed : 11.82 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.24), residues: 1231 helix: 1.08 (0.23), residues: 518 sheet: 0.33 (0.38), residues: 181 loop : -0.76 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 402 TYR 0.022 0.002 TYR B 218 PHE 0.013 0.002 PHE B 264 TRP 0.009 0.002 TRP A 231 HIS 0.005 0.001 HIS A 606 Details of bonding type rmsd covalent geometry : bond 0.00561 (10234) covalent geometry : angle 0.60376 (13813) hydrogen bonds : bond 0.03494 ( 470) hydrogen bonds : angle 4.87951 ( 1389) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.324 Fit side-chains REVERT: A 317 TYR cc_start: 0.8133 (t80) cc_final: 0.7800 (t80) REVERT: A 532 ASP cc_start: 0.8154 (m-30) cc_final: 0.7711 (m-30) REVERT: B 301 MET cc_start: 0.7303 (pmm) cc_final: 0.6863 (ptt) outliers start: 7 outliers final: 4 residues processed: 142 average time/residue: 0.0972 time to fit residues: 19.3949 Evaluate side-chains 126 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 379 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 112 optimal weight: 0.1980 chunk 113 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN A 279 ASN B 146 GLN B 504 ASN B 510 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107321 restraints weight = 14164.451| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.47 r_work: 0.3182 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10234 Z= 0.126 Angle : 0.506 7.567 13813 Z= 0.262 Chirality : 0.041 0.159 1557 Planarity : 0.003 0.031 1752 Dihedral : 5.404 53.554 1427 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.73 % Allowed : 14.02 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.25), residues: 1231 helix: 1.11 (0.23), residues: 526 sheet: 0.41 (0.39), residues: 180 loop : -0.76 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 692 TYR 0.011 0.001 TYR B 437 PHE 0.013 0.001 PHE B 621 TRP 0.012 0.002 TRP A 231 HIS 0.003 0.001 HIS A 538 Details of bonding type rmsd covalent geometry : bond 0.00286 (10234) covalent geometry : angle 0.50573 (13813) hydrogen bonds : bond 0.03132 ( 470) hydrogen bonds : angle 4.61353 ( 1389) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 614 GLU cc_start: 0.7276 (pt0) cc_final: 0.7066 (pt0) REVERT: A 682 LEU cc_start: 0.8685 (mt) cc_final: 0.8470 (mt) REVERT: B 141 MET cc_start: 0.8723 (mmm) cc_final: 0.8521 (mtp) REVERT: B 301 MET cc_start: 0.7416 (pmm) cc_final: 0.6900 (ptt) outliers start: 8 outliers final: 5 residues processed: 144 average time/residue: 0.1036 time to fit residues: 20.8403 Evaluate side-chains 135 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 379 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 0.0570 chunk 40 optimal weight: 4.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 510 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.136966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.109147 restraints weight = 14283.576| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.28 r_work: 0.3192 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10234 Z= 0.116 Angle : 0.497 7.023 13813 Z= 0.256 Chirality : 0.041 0.191 1557 Planarity : 0.003 0.039 1752 Dihedral : 5.224 49.455 1427 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.47 % Allowed : 14.39 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.25), residues: 1231 helix: 1.15 (0.23), residues: 526 sheet: 0.36 (0.38), residues: 179 loop : -0.71 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 495 TYR 0.011 0.001 TYR B 437 PHE 0.007 0.001 PHE A 112 TRP 0.012 0.001 TRP A 231 HIS 0.003 0.001 HIS A 538 Details of bonding type rmsd covalent geometry : bond 0.00262 (10234) covalent geometry : angle 0.49743 (13813) hydrogen bonds : bond 0.02989 ( 470) hydrogen bonds : angle 4.45945 ( 1389) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: B 301 MET cc_start: 0.7449 (pmm) cc_final: 0.6991 (ptt) REVERT: B 352 MET cc_start: 0.8110 (tpp) cc_final: 0.7770 (tpt) REVERT: B 693 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8356 (tt) outliers start: 16 outliers final: 11 residues processed: 148 average time/residue: 0.1015 time to fit residues: 21.3311 Evaluate side-chains 140 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 693 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 57 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN B 230 GLN ** B 655 ASN ** 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 = 0.3643 r_free = 0.3643 target = 0.131139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102710 restraints weight = 14326.052| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.47 r_work: 0.3113 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10234 Z= 0.211 Angle : 0.570 7.840 13813 Z= 0.293 Chirality : 0.043 0.193 1557 Planarity : 0.003 0.044 1752 Dihedral : 5.611 54.434 1427 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.11 % Allowed : 16.04 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.24), residues: 1231 helix: 1.07 (0.23), residues: 526 sheet: 0.13 (0.37), residues: 187 loop : -0.82 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 495 TYR 0.014 0.002 TYR A 206 PHE 0.011 0.001 PHE B 264 TRP 0.013 0.002 TRP A 231 HIS 0.004 0.001 HIS A 606 Details of bonding type rmsd covalent geometry : bond 0.00495 (10234) covalent geometry : angle 0.56964 (13813) hydrogen bonds : bond 0.03370 ( 470) hydrogen bonds : angle 4.70744 ( 1389) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.389 Fit side-chains REVERT: A 99 ASP cc_start: 0.8405 (t0) cc_final: 0.8114 (t0) REVERT: A 620 HIS cc_start: 0.8207 (t-170) cc_final: 0.7645 (t-170) REVERT: B 340 ARG cc_start: 0.8712 (mmt-90) cc_final: 0.8379 (mmt-90) REVERT: B 585 TRP cc_start: 0.8413 (t60) cc_final: 0.8202 (t60) REVERT: B 693 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8406 (tt) outliers start: 23 outliers final: 14 residues processed: 153 average time/residue: 0.1007 time to fit residues: 21.6660 Evaluate side-chains 137 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 693 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 87 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 26 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 GLN ** B 655 ASN ** 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 = 0.3675 r_free = 0.3675 target = 0.133637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105968 restraints weight = 14322.235| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.39 r_work: 0.3153 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10234 Z= 0.136 Angle : 0.524 7.437 13813 Z= 0.269 Chirality : 0.041 0.190 1557 Planarity : 0.003 0.036 1752 Dihedral : 5.340 49.676 1427 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.83 % Allowed : 16.32 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.24), residues: 1231 helix: 1.10 (0.23), residues: 531 sheet: 0.17 (0.37), residues: 185 loop : -0.81 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 703 TYR 0.012 0.001 TYR B 437 PHE 0.008 0.001 PHE B 621 TRP 0.018 0.002 TRP A 231 HIS 0.004 0.001 HIS A 538 Details of bonding type rmsd covalent geometry : bond 0.00316 (10234) covalent geometry : angle 0.52411 (13813) hydrogen bonds : bond 0.03100 ( 470) hydrogen bonds : angle 4.55476 ( 1389) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8329 (t0) cc_final: 0.8049 (t0) REVERT: A 583 MET cc_start: 0.7017 (mtp) cc_final: 0.6790 (mtm) REVERT: B 340 ARG cc_start: 0.8668 (mmt-90) cc_final: 0.8351 (mmt-90) REVERT: B 352 MET cc_start: 0.8032 (tpp) cc_final: 0.7713 (tpt) REVERT: B 693 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8406 (tt) outliers start: 20 outliers final: 16 residues processed: 145 average time/residue: 0.0920 time to fit residues: 19.1528 Evaluate side-chains 143 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 693 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 93 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.131765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103811 restraints weight = 14209.929| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.41 r_work: 0.3120 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10234 Z= 0.189 Angle : 0.554 9.342 13813 Z= 0.285 Chirality : 0.043 0.189 1557 Planarity : 0.003 0.047 1752 Dihedral : 5.502 52.389 1427 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.11 % Allowed : 15.86 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1231 helix: 1.10 (0.23), residues: 524 sheet: 0.12 (0.37), residues: 186 loop : -0.74 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 634 TYR 0.013 0.001 TYR B 437 PHE 0.010 0.001 PHE B 264 TRP 0.017 0.002 TRP A 231 HIS 0.005 0.001 HIS A 538 Details of bonding type rmsd covalent geometry : bond 0.00445 (10234) covalent geometry : angle 0.55402 (13813) hydrogen bonds : bond 0.03278 ( 470) hydrogen bonds : angle 4.62164 ( 1389) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8355 (t0) cc_final: 0.8044 (t0) REVERT: A 295 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8372 (tt) REVERT: B 352 MET cc_start: 0.8080 (tpp) cc_final: 0.7819 (tpt) REVERT: B 585 TRP cc_start: 0.8411 (t60) cc_final: 0.8185 (t60) REVERT: B 693 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8449 (tt) outliers start: 23 outliers final: 17 residues processed: 144 average time/residue: 0.0955 time to fit residues: 19.8675 Evaluate side-chains 141 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 693 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 116 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 655 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107250 restraints weight = 14094.179| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.35 r_work: 0.3167 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10234 Z= 0.119 Angle : 0.532 10.449 13813 Z= 0.274 Chirality : 0.041 0.187 1557 Planarity : 0.003 0.037 1752 Dihedral : 5.266 47.525 1427 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.92 % Allowed : 17.14 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.25), residues: 1231 helix: 1.09 (0.23), residues: 530 sheet: 0.16 (0.38), residues: 185 loop : -0.73 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 634 TYR 0.011 0.001 TYR B 437 PHE 0.008 0.001 PHE A 112 TRP 0.017 0.002 TRP B 231 HIS 0.013 0.001 HIS A 620 Details of bonding type rmsd covalent geometry : bond 0.00272 (10234) covalent geometry : angle 0.53168 (13813) hydrogen bonds : bond 0.03082 ( 470) hydrogen bonds : angle 4.49994 ( 1389) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8349 (t0) cc_final: 0.8052 (t0) REVERT: A 103 ARG cc_start: 0.8513 (mtm110) cc_final: 0.8269 (mtm110) REVERT: A 185 ASP cc_start: 0.7711 (m-30) cc_final: 0.7428 (m-30) REVERT: A 295 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8387 (tt) REVERT: A 312 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7919 (mt-10) REVERT: B 340 ARG cc_start: 0.8684 (mmt-90) cc_final: 0.8277 (mmt-90) REVERT: B 585 TRP cc_start: 0.8360 (t60) cc_final: 0.8149 (t60) REVERT: B 693 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8384 (tt) outliers start: 21 outliers final: 18 residues processed: 150 average time/residue: 0.0960 time to fit residues: 20.1170 Evaluate side-chains 151 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 693 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 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 = 0.3620 r_free = 0.3620 target = 0.129331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.101550 restraints weight = 14219.190| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.18 r_work: 0.3105 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10234 Z= 0.261 Angle : 0.635 11.341 13813 Z= 0.324 Chirality : 0.044 0.187 1557 Planarity : 0.004 0.048 1752 Dihedral : 5.812 55.388 1427 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.02 % Allowed : 17.23 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.24), residues: 1231 helix: 0.92 (0.23), residues: 523 sheet: 0.00 (0.37), residues: 186 loop : -0.72 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 634 TYR 0.015 0.002 TYR A 317 PHE 0.028 0.002 PHE C 146 TRP 0.016 0.002 TRP A 231 HIS 0.017 0.002 HIS A 620 Details of bonding type rmsd covalent geometry : bond 0.00616 (10234) covalent geometry : angle 0.63534 (13813) hydrogen bonds : bond 0.03531 ( 470) hydrogen bonds : angle 4.82788 ( 1389) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8603 (t0) cc_final: 0.8285 (t0) REVERT: A 290 ARG cc_start: 0.8162 (ptm160) cc_final: 0.7860 (ptm-80) REVERT: A 295 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8496 (tt) REVERT: A 312 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 362 SER cc_start: 0.8702 (m) cc_final: 0.8328 (p) REVERT: B 495 ARG cc_start: 0.7925 (pmt-80) cc_final: 0.7569 (ptp-110) REVERT: B 693 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8531 (tt) outliers start: 22 outliers final: 18 residues processed: 144 average time/residue: 0.1041 time to fit residues: 20.6521 Evaluate side-chains 143 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 693 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 82 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.132502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105057 restraints weight = 14146.233| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.32 r_work: 0.3148 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10234 Z= 0.151 Angle : 0.571 10.855 13813 Z= 0.291 Chirality : 0.042 0.188 1557 Planarity : 0.003 0.032 1752 Dihedral : 5.501 50.509 1427 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.11 % Allowed : 17.42 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.19 (0.25), residues: 1231 helix: 1.00 (0.23), residues: 525 sheet: 0.04 (0.37), residues: 186 loop : -0.67 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 634 TYR 0.012 0.001 TYR B 206 PHE 0.021 0.001 PHE A 280 TRP 0.033 0.002 TRP B 585 HIS 0.020 0.001 HIS A 620 Details of bonding type rmsd covalent geometry : bond 0.00352 (10234) covalent geometry : angle 0.57060 (13813) hydrogen bonds : bond 0.03253 ( 470) hydrogen bonds : angle 4.68061 ( 1389) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8355 (t0) cc_final: 0.8067 (t0) REVERT: A 290 ARG cc_start: 0.7960 (ptm160) cc_final: 0.7665 (ptm-80) REVERT: A 295 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8411 (tt) REVERT: A 312 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7974 (mt-10) REVERT: B 340 ARG cc_start: 0.8698 (mmt-90) cc_final: 0.8282 (mmt-90) REVERT: B 352 MET cc_start: 0.8251 (tpp) cc_final: 0.7986 (tpp) REVERT: B 693 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8401 (tt) outliers start: 23 outliers final: 19 residues processed: 148 average time/residue: 0.0949 time to fit residues: 19.8537 Evaluate side-chains 147 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 693 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 0.0270 chunk 110 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN ** B 636 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 = 0.3677 r_free = 0.3677 target = 0.133813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106351 restraints weight = 14126.372| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.35 r_work: 0.3155 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10234 Z= 0.133 Angle : 0.572 10.522 13813 Z= 0.290 Chirality : 0.041 0.185 1557 Planarity : 0.003 0.026 1752 Dihedral : 5.342 47.618 1427 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.02 % Allowed : 17.05 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.25), residues: 1231 helix: 1.01 (0.23), residues: 525 sheet: 0.14 (0.37), residues: 186 loop : -0.64 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 634 TYR 0.012 0.001 TYR B 437 PHE 0.008 0.001 PHE A 112 TRP 0.026 0.002 TRP B 585 HIS 0.019 0.001 HIS A 620 Details of bonding type rmsd covalent geometry : bond 0.00308 (10234) covalent geometry : angle 0.57226 (13813) hydrogen bonds : bond 0.03221 ( 470) hydrogen bonds : angle 4.60314 ( 1389) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2172.09 seconds wall clock time: 38 minutes 3.31 seconds (2283.31 seconds total)