Starting phenix.real_space_refine on Thu Jul 2 22:20:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kcl_22812/07_2026/7kcl_22812.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kcl_22812/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7kcl_22812/07_2026/7kcl_22812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kcl_22812/07_2026/7kcl_22812.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kcl_22812/07_2026/7kcl_22812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kcl_22812/07_2026/7kcl_22812.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7kcl_22812/07_2026/7kcl_22812.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kcl_22812/07_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-6108/lib/python3.11/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: 1.87, per 1000 atoms: 0.19 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: 1.06 Conformation dependent library (CDL) restraints added in 367.4 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: 0.21 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: 1.41 Time building geometry restraints manager: 1.35 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: 5539 17.96 - 35.92: 545 35.92 - 53.87: 109 53.87 - 71.83: 30 71.83 - 89.79: 17 Dihedral angle restraints: 6240 sinusoidal: 2571 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 6237 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: 2.130 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.410 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.010 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 : 15.740 89.789 3856 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/Z covalent geometry : bond 0.00394 / 0.19 (10234) covalent geometry : angle 0.62119 / 0.31 (13813) hydrogen bonds : bond 0.12679 / 8.98 ( 470) hydrogen bonds : angle 6.11222 / 4.39 ( 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 : 0.292 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: 0.0851 time to fit residues: 18.0734 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 : 0.327 ------------------------------------------------------------------------------- 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... 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 = 0.3663 r_free = 0.3663 target = 0.132824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104170 restraints weight = 14289.095| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.48 r_work: 0.3131 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1403 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= 0.237 Angle : 0.598 8.254 13813 Z= 0.308 Chirality : 0.045 0.209 1557 Planarity : 0.004 0.043 1752 Dihedral : 5.093 54.732 1371 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.64 % Allowed : 11.55 % Favored : 87.81 % 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: 0.27 (0.24), residues: 1231 helix: 1.09 (0.23), residues: 518 sheet: 0.38 (0.38), residues: 180 loop : -0.76 (0.28), residues: 533 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 0.010 0.002 TRP A 231 HIS 0.005 0.001 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 (10234) covalent geometry : angle 0.59838 / 0.31 (13813) hydrogen bonds : bond 0.03516 / 2.41 ( 470) hydrogen bonds : angle 4.87462 / 3.46 ( 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 143 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.371 Fit side-chains REVERT: A 317 TYR cc_start: 0.8151 (t80) cc_final: 0.7868 (t80) REVERT: A 532 ASP cc_start: 0.8105 (m-30) cc_final: 0.7666 (m-30) REVERT: B 301 MET cc_start: 0.7287 (pmm) cc_final: 0.6804 (ptt) outliers start: 7 outliers final: 4 residues processed: 139 average time/residue: 0.0914 time to fit residues: 18.1678 Evaluate side-chains 129 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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: 0.6980 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 111 optimal weight: 0.0870 chunk 44 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3698 r_free = 0.3698 target = 0.135498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107234 restraints weight = 14175.298| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.46 r_work: 0.3178 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1438 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= 0.131 Angle : 0.510 7.500 13813 Z= 0.264 Chirality : 0.041 0.167 1557 Planarity : 0.003 0.031 1752 Dihedral : 4.821 56.546 1371 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.92 % Allowed : 13.57 % Favored : 85.52 % 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: 0.29 (0.25), residues: 1231 helix: 1.09 (0.23), residues: 526 sheet: 0.40 (0.39), residues: 180 loop : -0.75 (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 0.016 0.001 PHE B 621 TRP 0.011 0.002 TRP A 231 HIS 0.003 0.001 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10234) covalent geometry : angle 0.51023 / 0.26 (13813) hydrogen bonds : bond 0.03145 / 2.16 ( 470) hydrogen bonds : angle 4.63554 / 3.28 ( 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: 10 poor density : 138 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 682 LEU cc_start: 0.8685 (mt) cc_final: 0.8472 (mt) REVERT: B 75 ILE cc_start: 0.6949 (mm) cc_final: 0.6725 (mm) REVERT: B 141 MET cc_start: 0.8742 (mmm) cc_final: 0.8534 (mtp) REVERT: B 301 MET cc_start: 0.7420 (pmm) cc_final: 0.6913 (ptt) outliers start: 10 outliers final: 5 residues processed: 143 average time/residue: 0.0914 time to fit residues: 18.3441 Evaluate side-chains 133 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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: 0.9980 chunk 27 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 510 HIS ** 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 = 0.3639 r_free = 0.3639 target = 0.130835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.103479 restraints weight = 14348.230| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.19 r_work: 0.3148 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10234 Z= 0.190 Angle : 0.554 6.960 13813 Z= 0.284 Chirality : 0.043 0.199 1557 Planarity : 0.003 0.041 1752 Dihedral : 4.939 56.798 1371 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.65 % Allowed : 14.94 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.20 (0.24), residues: 1231 helix: 1.05 (0.23), residues: 525 sheet: 0.14 (0.37), residues: 187 loop : -0.77 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 495 TYR 0.013 0.002 TYR B 437 PHE 0.010 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/Z covalent geometry : bond 0.00443 / 0.19 (10234) covalent geometry : angle 0.55369 / 0.28 (13813) hydrogen bonds : bond 0.03295 / 2.25 ( 470) hydrogen bonds : angle 4.69050 / 3.33 ( 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 144 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.394 Fit side-chains REVERT: A 620 HIS cc_start: 0.8217 (t-170) cc_final: 0.7670 (t-170) REVERT: A 625 GLN cc_start: 0.6437 (mm-40) cc_final: 0.5880 (tt0) REVERT: B 693 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8534 (tt) outliers start: 18 outliers final: 11 residues processed: 140 average time/residue: 0.0947 time to fit residues: 18.5542 Evaluate side-chains 131 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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: 4.9990 chunk 89 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 ASN A 704 HIS B 230 GLN B 530 GLN ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.127572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.099342 restraints weight = 14392.031| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.26 r_work: 0.3069 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 10234 Z= 0.321 Angle : 0.657 8.489 13813 Z= 0.337 Chirality : 0.046 0.204 1557 Planarity : 0.004 0.035 1752 Dihedral : 5.378 58.580 1371 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.47 % Allowed : 15.95 % Favored : 81.58 % 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: 0.68 (0.23), residues: 528 sheet: -0.19 (0.36), residues: 188 loop : -0.92 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 402 TYR 0.015 0.002 TYR B 317 PHE 0.014 0.002 PHE B 264 TRP 0.016 0.003 TRP A 585 HIS 0.005 0.001 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.32 (10234) covalent geometry : angle 0.65709 / 0.34 (13813) hydrogen bonds : bond 0.03751 / 2.56 ( 470) hydrogen bonds : angle 5.00088 / 3.55 ( 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 152 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.381 Fit side-chains REVERT: A 587 ARG cc_start: 0.7162 (mtt90) cc_final: 0.6916 (mtt-85) REVERT: A 620 HIS cc_start: 0.8452 (t-170) cc_final: 0.7865 (t-170) REVERT: A 625 GLN cc_start: 0.6508 (mm-40) cc_final: 0.5999 (tt0) REVERT: B 110 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8653 (pt0) REVERT: B 362 SER cc_start: 0.8690 (m) cc_final: 0.8281 (p) REVERT: B 495 ARG cc_start: 0.7818 (pmt-80) cc_final: 0.7540 (ptp-110) REVERT: B 585 TRP cc_start: 0.8582 (t60) cc_final: 0.8352 (t60) REVERT: B 693 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8509 (tt) outliers start: 27 outliers final: 16 residues processed: 147 average time/residue: 0.0935 time to fit residues: 19.2686 Evaluate side-chains 135 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 597 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 110 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 87 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 26 optimal weight: 0.0040 chunk 65 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 230 GLN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.105639 restraints weight = 14294.912| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.38 r_work: 0.3154 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10234 Z= 0.117 Angle : 0.524 7.436 13813 Z= 0.271 Chirality : 0.041 0.199 1557 Planarity : 0.003 0.027 1752 Dihedral : 4.812 50.388 1371 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.83 % Allowed : 16.96 % Favored : 81.21 % 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: 0.11 (0.24), residues: 1231 helix: 0.98 (0.23), residues: 525 sheet: 0.09 (0.37), residues: 186 loop : -0.82 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 703 TYR 0.012 0.001 TYR A 437 PHE 0.009 0.001 PHE B 621 TRP 0.019 0.002 TRP A 231 HIS 0.003 0.001 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (10234) covalent geometry : angle 0.52445 / 0.27 (13813) hydrogen bonds : bond 0.03161 / 2.16 ( 470) hydrogen bonds : angle 4.58190 / 3.24 ( 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 163 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8277 (t0) cc_final: 0.7991 (t0) REVERT: A 583 MET cc_start: 0.7570 (mtm) cc_final: 0.7314 (mtp) REVERT: A 625 GLN cc_start: 0.6611 (mm-40) cc_final: 0.6155 (tt0) REVERT: A 682 LEU cc_start: 0.8693 (mt) cc_final: 0.8486 (mt) REVERT: B 75 ILE cc_start: 0.7045 (mm) cc_final: 0.6827 (mm) REVERT: B 352 MET cc_start: 0.8094 (tpp) cc_final: 0.7852 (tpt) REVERT: B 585 TRP cc_start: 0.8380 (t60) cc_final: 0.8170 (t60) REVERT: B 693 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8392 (tt) outliers start: 20 outliers final: 14 residues processed: 157 average time/residue: 0.0958 time to fit residues: 21.8839 Evaluate side-chains 143 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 B residue 108 GLU 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 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=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: 2.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 ASN B 230 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.131702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.104134 restraints weight = 14258.689| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.20 r_work: 0.3137 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10234 Z= 0.162 Angle : 0.553 7.285 13813 Z= 0.283 Chirality : 0.042 0.192 1557 Planarity : 0.003 0.027 1752 Dihedral : 4.839 52.622 1371 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.38 % Allowed : 16.59 % Favored : 81.03 % 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: 0.15 (0.24), residues: 1231 helix: 1.00 (0.23), residues: 519 sheet: 0.10 (0.38), residues: 186 loop : -0.76 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 692 TYR 0.013 0.001 TYR B 437 PHE 0.011 0.001 PHE B 112 TRP 0.017 0.002 TRP A 231 HIS 0.005 0.001 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (10234) covalent geometry : angle 0.55297 / 0.28 (13813) hydrogen bonds : bond 0.03236 / 2.22 ( 470) hydrogen bonds : angle 4.61468 / 3.27 ( 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 153 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8540 (t0) cc_final: 0.8190 (t0) REVERT: A 292 MET cc_start: 0.7660 (ptp) cc_final: 0.7033 (ptp) REVERT: A 583 MET cc_start: 0.7718 (mtm) cc_final: 0.7440 (mtp) REVERT: A 625 GLN cc_start: 0.6522 (mm-40) cc_final: 0.6048 (tt0) REVERT: B 340 ARG cc_start: 0.8876 (mmt-90) cc_final: 0.8507 (mmt-90) REVERT: B 352 MET cc_start: 0.8067 (tpp) cc_final: 0.7819 (tpt) REVERT: B 636 GLN cc_start: 0.8204 (pt0) cc_final: 0.7983 (pp30) REVERT: B 693 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8519 (tt) outliers start: 26 outliers final: 20 residues processed: 145 average time/residue: 0.1005 time to fit residues: 20.9106 Evaluate side-chains 145 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 23 optimal weight: 0.0170 chunk 37 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 61 optimal weight: 0.0000 chunk 41 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 overall best weight: 0.8028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3672 r_free = 0.3672 target = 0.133463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105318 restraints weight = 14133.366| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.45 r_work: 0.3146 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10234 Z= 0.129 Angle : 0.538 6.960 13813 Z= 0.277 Chirality : 0.041 0.190 1557 Planarity : 0.003 0.027 1752 Dihedral : 4.701 49.901 1371 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.20 % Allowed : 17.05 % 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: 0.19 (0.24), residues: 1231 helix: 1.07 (0.23), residues: 518 sheet: 0.14 (0.38), residues: 186 loop : -0.77 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 692 TYR 0.012 0.001 TYR B 437 PHE 0.010 0.001 PHE B 112 TRP 0.018 0.002 TRP B 231 HIS 0.007 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10234) covalent geometry : angle 0.53802 / 0.28 (13813) hydrogen bonds : bond 0.03159 / 2.17 ( 470) hydrogen bonds : angle 4.54360 / 3.22 ( 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 158 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8318 (t0) cc_final: 0.7991 (t0) REVERT: A 292 MET cc_start: 0.7134 (ptp) cc_final: 0.6544 (ptp) REVERT: A 583 MET cc_start: 0.7672 (mtm) cc_final: 0.7397 (mtp) REVERT: B 340 ARG cc_start: 0.8705 (mmt-90) cc_final: 0.8298 (mmt-90) REVERT: B 354 ASP cc_start: 0.6354 (m-30) cc_final: 0.5450 (m-30) REVERT: B 636 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7958 (pp30) REVERT: B 693 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8401 (tt) outliers start: 24 outliers final: 20 residues processed: 152 average time/residue: 0.0929 time to fit residues: 20.4213 Evaluate side-chains 150 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 238 VAL 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 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 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 636 GLN 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: 7.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 91 optimal weight: 0.0050 chunk 19 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 ASN ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 293 ASN B 655 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.129712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.101499 restraints weight = 14241.624| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.26 r_work: 0.3109 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10234 Z= 0.227 Angle : 0.615 9.231 13813 Z= 0.311 Chirality : 0.044 0.195 1557 Planarity : 0.003 0.028 1752 Dihedral : 5.036 54.642 1371 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.84 % Allowed : 16.50 % Favored : 80.66 % 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: 0.06 (0.24), residues: 1231 helix: 0.95 (0.23), residues: 517 sheet: -0.03 (0.38), residues: 186 loop : -0.79 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 692 TYR 0.014 0.002 TYR A 317 PHE 0.022 0.002 PHE C 146 TRP 0.027 0.002 TRP B 585 HIS 0.022 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 (10234) covalent geometry : angle 0.61488 / 0.31 (13813) hydrogen bonds : bond 0.03447 / 2.36 ( 470) hydrogen bonds : angle 4.79422 / 3.42 ( 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 159 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8553 (t0) cc_final: 0.8172 (t0) REVERT: A 292 MET cc_start: 0.8013 (ptp) cc_final: 0.7503 (ptp) REVERT: A 587 ARG cc_start: 0.7256 (mtt90) cc_final: 0.6981 (mtt-85) REVERT: B 354 ASP cc_start: 0.6635 (m-30) cc_final: 0.5942 (m-30) REVERT: B 362 SER cc_start: 0.8623 (m) cc_final: 0.8256 (p) REVERT: B 495 ARG cc_start: 0.7959 (pmt-80) cc_final: 0.7528 (ptp-110) REVERT: B 636 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8040 (pp30) REVERT: B 693 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8475 (tt) outliers start: 31 outliers final: 23 residues processed: 149 average time/residue: 0.0980 time to fit residues: 20.6318 Evaluate side-chains 148 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 279 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 597 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 622 LEU Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 655 ASN 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: 0.7980 chunk 103 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 ASN ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.131814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104505 restraints weight = 14446.231| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.34 r_work: 0.3115 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10234 Z= 0.211 Angle : 0.609 8.672 13813 Z= 0.310 Chirality : 0.044 0.196 1557 Planarity : 0.003 0.030 1752 Dihedral : 5.065 54.575 1371 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.47 % Allowed : 16.59 % 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: -0.03 (0.24), residues: 1231 helix: 0.83 (0.23), residues: 523 sheet: -0.07 (0.38), residues: 186 loop : -0.79 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 692 TYR 0.013 0.002 TYR B 437 PHE 0.020 0.002 PHE A 280 TRP 0.026 0.002 TRP B 585 HIS 0.021 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (10234) covalent geometry : angle 0.60936 / 0.31 (13813) hydrogen bonds : bond 0.03463 / 2.39 ( 470) hydrogen bonds : angle 4.81422 / 3.42 ( 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 153 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8212 (t0) cc_final: 0.7960 (t0) REVERT: A 292 MET cc_start: 0.7362 (ptp) cc_final: 0.6899 (ptp) REVERT: A 587 ARG cc_start: 0.7302 (mtt90) cc_final: 0.7079 (mtt-85) REVERT: B 340 ARG cc_start: 0.8661 (mmt-90) cc_final: 0.8307 (mmt-90) REVERT: B 354 ASP cc_start: 0.6597 (m-30) cc_final: 0.5781 (m-30) REVERT: B 693 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8541 (tt) outliers start: 27 outliers final: 24 residues processed: 144 average time/residue: 0.1092 time to fit residues: 22.2045 Evaluate side-chains 148 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 132 VAL 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 279 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 597 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 622 LEU Chi-restraints excluded: chain B residue 655 ASN 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: 0.7980 chunk 118 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 ASN ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.132065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.104441 restraints weight = 14165.083| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.19 r_work: 0.3157 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10234 Z= 0.137 Angle : 0.570 8.605 13813 Z= 0.291 Chirality : 0.042 0.192 1557 Planarity : 0.003 0.027 1752 Dihedral : 4.829 50.617 1371 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.11 % Allowed : 16.87 % Favored : 81.03 % 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: 0.13 (0.24), residues: 1231 helix: 0.95 (0.23), residues: 517 sheet: 0.12 (0.40), residues: 175 loop : -0.71 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 692 TYR 0.012 0.001 TYR B 437 PHE 0.017 0.001 PHE A 280 TRP 0.025 0.002 TRP B 585 HIS 0.021 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (10234) covalent geometry : angle 0.56983 / 0.29 (13813) hydrogen bonds : bond 0.03319 / 2.30 ( 470) hydrogen bonds : angle 4.67025 / 3.32 ( 1389) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2324.00 seconds wall clock time: 40 minutes 38.36 seconds (2438.36 seconds total)