Starting phenix.real_space_refine on Fri Feb 14 20:33:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kcl_22812/02_2025/7kcl_22812.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kcl_22812/02_2025/7kcl_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_22812/02_2025/7kcl_22812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kcl_22812/02_2025/7kcl_22812.map" model { file = "/net/cci-nas-00/data/ceres_data/7kcl_22812/02_2025/7kcl_22812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kcl_22812/02_2025/7kcl_22812.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.80, per 1000 atoms: 0.68 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: 2.23 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.35 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: 3.92 Time building geometry restraints manager: 2.65 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 704 or resid 801 through 803)) selection = (chain 'B' and (resid 70 through 355 or resid 361 through 625 or resid 631 or re \ sid 636 through 704 or resid 801 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.240 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.990 ------------------------------------------------------------------------------- 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= 0.222 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (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 TRP 0.009 0.001 TRP A 231 HIS 0.004 0.001 HIS A 311 PHE 0.019 0.001 PHE C 146 TYR 0.010 0.001 TYR A 317 ARG 0.006 0.000 ARG A 692 *********************** 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 : 1.139 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: 0.2372 time to fit residues: 49.8410 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 : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 506 HIS B 72 HIS B 288 ASN B 406 GLN B 510 HIS B 648 HIS B 655 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.133899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.104894 restraints weight = 14131.008| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.54 r_work: 0.3141 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10234 Z= 0.317 Angle : 0.575 8.118 13813 Z= 0.296 Chirality : 0.044 0.199 1557 Planarity : 0.004 0.042 1752 Dihedral : 5.725 56.075 1427 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.55 % Allowed : 11.00 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.25), residues: 1231 helix: 1.15 (0.23), residues: 518 sheet: 0.44 (0.39), residues: 180 loop : -0.75 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.004 0.001 HIS A 606 PHE 0.011 0.002 PHE B 264 TYR 0.020 0.002 TYR B 218 ARG 0.005 0.001 ARG A 402 *********************** 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: 6 poor density : 137 time to evaluate : 1.138 Fit side-chains REVERT: A 317 TYR cc_start: 0.8133 (t80) cc_final: 0.7898 (t80) outliers start: 6 outliers final: 4 residues processed: 140 average time/residue: 0.2430 time to fit residues: 48.4195 Evaluate side-chains 130 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 76 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN B 146 GLN B 504 ASN B 671 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.136587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108445 restraints weight = 14137.724| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.44 r_work: 0.3191 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10234 Z= 0.176 Angle : 0.501 7.403 13813 Z= 0.260 Chirality : 0.041 0.175 1557 Planarity : 0.003 0.030 1752 Dihedral : 5.353 53.098 1427 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.73 % Allowed : 13.38 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1231 helix: 1.14 (0.23), residues: 526 sheet: 0.43 (0.38), residues: 185 loop : -0.75 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 231 HIS 0.003 0.001 HIS A 538 PHE 0.008 0.001 PHE C 146 TYR 0.011 0.001 TYR A 437 ARG 0.003 0.000 ARG A 692 *********************** 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 146 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 317 TYR cc_start: 0.8129 (t80) cc_final: 0.7845 (t80) REVERT: A 614 GLU cc_start: 0.7262 (pt0) cc_final: 0.7060 (pt0) REVERT: A 682 LEU cc_start: 0.8651 (mt) cc_final: 0.8433 (mt) REVERT: B 141 MET cc_start: 0.8719 (mmm) cc_final: 0.8517 (mtp) REVERT: B 156 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8520 (mt) outliers start: 8 outliers final: 6 residues processed: 143 average time/residue: 0.2322 time to fit residues: 46.5111 Evaluate side-chains 137 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 379 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107766 restraints weight = 14223.705| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.46 r_work: 0.3189 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10234 Z= 0.173 Angle : 0.495 7.031 13813 Z= 0.256 Chirality : 0.041 0.168 1557 Planarity : 0.003 0.042 1752 Dihedral : 5.220 50.290 1427 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.37 % Allowed : 14.39 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1231 helix: 1.17 (0.23), residues: 526 sheet: 0.41 (0.38), residues: 186 loop : -0.77 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 231 HIS 0.003 0.001 HIS A 538 PHE 0.007 0.001 PHE C 146 TYR 0.011 0.001 TYR A 206 ARG 0.002 0.000 ARG B 692 *********************** 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 156 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 317 TYR cc_start: 0.8142 (t80) cc_final: 0.7835 (t80) REVERT: B 301 MET cc_start: 0.7401 (pmm) cc_final: 0.6875 (ptt) REVERT: B 352 MET cc_start: 0.8107 (tpp) cc_final: 0.7825 (tpt) REVERT: B 637 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8421 (pp) REVERT: B 693 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8379 (tt) outliers start: 15 outliers final: 10 residues processed: 148 average time/residue: 0.2400 time to fit residues: 49.7818 Evaluate side-chains 141 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 279 ASN 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 637 LEU Chi-restraints excluded: chain B residue 650 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 1 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 29 optimal weight: 0.0070 chunk 22 optimal weight: 3.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107229 restraints weight = 14081.801| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.18 r_work: 0.3193 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10234 Z= 0.227 Angle : 0.514 7.126 13813 Z= 0.267 Chirality : 0.042 0.239 1557 Planarity : 0.003 0.046 1752 Dihedral : 5.320 51.255 1427 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.92 % Allowed : 15.31 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.24), residues: 1231 helix: 1.15 (0.23), residues: 531 sheet: 0.38 (0.38), residues: 185 loop : -0.81 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 231 HIS 0.003 0.001 HIS A 606 PHE 0.011 0.001 PHE A 112 TYR 0.012 0.001 TYR B 437 ARG 0.003 0.000 ARG A 495 *********************** 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 153 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8627 (t0) cc_final: 0.8327 (t0) REVERT: A 317 TYR cc_start: 0.8323 (t80) cc_final: 0.8011 (t80) REVERT: B 301 MET cc_start: 0.7559 (pmm) cc_final: 0.7190 (ptt) REVERT: B 693 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8507 (tt) outliers start: 21 outliers final: 12 residues processed: 145 average time/residue: 0.2414 time to fit residues: 49.3264 Evaluate side-chains 141 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 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 55 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 120 optimal weight: 0.0770 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- 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 256 HIS ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.131453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103236 restraints weight = 14196.419| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.44 r_work: 0.3120 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1992 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= 0.303 Angle : 0.566 7.141 13813 Z= 0.290 Chirality : 0.043 0.236 1557 Planarity : 0.003 0.040 1752 Dihedral : 5.570 53.761 1427 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.83 % Allowed : 15.86 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1231 helix: 1.05 (0.23), residues: 528 sheet: 0.19 (0.37), residues: 187 loop : -0.85 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 231 HIS 0.004 0.001 HIS A 538 PHE 0.010 0.001 PHE A 112 TYR 0.013 0.002 TYR B 437 ARG 0.004 0.000 ARG A 495 *********************** 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 159 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8357 (t0) cc_final: 0.8042 (t0) REVERT: A 620 HIS cc_start: 0.8233 (t-170) cc_final: 0.7706 (t-170) REVERT: B 693 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8405 (tt) outliers start: 20 outliers final: 15 residues processed: 153 average time/residue: 0.2425 time to fit residues: 51.9298 Evaluate side-chains 147 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 480 LEU Chi-restraints excluded: chain A residue 524 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 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 47 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.0670 chunk 86 optimal weight: 5.9990 chunk 54 optimal weight: 0.0870 chunk 48 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.134596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106756 restraints weight = 14295.761| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.43 r_work: 0.3160 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2030 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= 0.184 Angle : 0.532 7.302 13813 Z= 0.273 Chirality : 0.041 0.230 1557 Planarity : 0.003 0.033 1752 Dihedral : 5.309 48.472 1427 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.74 % Allowed : 16.87 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.24), residues: 1231 helix: 1.18 (0.23), residues: 531 sheet: 0.22 (0.38), residues: 185 loop : -0.85 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 585 HIS 0.004 0.001 HIS A 538 PHE 0.010 0.001 PHE A 112 TYR 0.013 0.001 TYR A 317 ARG 0.003 0.000 ARG B 703 *********************** 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 155 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8389 (t0) cc_final: 0.8097 (t0) REVERT: A 295 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8330 (tt) REVERT: A 312 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7928 (mt-10) REVERT: B 340 ARG cc_start: 0.8677 (mmt-90) cc_final: 0.8376 (mmt-90) REVERT: B 636 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7802 (pp30) REVERT: B 693 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8404 (tt) outliers start: 19 outliers final: 15 residues processed: 150 average time/residue: 0.2339 time to fit residues: 49.5775 Evaluate side-chains 147 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 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 536 LEU Chi-restraints excluded: chain B residue 636 GLN 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 16 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.132526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.105242 restraints weight = 14206.115| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.33 r_work: 0.3141 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10234 Z= 0.259 Angle : 0.569 8.561 13813 Z= 0.288 Chirality : 0.042 0.232 1557 Planarity : 0.003 0.031 1752 Dihedral : 5.435 50.826 1427 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.02 % Allowed : 16.87 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.24), residues: 1231 helix: 1.10 (0.23), residues: 534 sheet: 0.18 (0.37), residues: 185 loop : -0.82 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 585 HIS 0.015 0.001 HIS A 620 PHE 0.011 0.001 PHE A 112 TYR 0.013 0.001 TYR B 437 ARG 0.003 0.000 ARG B 703 *********************** 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 153 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8382 (t0) cc_final: 0.8093 (t0) REVERT: A 312 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7941 (mt-10) REVERT: B 340 ARG cc_start: 0.8675 (mmt-90) cc_final: 0.8273 (mmt-90) REVERT: B 636 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7875 (pp30) REVERT: B 693 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8419 (tt) outliers start: 22 outliers final: 17 residues processed: 147 average time/residue: 0.2387 time to fit residues: 49.3129 Evaluate side-chains 145 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 113 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 227 LEU 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 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 53 optimal weight: 5.9990 chunk 3 optimal weight: 0.0570 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 73 optimal weight: 0.0270 chunk 9 optimal weight: 0.7980 chunk 111 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.134295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.106159 restraints weight = 14227.972| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.45 r_work: 0.3153 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10234 Z= 0.182 Angle : 0.554 10.101 13813 Z= 0.279 Chirality : 0.041 0.222 1557 Planarity : 0.003 0.030 1752 Dihedral : 5.261 47.039 1427 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.20 % Allowed : 16.68 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.24), residues: 1231 helix: 1.19 (0.24), residues: 521 sheet: 0.21 (0.37), residues: 185 loop : -0.71 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 585 HIS 0.013 0.001 HIS A 620 PHE 0.011 0.001 PHE A 112 TYR 0.011 0.001 TYR B 437 ARG 0.003 0.000 ARG B 703 *********************** 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 157 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8376 (t0) cc_final: 0.8084 (t0) REVERT: A 295 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8339 (tt) REVERT: A 312 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7915 (mt-10) REVERT: B 340 ARG cc_start: 0.8680 (mmt-90) cc_final: 0.8261 (mmt-90) REVERT: B 636 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7874 (pp30) REVERT: B 693 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8392 (tt) outliers start: 24 outliers final: 20 residues processed: 149 average time/residue: 0.2496 time to fit residues: 52.4147 Evaluate side-chains 151 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 517 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 622 LEU 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 227 LEU 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 636 GLN 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 111 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.130575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102931 restraints weight = 14339.594| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.19 r_work: 0.3135 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2335 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= 0.333 Angle : 0.617 10.964 13813 Z= 0.312 Chirality : 0.043 0.236 1557 Planarity : 0.003 0.029 1752 Dihedral : 5.642 53.400 1427 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.29 % Allowed : 16.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.24), residues: 1231 helix: 1.06 (0.23), residues: 520 sheet: 0.15 (0.37), residues: 186 loop : -0.70 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 585 HIS 0.022 0.001 HIS A 620 PHE 0.011 0.002 PHE B 264 TYR 0.014 0.002 TYR B 437 ARG 0.003 0.000 ARG A 402 ********************** 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 154 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8627 (t0) cc_final: 0.8283 (t0) REVERT: A 295 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8466 (tt) REVERT: A 312 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8210 (mt-10) REVERT: A 643 GLU cc_start: 0.8048 (mp0) cc_final: 0.7815 (mp0) REVERT: B 352 MET cc_start: 0.8082 (tpp) cc_final: 0.7813 (tpt) REVERT: B 636 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7948 (pp30) REVERT: B 693 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8507 (tt) outliers start: 25 outliers final: 21 residues processed: 146 average time/residue: 0.2366 time to fit residues: 48.5329 Evaluate side-chains 146 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 295 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 517 MET 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 227 LEU 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 636 GLN 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 26 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 83 optimal weight: 0.0970 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.134095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106751 restraints weight = 14171.076| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.18 r_work: 0.3181 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10234 Z= 0.189 Angle : 0.579 10.686 13813 Z= 0.291 Chirality : 0.042 0.225 1557 Planarity : 0.003 0.030 1752 Dihedral : 5.381 48.304 1427 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.11 % Allowed : 17.05 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.24), residues: 1231 helix: 1.11 (0.23), residues: 520 sheet: 0.16 (0.37), residues: 185 loop : -0.70 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 585 HIS 0.021 0.001 HIS A 620 PHE 0.018 0.001 PHE A 280 TYR 0.012 0.001 TYR B 437 ARG 0.003 0.000 ARG B 703 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4699.07 seconds wall clock time: 84 minutes 22.83 seconds (5062.83 seconds total)