Starting phenix.real_space_refine on Fri Feb 6 12:15:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n0o_48788/02_2026/9n0o_48788_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n0o_48788/02_2026/9n0o_48788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n0o_48788/02_2026/9n0o_48788_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n0o_48788/02_2026/9n0o_48788_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n0o_48788/02_2026/9n0o_48788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n0o_48788/02_2026/9n0o_48788.map" } resolution = 2.8 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 42 5.16 5 C 7851 2.51 5 N 2194 2.21 5 O 2276 1.98 5 H 12157 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24522 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 12219 Classifications: {'peptide': 768} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 739} Chain breaks: 6 Chain: "B" Number of atoms: 12273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 12273 Classifications: {'peptide': 771} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 742} Chain breaks: 6 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 3.96, per 1000 atoms: 0.16 Number of scatterers: 24522 At special positions: 0 Unit cell: (120.24, 110.16, 106.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 2 15.00 O 2276 8.00 N 2194 7.00 C 7851 6.00 H 12157 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 664.8 milliseconds 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2950 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 12 sheets defined 60.4% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 15 through 19 Processing helix chain 'A' and resid 21 through 24 removed outlier: 3.521A pdb=" N TYR A 24 " --> pdb=" O ASN A 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 21 through 24' Processing helix chain 'A' and resid 25 through 46 removed outlier: 3.614A pdb=" N ALA A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 66 removed outlier: 3.538A pdb=" N ALA A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 90 through 109 removed outlier: 3.844A pdb=" N GLU A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 175 through 186 Processing helix chain 'A' and resid 229 through 239 Processing helix chain 'A' and resid 272 through 289 removed outlier: 3.629A pdb=" N LEU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 301 Processing helix chain 'A' and resid 355 through 368 Processing helix chain 'A' and resid 379 through 392 removed outlier: 3.650A pdb=" N LYS A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 416 removed outlier: 3.812A pdb=" N HIS A 409 " --> pdb=" O HIS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 451 Processing helix chain 'A' and resid 473 through 485 removed outlier: 3.652A pdb=" N ILE A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 502 removed outlier: 4.309A pdb=" N ALA A 498 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N PHE A 499 " --> pdb=" O TRP A 496 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 501 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 510 through 524 Processing helix chain 'A' and resid 524 through 538 Processing helix chain 'A' and resid 542 through 548 removed outlier: 3.861A pdb=" N VAL A 547 " --> pdb=" O SER A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 Processing helix chain 'A' and resid 591 through 604 removed outlier: 4.614A pdb=" N ALA A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 625 Processing helix chain 'A' and resid 626 through 648 Processing helix chain 'A' and resid 648 through 653 Processing helix chain 'A' and resid 659 through 664 Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 685 through 694 Processing helix chain 'A' and resid 708 through 711 Processing helix chain 'A' and resid 713 through 721 Processing helix chain 'A' and resid 721 through 727 Processing helix chain 'A' and resid 747 through 772 Processing helix chain 'A' and resid 773 through 789 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 832 through 843 removed outlier: 3.622A pdb=" N GLY A 837 " --> pdb=" O ILE A 833 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG A 838 " --> pdb=" O GLY A 834 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 841 " --> pdb=" O GLY A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 878 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'B' and resid 15 through 19 Processing helix chain 'B' and resid 25 through 46 removed outlier: 3.655A pdb=" N ALA B 46 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 65 Processing helix chain 'B' and resid 66 through 71 removed outlier: 5.873A pdb=" N ARG B 69 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 88 Processing helix chain 'B' and resid 90 through 108 removed outlier: 3.771A pdb=" N GLU B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 Processing helix chain 'B' and resid 152 through 160 Processing helix chain 'B' and resid 175 through 186 Processing helix chain 'B' and resid 229 through 239 Processing helix chain 'B' and resid 272 through 289 Processing helix chain 'B' and resid 290 through 301 Processing helix chain 'B' and resid 355 through 368 Processing helix chain 'B' and resid 378 through 392 removed outlier: 3.687A pdb=" N THR B 382 " --> pdb=" O ASN B 378 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 416 removed outlier: 3.654A pdb=" N HIS B 409 " --> pdb=" O HIS B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 473 through 485 removed outlier: 3.590A pdb=" N ILE B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 502 removed outlier: 4.187A pdb=" N ALA B 498 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE B 499 " --> pdb=" O TRP B 496 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 501 " --> pdb=" O ALA B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 510 through 524 Processing helix chain 'B' and resid 524 through 538 Processing helix chain 'B' and resid 543 through 548 removed outlier: 3.759A pdb=" N VAL B 547 " --> pdb=" O SER B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 572 Processing helix chain 'B' and resid 592 through 604 Processing helix chain 'B' and resid 609 through 625 removed outlier: 3.543A pdb=" N LEU B 613 " --> pdb=" O ASN B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 648 Processing helix chain 'B' and resid 648 through 653 Processing helix chain 'B' and resid 659 through 664 Processing helix chain 'B' and resid 665 through 669 Processing helix chain 'B' and resid 685 through 694 Processing helix chain 'B' and resid 708 through 711 Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'B' and resid 721 through 727 Processing helix chain 'B' and resid 747 through 772 Processing helix chain 'B' and resid 773 through 789 Processing helix chain 'B' and resid 814 through 822 Processing helix chain 'B' and resid 832 through 843 removed outlier: 3.625A pdb=" N GLY B 837 " --> pdb=" O ILE B 833 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG B 838 " --> pdb=" O GLY B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 878 Processing helix chain 'B' and resid 897 through 910 Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 173 removed outlier: 6.287A pdb=" N GLN A 134 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N GLU A 169 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TYR A 136 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU A 171 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A 138 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 173 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU A 140 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE A 189 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR A 137 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 191 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLN A 190 " --> pdb=" O ASP A 243 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N TYR A 245 " --> pdb=" O GLN A 190 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA A 192 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU A 247 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE A 194 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N PHE A 267 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 246 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 372 through 376 removed outlier: 6.119A pdb=" N PHE A 490 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N THR A 565 " --> pdb=" O PHE A 490 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TRP A 492 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N SER A 567 " --> pdb=" O TRP A 492 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE A 397 " --> pdb=" O MET A 459 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N LEU A 461 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 399 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 398 " --> pdb=" O MET A 420 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU A 422 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE A 400 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 470 through 472 Processing sheet with id=AA4, first strand: chain 'A' and resid 656 through 657 removed outlier: 3.678A pdb=" N LYS A 732 " --> pdb=" O LEU A 739 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 828 through 831 Processing sheet with id=AA6, first strand: chain 'A' and resid 853 through 854 Processing sheet with id=AA7, first strand: chain 'B' and resid 166 through 173 removed outlier: 6.257A pdb=" N GLN B 134 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N GLU B 169 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR B 136 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU B 171 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL B 138 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N VAL B 173 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU B 140 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE B 189 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR B 137 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 191 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLN B 190 " --> pdb=" O ASP B 243 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N TYR B 245 " --> pdb=" O GLN B 190 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA B 192 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU B 247 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE B 194 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N PHE B 267 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 246 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 372 through 376 removed outlier: 6.906A pdb=" N ILE B 397 " --> pdb=" O MET B 459 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LEU B 461 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 399 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 398 " --> pdb=" O MET B 420 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU B 422 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE B 400 " --> pdb=" O LEU B 422 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 470 through 472 Processing sheet with id=AB1, first strand: chain 'B' and resid 656 through 657 removed outlier: 3.784A pdb=" N LYS B 732 " --> pdb=" O LEU B 739 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 828 through 831 Processing sheet with id=AB3, first strand: chain 'B' and resid 853 through 854 removed outlier: 3.740A pdb=" N HIS B 885 " --> pdb=" O VAL B 853 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1905 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: 6.00 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 12143 1.00 - 1.21: 14 1.21 - 1.41: 5366 1.41 - 1.61: 7199 1.61 - 1.82: 70 Bond restraints: 24792 Sorted by residual: bond pdb=" N ALA B 15 " pdb=" H1 ALA B 15 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N ALA A 15 " pdb=" H1 ALA A 15 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" ND2 ASN A 909 " pdb="HD22 ASN A 909 " ideal model delta sigma weight residual 0.860 0.798 0.062 2.00e-02 2.50e+03 9.65e+00 bond pdb=" ND2 ASN B 186 " pdb="HD22 ASN B 186 " ideal model delta sigma weight residual 0.860 0.800 0.060 2.00e-02 2.50e+03 9.03e+00 bond pdb=" ND2 ASN A 464 " pdb="HD22 ASN A 464 " ideal model delta sigma weight residual 0.860 0.801 0.059 2.00e-02 2.50e+03 8.83e+00 ... (remaining 24787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.31: 44563 5.31 - 10.62: 14 10.62 - 15.93: 2 15.93 - 21.24: 8 21.24 - 26.55: 5 Bond angle restraints: 44592 Sorted by residual: angle pdb=" CG ASN A 473 " pdb=" ND2 ASN A 473 " pdb="HD22 ASN A 473 " ideal model delta sigma weight residual 120.00 146.55 -26.55 3.00e+00 1.11e-01 7.83e+01 angle pdb="HD21 ASN A 473 " pdb=" ND2 ASN A 473 " pdb="HD22 ASN A 473 " ideal model delta sigma weight residual 120.00 93.50 26.50 3.00e+00 1.11e-01 7.80e+01 angle pdb=" CG ASN A 473 " pdb=" ND2 ASN A 473 " pdb="HD21 ASN A 473 " ideal model delta sigma weight residual 120.00 94.53 25.47 3.00e+00 1.11e-01 7.21e+01 angle pdb=" CG ASN A 464 " pdb=" ND2 ASN A 464 " pdb="HD22 ASN A 464 " ideal model delta sigma weight residual 120.00 142.02 -22.02 3.00e+00 1.11e-01 5.39e+01 angle pdb="HD21 ASN A 464 " pdb=" ND2 ASN A 464 " pdb="HD22 ASN A 464 " ideal model delta sigma weight residual 120.00 98.02 21.98 3.00e+00 1.11e-01 5.37e+01 ... (remaining 44587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 10506 17.98 - 35.95: 664 35.95 - 53.93: 272 53.93 - 71.90: 160 71.90 - 89.88: 37 Dihedral angle restraints: 11639 sinusoidal: 6232 harmonic: 5407 Sorted by residual: dihedral pdb=" CA ARG A 692 " pdb=" C ARG A 692 " pdb=" N SER A 693 " pdb=" CA SER A 693 " ideal model delta harmonic sigma weight residual -180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA ARG B 692 " pdb=" C ARG B 692 " pdb=" N SER B 693 " pdb=" CA SER B 693 " ideal model delta harmonic sigma weight residual -180.00 -155.71 -24.29 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA PRO B 419 " pdb=" C PRO B 419 " pdb=" N MET B 420 " pdb=" CA MET B 420 " ideal model delta harmonic sigma weight residual 180.00 157.83 22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 11636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1379 0.036 - 0.073: 397 0.073 - 0.109: 125 0.109 - 0.145: 25 0.145 - 0.182: 3 Chirality restraints: 1929 Sorted by residual: chirality pdb=" CA TYR B 855 " pdb=" N TYR B 855 " pdb=" C TYR B 855 " pdb=" CB TYR B 855 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CA TYR A 497 " pdb=" N TYR A 497 " pdb=" C TYR A 497 " pdb=" CB TYR A 497 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" CA TYR B 497 " pdb=" N TYR B 497 " pdb=" C TYR B 497 " pdb=" CB TYR B 497 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 1926 not shown) Planarity restraints: 3682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 378 " 0.048 2.00e-02 2.50e+03 9.77e-02 1.43e+02 pdb=" CG ASN A 378 " -0.114 2.00e-02 2.50e+03 pdb=" OD1 ASN A 378 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 378 " 0.162 2.00e-02 2.50e+03 pdb="HD21 ASN A 378 " 0.034 2.00e-02 2.50e+03 pdb="HD22 ASN A 378 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 909 " 0.067 2.00e-02 2.50e+03 9.74e-02 1.42e+02 pdb=" CG ASN A 909 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 909 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 909 " -0.160 2.00e-02 2.50e+03 pdb="HD21 ASN A 909 " -0.030 2.00e-02 2.50e+03 pdb="HD22 ASN A 909 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 186 " 0.058 2.00e-02 2.50e+03 9.46e-02 1.34e+02 pdb=" CG ASN B 186 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN B 186 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 186 " -0.161 2.00e-02 2.50e+03 pdb="HD21 ASN B 186 " -0.034 2.00e-02 2.50e+03 pdb="HD22 ASN B 186 " 0.152 2.00e-02 2.50e+03 ... (remaining 3679 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.12: 712 2.12 - 2.74: 45192 2.74 - 3.36: 77481 3.36 - 3.98: 99933 3.98 - 4.60: 155872 Nonbonded interactions: 379190 Sorted by model distance: nonbonded pdb=" HG SER B 798 " pdb=" O LEU B 867 " model vdw 1.494 2.450 nonbonded pdb=" OG1 THR A 701 " pdb="HH11 ARG A 702 " model vdw 1.557 2.450 nonbonded pdb=" OE1 GLU B 842 " pdb=" HZ3 LYS B 844 " model vdw 1.574 2.450 nonbonded pdb="HH12 ARG A 160 " pdb=" OE1 GLU A 169 " model vdw 1.589 2.450 nonbonded pdb=" HH TYR A 527 " pdb=" O PRO A 553 " model vdw 1.611 2.450 ... (remaining 379185 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' selection = (chain 'B' and (resid 15 through 201 or resid 228 through 855 or (resid 856 and \ (name N or name CA or name C or name O or name CB or name CG or name CD )) or re \ sid 857 through 1001)) } 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: 8.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.310 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.006 0.469 12637 Z= 0.540 Angle : 0.614 7.444 17177 Z= 0.337 Chirality : 0.039 0.182 1929 Planarity : 0.007 0.085 2213 Dihedral : 15.576 89.875 4571 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.00 % Allowed : 12.12 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.21), residues: 1511 helix: -0.17 (0.17), residues: 780 sheet: -0.52 (0.45), residues: 144 loop : 0.16 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A 287 TYR 0.026 0.003 TYR B 527 PHE 0.016 0.002 PHE A 135 TRP 0.018 0.002 TRP B 71 HIS 0.008 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00302 (12635) covalent geometry : angle 0.61393 (17177) hydrogen bonds : bond 0.14922 ( 672) hydrogen bonds : angle 7.48457 ( 1905) Misc. bond : bond 0.41658 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 828 ARG cc_start: 0.8485 (tmm-80) cc_final: 0.8272 (ttm-80) outliers start: 13 outliers final: 7 residues processed: 152 average time/residue: 1.5659 time to fit residues: 256.7252 Evaluate side-chains 150 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 734 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS B 569 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.180184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.140708 restraints weight = 36260.231| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.62 r_work: 0.3559 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12637 Z= 0.167 Angle : 0.553 6.407 17177 Z= 0.297 Chirality : 0.040 0.172 1929 Planarity : 0.004 0.033 2213 Dihedral : 6.161 74.186 1733 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.31 % Allowed : 11.04 % Favored : 87.64 % 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: 1.22 (0.22), residues: 1511 helix: 1.32 (0.18), residues: 792 sheet: -0.49 (0.45), residues: 140 loop : 0.66 (0.28), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 160 TYR 0.020 0.002 TYR B 527 PHE 0.014 0.001 PHE B 819 TRP 0.008 0.001 TRP B 687 HIS 0.005 0.001 HIS B 603 Details of bonding type rmsd covalent geometry : bond 0.00385 (12635) covalent geometry : angle 0.55314 (17177) hydrogen bonds : bond 0.04109 ( 672) hydrogen bonds : angle 5.66264 ( 1905) Misc. bond : bond 0.00095 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.6282 (OUTLIER) cc_final: 0.5872 (mm-30) REVERT: A 497 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.6721 (m-10) REVERT: A 878 GLN cc_start: 0.7453 (mm110) cc_final: 0.7216 (mm-40) REVERT: B 497 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7046 (m-10) REVERT: B 538 MET cc_start: 0.8521 (mmp) cc_final: 0.8169 (mmt) REVERT: B 785 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6440 (mp0) outliers start: 17 outliers final: 7 residues processed: 160 average time/residue: 1.3579 time to fit residues: 234.8061 Evaluate side-chains 148 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 785 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 107 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 0.3980 chunk 75 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.179708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.140218 restraints weight = 36019.511| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.60 r_work: 0.3545 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12637 Z= 0.145 Angle : 0.502 6.496 17177 Z= 0.267 Chirality : 0.038 0.162 1929 Planarity : 0.004 0.039 2213 Dihedral : 5.599 61.479 1730 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.47 % Allowed : 10.73 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.22), residues: 1511 helix: 1.80 (0.18), residues: 793 sheet: -0.72 (0.43), residues: 154 loop : 0.77 (0.29), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 195 TYR 0.023 0.001 TYR B 527 PHE 0.012 0.001 PHE B 819 TRP 0.009 0.001 TRP B 687 HIS 0.006 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00335 (12635) covalent geometry : angle 0.50158 (17177) hydrogen bonds : bond 0.03785 ( 672) hydrogen bonds : angle 5.27180 ( 1905) Misc. bond : bond 0.00095 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 108 TYR cc_start: 0.3297 (OUTLIER) cc_final: 0.2509 (m-10) REVERT: A 154 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.6001 (mm-30) REVERT: A 233 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7459 (mt-10) REVERT: A 497 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.6865 (m-80) REVERT: A 538 MET cc_start: 0.8575 (mmp) cc_final: 0.8339 (mmt) REVERT: A 545 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: A 716 ASP cc_start: 0.6841 (p0) cc_final: 0.6588 (m-30) REVERT: A 878 GLN cc_start: 0.7485 (mm110) cc_final: 0.7243 (mm-40) REVERT: B 497 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.6968 (m-10) REVERT: B 538 MET cc_start: 0.8523 (mmp) cc_final: 0.8320 (mmt) REVERT: B 716 ASP cc_start: 0.7172 (p0) cc_final: 0.6753 (m-30) REVERT: B 785 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6528 (mp0) REVERT: B 824 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6557 (mt-10) outliers start: 19 outliers final: 7 residues processed: 157 average time/residue: 1.4257 time to fit residues: 242.4003 Evaluate side-chains 149 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 785 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 15 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 135 optimal weight: 0.6980 chunk 122 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.179900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.140561 restraints weight = 36022.101| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.59 r_work: 0.3545 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12637 Z= 0.133 Angle : 0.481 6.269 17177 Z= 0.255 Chirality : 0.038 0.157 1929 Planarity : 0.004 0.038 2213 Dihedral : 5.410 59.047 1730 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.24 % Allowed : 11.81 % Favored : 86.95 % 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: 1.80 (0.23), residues: 1511 helix: 1.98 (0.19), residues: 794 sheet: -0.77 (0.43), residues: 154 loop : 0.81 (0.29), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 195 TYR 0.020 0.001 TYR B 527 PHE 0.010 0.001 PHE B 819 TRP 0.006 0.001 TRP B 687 HIS 0.003 0.001 HIS B 603 Details of bonding type rmsd covalent geometry : bond 0.00304 (12635) covalent geometry : angle 0.48063 (17177) hydrogen bonds : bond 0.03492 ( 672) hydrogen bonds : angle 5.10909 ( 1905) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 108 TYR cc_start: 0.3600 (OUTLIER) cc_final: 0.2753 (m-80) REVERT: A 154 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6094 (mm-30) REVERT: A 188 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8708 (mt-10) REVERT: A 497 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.6790 (m-10) REVERT: A 545 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7493 (mt-10) REVERT: A 716 ASP cc_start: 0.6881 (p0) cc_final: 0.6610 (m-30) REVERT: A 878 GLN cc_start: 0.7465 (mm110) cc_final: 0.7233 (mm-40) REVERT: B 497 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.6913 (m-10) REVERT: B 716 ASP cc_start: 0.7221 (p0) cc_final: 0.6833 (m-30) REVERT: B 785 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6572 (mp0) REVERT: B 824 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6564 (mt-10) outliers start: 16 outliers final: 4 residues processed: 151 average time/residue: 1.4510 time to fit residues: 236.7164 Evaluate side-chains 143 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 785 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN B 885 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.180176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.141052 restraints weight = 35899.346| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.61 r_work: 0.3509 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12637 Z= 0.152 Angle : 0.486 6.355 17177 Z= 0.258 Chirality : 0.038 0.155 1929 Planarity : 0.004 0.039 2213 Dihedral : 5.363 60.031 1728 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.31 % Allowed : 12.36 % Favored : 86.33 % 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: 1.83 (0.23), residues: 1511 helix: 2.04 (0.19), residues: 795 sheet: -0.82 (0.42), residues: 156 loop : 0.80 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 195 TYR 0.020 0.001 TYR B 527 PHE 0.010 0.001 PHE B 819 TRP 0.007 0.001 TRP B 687 HIS 0.004 0.001 HIS B 603 Details of bonding type rmsd covalent geometry : bond 0.00356 (12635) covalent geometry : angle 0.48555 (17177) hydrogen bonds : bond 0.03578 ( 672) hydrogen bonds : angle 5.07360 ( 1905) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.6101 (mm-30) REVERT: A 497 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.6747 (m-10) REVERT: A 545 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: A 716 ASP cc_start: 0.6861 (p0) cc_final: 0.6631 (m-30) REVERT: A 878 GLN cc_start: 0.7367 (mm110) cc_final: 0.7138 (mm-40) REVERT: B 497 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.6825 (m-10) REVERT: B 785 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6486 (mp0) outliers start: 17 outliers final: 5 residues processed: 149 average time/residue: 1.4649 time to fit residues: 234.6376 Evaluate side-chains 146 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 785 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 885 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.179942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.140987 restraints weight = 35947.320| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.60 r_work: 0.3505 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12637 Z= 0.150 Angle : 0.483 6.361 17177 Z= 0.256 Chirality : 0.038 0.154 1929 Planarity : 0.004 0.038 2213 Dihedral : 5.113 59.625 1725 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.24 % Allowed : 13.05 % Favored : 85.71 % 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: 1.85 (0.23), residues: 1511 helix: 2.07 (0.19), residues: 794 sheet: -0.80 (0.43), residues: 152 loop : 0.76 (0.29), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 195 TYR 0.018 0.001 TYR B 527 PHE 0.010 0.001 PHE A 819 TRP 0.005 0.001 TRP A 687 HIS 0.003 0.001 HIS B 603 Details of bonding type rmsd covalent geometry : bond 0.00348 (12635) covalent geometry : angle 0.48252 (17177) hydrogen bonds : bond 0.03541 ( 672) hydrogen bonds : angle 5.03213 ( 1905) Misc. bond : bond 0.00006 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.6150 (mm-30) REVERT: A 497 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.6708 (m-10) REVERT: A 545 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: A 716 ASP cc_start: 0.6942 (p0) cc_final: 0.6702 (m-30) REVERT: A 878 GLN cc_start: 0.7414 (mm110) cc_final: 0.7199 (mm-40) REVERT: B 236 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6886 (mmt-90) REVERT: B 497 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.6955 (m-10) REVERT: B 593 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7462 (ttp80) REVERT: B 785 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6511 (mp0) outliers start: 16 outliers final: 6 residues processed: 156 average time/residue: 1.4085 time to fit residues: 238.0896 Evaluate side-chains 151 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 785 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 114 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.178418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.139149 restraints weight = 35964.405| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.60 r_work: 0.3438 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12637 Z= 0.188 Angle : 0.509 6.505 17177 Z= 0.270 Chirality : 0.039 0.154 1929 Planarity : 0.004 0.040 2213 Dihedral : 5.231 61.194 1725 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.78 % Favored : 97.15 % Rotamer: Outliers : 1.47 % Allowed : 13.59 % Favored : 84.94 % 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: 1.72 (0.23), residues: 1511 helix: 1.99 (0.19), residues: 794 sheet: -0.97 (0.43), residues: 159 loop : 0.71 (0.29), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 195 TYR 0.019 0.001 TYR B 527 PHE 0.011 0.002 PHE B 819 TRP 0.007 0.001 TRP A 748 HIS 0.004 0.001 HIS B 603 Details of bonding type rmsd covalent geometry : bond 0.00443 (12635) covalent geometry : angle 0.50872 (17177) hydrogen bonds : bond 0.03737 ( 672) hydrogen bonds : angle 5.09281 ( 1905) Misc. bond : bond 0.00018 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.6150 (mm-30) REVERT: A 236 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6914 (mmt-90) REVERT: A 497 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.6844 (m-80) REVERT: A 545 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: A 716 ASP cc_start: 0.6943 (p0) cc_final: 0.6664 (m-30) REVERT: A 878 GLN cc_start: 0.7399 (mm110) cc_final: 0.7188 (mm-40) REVERT: B 497 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.6932 (m-10) REVERT: B 593 ARG cc_start: 0.7787 (ttm-80) cc_final: 0.7456 (ttp-110) REVERT: B 785 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6401 (mp0) outliers start: 19 outliers final: 8 residues processed: 152 average time/residue: 1.4763 time to fit residues: 242.1171 Evaluate side-chains 152 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 785 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 73 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 636 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 = 0.4049 r_free = 0.4049 target = 0.179462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.139576 restraints weight = 35575.489| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.64 r_work: 0.3456 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12637 Z= 0.140 Angle : 0.476 6.379 17177 Z= 0.252 Chirality : 0.038 0.153 1929 Planarity : 0.004 0.038 2213 Dihedral : 5.066 58.985 1725 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 1.31 % Allowed : 13.98 % Favored : 84.71 % 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: 1.83 (0.23), residues: 1511 helix: 2.11 (0.19), residues: 794 sheet: -0.96 (0.43), residues: 157 loop : 0.73 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 509 TYR 0.017 0.001 TYR B 527 PHE 0.010 0.001 PHE B 819 TRP 0.010 0.001 TRP A 687 HIS 0.003 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00322 (12635) covalent geometry : angle 0.47591 (17177) hydrogen bonds : bond 0.03484 ( 672) hydrogen bonds : angle 4.98816 ( 1905) Misc. bond : bond 0.00007 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6908 (mmt-90) REVERT: A 497 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.6829 (m-80) REVERT: A 538 MET cc_start: 0.8487 (mmp) cc_final: 0.8090 (mmt) REVERT: A 545 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: A 593 ARG cc_start: 0.7593 (ttm-80) cc_final: 0.7338 (ttp-110) REVERT: A 878 GLN cc_start: 0.7409 (mm110) cc_final: 0.7199 (mm-40) REVERT: B 497 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.6949 (m-10) REVERT: B 545 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7834 (mt-10) REVERT: B 593 ARG cc_start: 0.7757 (ttm-80) cc_final: 0.7412 (ttp80) REVERT: B 785 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6458 (mp0) outliers start: 17 outliers final: 7 residues processed: 152 average time/residue: 1.5734 time to fit residues: 257.9879 Evaluate side-chains 146 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 785 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 81 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.179304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.140335 restraints weight = 35818.714| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.60 r_work: 0.3457 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12637 Z= 0.148 Angle : 0.483 6.400 17177 Z= 0.256 Chirality : 0.038 0.152 1929 Planarity : 0.004 0.039 2213 Dihedral : 5.064 59.288 1725 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.82 % Rotamer: Outliers : 0.93 % Allowed : 14.44 % Favored : 84.63 % 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: 1.83 (0.23), residues: 1511 helix: 2.11 (0.19), residues: 794 sheet: -0.93 (0.44), residues: 157 loop : 0.71 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 509 TYR 0.017 0.001 TYR B 527 PHE 0.010 0.001 PHE B 819 TRP 0.013 0.001 TRP A 748 HIS 0.003 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00343 (12635) covalent geometry : angle 0.48259 (17177) hydrogen bonds : bond 0.03512 ( 672) hydrogen bonds : angle 4.98068 ( 1905) Misc. bond : bond 0.00016 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6902 (mmt-90) REVERT: A 497 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.6862 (m-80) REVERT: A 545 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: A 593 ARG cc_start: 0.7588 (ttm-80) cc_final: 0.7354 (ttp-110) REVERT: B 497 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.6987 (m-10) REVERT: B 545 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7847 (mt-10) REVERT: B 785 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6528 (mp0) outliers start: 12 outliers final: 6 residues processed: 144 average time/residue: 1.4813 time to fit residues: 230.8588 Evaluate side-chains 146 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 785 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 5 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 chunk 137 optimal weight: 0.5980 chunk 88 optimal weight: 0.0570 chunk 9 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 636 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 = 0.4020 r_free = 0.4020 target = 0.177745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137756 restraints weight = 35779.678| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.65 r_work: 0.3531 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12637 Z= 0.104 Angle : 0.452 6.226 17177 Z= 0.238 Chirality : 0.037 0.150 1929 Planarity : 0.004 0.038 2213 Dihedral : 4.810 56.383 1725 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.71 % Favored : 97.22 % Rotamer: Outliers : 0.77 % Allowed : 14.90 % Favored : 84.32 % 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: 2.06 (0.23), residues: 1511 helix: 2.28 (0.19), residues: 794 sheet: -0.73 (0.45), residues: 150 loop : 0.79 (0.29), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 509 TYR 0.014 0.001 TYR B 527 PHE 0.010 0.001 PHE B 819 TRP 0.011 0.001 TRP A 687 HIS 0.003 0.000 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00232 (12635) covalent geometry : angle 0.45197 (17177) hydrogen bonds : bond 0.03209 ( 672) hydrogen bonds : angle 4.86842 ( 1905) Misc. bond : bond 0.00003 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 236 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6851 (mmt-90) REVERT: A 392 THR cc_start: 0.8986 (p) cc_final: 0.8630 (p) REVERT: A 497 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.6791 (m-10) REVERT: A 538 MET cc_start: 0.8401 (mmp) cc_final: 0.8054 (mmt) REVERT: A 593 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.7343 (ttp-110) REVERT: B 135 PHE cc_start: 0.8654 (t80) cc_final: 0.8449 (t80) REVERT: B 402 ARG cc_start: 0.8425 (ttp-170) cc_final: 0.8136 (ppp-140) REVERT: B 497 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.6952 (m-10) REVERT: B 545 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7877 (mt-10) REVERT: B 593 ARG cc_start: 0.7704 (ttm-80) cc_final: 0.7393 (ttp-110) REVERT: B 785 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6586 (mp0) outliers start: 10 outliers final: 4 residues processed: 145 average time/residue: 1.2956 time to fit residues: 204.3668 Evaluate side-chains 144 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 785 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 54 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 94 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 HIS A 885 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.175571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.134983 restraints weight = 35903.870| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.67 r_work: 0.3447 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12637 Z= 0.148 Angle : 0.481 6.353 17177 Z= 0.255 Chirality : 0.038 0.151 1929 Planarity : 0.004 0.040 2213 Dihedral : 4.992 59.155 1725 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.82 % Rotamer: Outliers : 0.69 % Allowed : 15.21 % Favored : 84.09 % 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: 1.94 (0.23), residues: 1511 helix: 2.19 (0.19), residues: 794 sheet: -0.88 (0.44), residues: 157 loop : 0.78 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 509 TYR 0.017 0.001 TYR B 527 PHE 0.010 0.001 PHE B 819 TRP 0.008 0.001 TRP A 687 HIS 0.003 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00343 (12635) covalent geometry : angle 0.48097 (17177) hydrogen bonds : bond 0.03462 ( 672) hydrogen bonds : angle 4.94531 ( 1905) Misc. bond : bond 0.00010 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8502.64 seconds wall clock time: 144 minutes 30.58 seconds (8670.58 seconds total)