Starting phenix.real_space_refine on Fri Jul 3 00:55:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8toi_41453/07_2026/8toi_41453.cif Found real_map, /net/cci-nas-00/data/ceres_data/8toi_41453/07_2026/8toi_41453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8toi_41453/07_2026/8toi_41453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8toi_41453/07_2026/8toi_41453.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8toi_41453/07_2026/8toi_41453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8toi_41453/07_2026/8toi_41453.map" } resolution = 2.64 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= 0.057 sd= 0.508 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 Ca 4 9.91 5 P 34 5.49 5 S 40 5.16 5 C 7502 2.51 5 N 1724 2.21 5 O 2110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11414 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5160 Classifications: {'peptide': 649} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 28, 'TRANS': 620} Chain breaks: 5 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 545 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'PGW': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain breaks: 2 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 394 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PGW:plan-3': 9} Unresolved non-hydrogen planarities: 27 Restraints were copied for chains: B Time building chain proxies: 4.72, per 1000 atoms: 0.41 Number of scatterers: 11414 At special positions: 0 Unit cell: (91.575, 137.775, 106.425, 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) Ca 4 19.99 S 40 16.00 P 34 15.00 O 2110 8.00 N 1724 7.00 C 7502 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 333.3 milliseconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 73.3% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 32 through 47 removed outlier: 3.644A pdb=" N GLY A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 90 removed outlier: 3.618A pdb=" N PHE A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.833A pdb=" N LEU A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 106 " --> pdb=" O GLN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.552A pdb=" N GLU A 129 " --> pdb=" O PRO A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 165 Processing helix chain 'A' and resid 170 through 182 removed outlier: 3.813A pdb=" N ILE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 199 removed outlier: 3.549A pdb=" N ALA A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 Processing helix chain 'A' and resid 217 through 246 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.578A pdb=" N ARG A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 320 Processing helix chain 'A' and resid 330 through 358 Proline residue: A 341 - end of helix Processing helix chain 'A' and resid 362 through 392 removed outlier: 6.230A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.627A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 453 removed outlier: 3.793A pdb=" N ASN A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 449 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 452 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 466 Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.584A pdb=" N GLU A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU A 481 " --> pdb=" O ASP A 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 477 through 481' Processing helix chain 'A' and resid 482 through 493 Processing helix chain 'A' and resid 499 through 518 removed outlier: 4.318A pdb=" N ASP A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 545 removed outlier: 3.987A pdb=" N ARG A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 585 removed outlier: 3.705A pdb=" N GLY A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N SER A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN A 585 " --> pdb=" O TYR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 625 removed outlier: 3.506A pdb=" N LEU A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 Processing helix chain 'A' and resid 667 through 685 Processing helix chain 'A' and resid 689 through 694 Processing helix chain 'A' and resid 701 through 716 removed outlier: 3.653A pdb=" N ILE A 705 " --> pdb=" O MET A 701 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 47 removed outlier: 3.644A pdb=" N GLY B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 90 removed outlier: 3.618A pdb=" N PHE B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.834A pdb=" N LEU B 105 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 106 " --> pdb=" O GLN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.552A pdb=" N GLU B 129 " --> pdb=" O PRO B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 165 Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.813A pdb=" N ILE B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 199 removed outlier: 3.549A pdb=" N ALA B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 Processing helix chain 'B' and resid 217 through 246 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.578A pdb=" N ARG B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 320 Processing helix chain 'B' and resid 330 through 358 Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 362 through 392 removed outlier: 6.230A pdb=" N ALA B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 413 removed outlier: 3.627A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 453 removed outlier: 3.793A pdb=" N ASN B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR B 443 " --> pdb=" O TYR B 439 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 449 " --> pdb=" O GLN B 445 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 452 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 466 Processing helix chain 'B' and resid 477 through 481 removed outlier: 3.584A pdb=" N GLU B 480 " --> pdb=" O GLU B 477 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU B 481 " --> pdb=" O ASP B 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 477 through 481' Processing helix chain 'B' and resid 482 through 493 Processing helix chain 'B' and resid 499 through 518 removed outlier: 4.317A pdb=" N ASP B 503 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 545 removed outlier: 3.986A pdb=" N ARG B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.705A pdb=" N GLY B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN B 585 " --> pdb=" O TYR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 625 removed outlier: 3.506A pdb=" N LEU B 602 " --> pdb=" O LYS B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 Processing helix chain 'B' and resid 667 through 685 Processing helix chain 'B' and resid 689 through 694 Processing helix chain 'B' and resid 701 through 716 removed outlier: 3.653A pdb=" N ILE B 705 " --> pdb=" O MET B 701 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 716 " --> pdb=" O ILE B 712 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 268 removed outlier: 3.784A pdb=" N HIS A 265 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 268 removed outlier: 3.784A pdb=" N HIS B 265 " --> pdb=" O VAL B 278 " (cutoff:3.500A) 694 hydrogen bonds defined for protein. 2046 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1722 1.31 - 1.44: 3226 1.44 - 1.57: 6564 1.57 - 1.70: 68 1.70 - 1.83: 66 Bond restraints: 11646 Sorted by residual: bond pdb=" C1 PGW A 820 " pdb=" O01 PGW A 820 " ideal model delta sigma weight residual 1.332 1.428 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C1 PGW A 809 " pdb=" O01 PGW A 809 " ideal model delta sigma weight residual 1.332 1.428 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C1 PGW B 820 " pdb=" O01 PGW B 820 " ideal model delta sigma weight residual 1.332 1.428 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C1 PGW B 809 " pdb=" O01 PGW B 809 " ideal model delta sigma weight residual 1.332 1.428 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C1 PGW A 817 " pdb=" O01 PGW A 817 " ideal model delta sigma weight residual 1.332 1.427 -0.095 2.00e-02 2.50e+03 2.24e+01 ... (remaining 11641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.90: 15536 9.90 - 19.80: 78 19.80 - 29.70: 2 29.70 - 39.60: 0 39.60 - 49.50: 6 Bond angle restraints: 15622 Sorted by residual: angle pdb=" C2 PGW A 805 " pdb=" C1 PGW A 805 " pdb=" O01 PGW A 805 " ideal model delta sigma weight residual 110.92 160.42 -49.50 3.00e+00 1.11e-01 2.72e+02 angle pdb=" C2 PGW B 805 " pdb=" C1 PGW B 805 " pdb=" O01 PGW B 805 " ideal model delta sigma weight residual 110.92 160.38 -49.46 3.00e+00 1.11e-01 2.72e+02 angle pdb=" C2 PGW B 805 " pdb=" C1 PGW B 805 " pdb=" O02 PGW B 805 " ideal model delta sigma weight residual 125.44 80.14 45.30 3.00e+00 1.11e-01 2.28e+02 angle pdb=" C2 PGW A 805 " pdb=" C1 PGW A 805 " pdb=" O02 PGW A 805 " ideal model delta sigma weight residual 125.44 80.21 45.23 3.00e+00 1.11e-01 2.27e+02 angle pdb=" O01 PGW A 805 " pdb=" C1 PGW A 805 " pdb=" O02 PGW A 805 " ideal model delta sigma weight residual 123.63 80.21 43.42 3.00e+00 1.11e-01 2.09e+02 ... (remaining 15617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.20: 6550 33.20 - 66.41: 400 66.41 - 99.61: 58 99.61 - 132.82: 20 132.82 - 166.02: 28 Dihedral angle restraints: 7056 sinusoidal: 3268 harmonic: 3788 Sorted by residual: dihedral pdb=" CA ILE A 101 " pdb=" C ILE A 101 " pdb=" N ALA A 102 " pdb=" CA ALA A 102 " ideal model delta harmonic sigma weight residual -180.00 -156.57 -23.43 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ILE B 101 " pdb=" C ILE B 101 " pdb=" N ALA B 102 " pdb=" CA ALA B 102 " ideal model delta harmonic sigma weight residual -180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" O01 PGW B 815 " pdb=" C01 PGW B 815 " pdb=" C02 PGW B 815 " pdb=" O03 PGW B 815 " ideal model delta sinusoidal sigma weight residual 59.30 -106.72 166.02 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 7053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1242 0.054 - 0.109: 292 0.109 - 0.163: 74 0.163 - 0.217: 20 0.217 - 0.272: 4 Chirality restraints: 1632 Sorted by residual: chirality pdb=" CA THR A 340 " pdb=" N THR A 340 " pdb=" C THR A 340 " pdb=" CB THR A 340 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA THR B 340 " pdb=" N THR B 340 " pdb=" C THR B 340 " pdb=" CB THR B 340 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB VAL B 111 " pdb=" CA VAL B 111 " pdb=" CG1 VAL B 111 " pdb=" CG2 VAL B 111 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1629 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 396 " 0.014 2.00e-02 2.50e+03 1.86e-02 6.03e+00 pdb=" CG PHE B 396 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 396 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 396 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 396 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 396 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 396 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 396 " -0.014 2.00e-02 2.50e+03 1.85e-02 5.98e+00 pdb=" CG PHE A 396 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 396 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 396 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 396 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 396 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 396 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 134 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C VAL B 134 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL B 134 " -0.016 2.00e-02 2.50e+03 pdb=" N THR B 135 " -0.014 2.00e-02 2.50e+03 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3412 2.83 - 3.35: 10087 3.35 - 3.87: 18858 3.87 - 4.38: 21109 4.38 - 4.90: 36789 Nonbonded interactions: 90255 Sorted by model distance: nonbonded pdb=" OH TYR A 188 " pdb=" OD2 ASP A 539 " model vdw 2.318 3.040 nonbonded pdb=" OH TYR B 188 " pdb=" OD2 ASP B 539 " model vdw 2.318 3.040 nonbonded pdb=" O TRP B 570 " pdb=" OG SER B 573 " model vdw 2.353 3.040 nonbonded pdb=" O TRP A 570 " pdb=" OG SER A 573 " model vdw 2.353 3.040 nonbonded pdb=" OE2 GLU B 358 " pdb=" OH TYR B 360 " model vdw 2.360 3.040 ... (remaining 90250 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.700 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 : 0.010 0.096 11646 Z= 0.469 Angle : 1.856 49.496 15622 Z= 0.718 Chirality : 0.054 0.272 1632 Planarity : 0.006 0.053 1914 Dihedral : 24.382 166.024 4596 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -1.60 (0.20), residues: 1274 helix: -0.55 (0.15), residues: 888 sheet: -1.94 (0.77), residues: 44 loop : -1.97 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 537 TYR 0.017 0.002 TYR B 457 PHE 0.043 0.002 PHE B 396 TRP 0.032 0.002 TRP A 141 HIS 0.004 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00950 / 0.47 (11646) covalent geometry : angle 1.85630 / 0.72 (15622) hydrogen bonds : bond 0.14143 / 9.30 ( 694) hydrogen bonds : angle 6.47489 / 4.83 ( 2046) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.452 Fit side-chains REVERT: A 320 TYR cc_start: 0.8068 (t80) cc_final: 0.7754 (t80) REVERT: B 55 GLU cc_start: 0.7866 (tp30) cc_final: 0.7066 (mm-30) REVERT: B 320 TYR cc_start: 0.8143 (t80) cc_final: 0.7800 (t80) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.6378 time to fit residues: 114.0336 Evaluate side-chains 131 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 GLN A 153 HIS A 265 HIS A 310 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 HIS A 696 GLN A 698 GLN B 79 GLN B 153 HIS B 265 HIS B 310 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 HIS B 696 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.128659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.092520 restraints weight = 16344.722| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.02 r_work: 0.3112 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11646 Z= 0.142 Angle : 1.072 46.211 15622 Z= 0.418 Chirality : 0.040 0.158 1632 Planarity : 0.004 0.043 1914 Dihedral : 26.057 161.392 2250 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.87 % Allowed : 9.24 % Favored : 88.90 % 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: 0.49 (0.23), residues: 1274 helix: 1.17 (0.17), residues: 892 sheet: -1.52 (0.82), residues: 44 loop : -1.64 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 697 TYR 0.014 0.001 TYR A 188 PHE 0.023 0.001 PHE A 406 TRP 0.014 0.001 TRP B 235 HIS 0.003 0.001 HIS B 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (11646) covalent geometry : angle 1.07248 / 0.42 (15622) hydrogen bonds : bond 0.04253 / 2.86 ( 694) hydrogen bonds : angle 3.87008 / 2.85 ( 2046) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.496 Fit side-chains REVERT: A 268 GLU cc_start: 0.8832 (pt0) cc_final: 0.8459 (pm20) REVERT: A 320 TYR cc_start: 0.7965 (t80) cc_final: 0.7568 (t80) REVERT: B 268 GLU cc_start: 0.8807 (pt0) cc_final: 0.8466 (pm20) REVERT: B 320 TYR cc_start: 0.8049 (t80) cc_final: 0.7703 (t80) outliers start: 20 outliers final: 5 residues processed: 143 average time/residue: 0.5307 time to fit residues: 82.7810 Evaluate side-chains 131 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 282 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 125 optimal weight: 20.0000 chunk 10 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS A 510 GLN A 531 ASN A 696 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.128720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.092808 restraints weight = 16438.342| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.01 r_work: 0.3112 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11646 Z= 0.120 Angle : 1.043 46.398 15622 Z= 0.401 Chirality : 0.040 0.152 1632 Planarity : 0.004 0.041 1914 Dihedral : 24.491 164.664 2250 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.89 % Allowed : 11.29 % Favored : 85.82 % 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: 1.19 (0.23), residues: 1274 helix: 1.72 (0.17), residues: 900 sheet: -1.15 (0.87), residues: 44 loop : -1.57 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 697 TYR 0.015 0.001 TYR A 26 PHE 0.012 0.001 PHE B 396 TRP 0.014 0.001 TRP B 235 HIS 0.003 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (11646) covalent geometry : angle 1.04331 / 0.40 (15622) hydrogen bonds : bond 0.03941 / 2.65 ( 694) hydrogen bonds : angle 3.60512 / 2.65 ( 2046) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.412 Fit side-chains REVERT: A 35 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: A 268 GLU cc_start: 0.8836 (pt0) cc_final: 0.8394 (pm20) REVERT: A 320 TYR cc_start: 0.7812 (t80) cc_final: 0.7440 (t80) REVERT: A 352 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8139 (mt-10) REVERT: A 400 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6687 (pp) REVERT: A 633 GLN cc_start: 0.8584 (tt0) cc_final: 0.8360 (tt0) REVERT: B 33 ARG cc_start: 0.8489 (ttp80) cc_final: 0.8275 (ttp80) REVERT: B 268 GLU cc_start: 0.8823 (pt0) cc_final: 0.8375 (pm20) REVERT: B 320 TYR cc_start: 0.7888 (t80) cc_final: 0.7416 (t80) REVERT: B 400 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6718 (pp) outliers start: 31 outliers final: 6 residues processed: 155 average time/residue: 0.4771 time to fit residues: 80.6363 Evaluate side-chains 144 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 627 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 51 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 12 optimal weight: 0.0070 chunk 48 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.9204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS A 641 GLN A 696 GLN B 310 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 HIS B 510 GLN B 531 ASN B 641 GLN B 696 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.127672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.091460 restraints weight = 16453.214| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.01 r_work: 0.3089 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11646 Z= 0.133 Angle : 1.043 46.259 15622 Z= 0.403 Chirality : 0.040 0.154 1632 Planarity : 0.004 0.039 1914 Dihedral : 23.520 166.498 2250 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.52 % Allowed : 12.97 % Favored : 84.51 % 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: 1.56 (0.24), residues: 1274 helix: 1.97 (0.17), residues: 904 sheet: -0.94 (0.89), residues: 44 loop : -1.43 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 697 TYR 0.015 0.001 TYR B 26 PHE 0.028 0.001 PHE B 406 TRP 0.014 0.001 TRP A 235 HIS 0.004 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (11646) covalent geometry : angle 1.04306 / 0.40 (15622) hydrogen bonds : bond 0.03927 / 2.65 ( 694) hydrogen bonds : angle 3.49809 / 2.57 ( 2046) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.424 Fit side-chains REVERT: A 268 GLU cc_start: 0.8729 (pt0) cc_final: 0.8315 (pm20) REVERT: A 320 TYR cc_start: 0.7894 (t80) cc_final: 0.7449 (t80) REVERT: A 400 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6688 (pp) REVERT: A 633 GLN cc_start: 0.8602 (tt0) cc_final: 0.8399 (tt0) REVERT: B 268 GLU cc_start: 0.8690 (pt0) cc_final: 0.8288 (pm20) REVERT: B 282 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8160 (tpp) REVERT: B 320 TYR cc_start: 0.7839 (t80) cc_final: 0.7338 (t80) outliers start: 27 outliers final: 5 residues processed: 154 average time/residue: 0.4853 time to fit residues: 81.6136 Evaluate side-chains 140 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 282 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 101 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN A 479 HIS A 696 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN B 479 HIS B 696 GLN B 698 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.128067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.091801 restraints weight = 16477.072| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.01 r_work: 0.3100 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11646 Z= 0.123 Angle : 1.042 46.214 15622 Z= 0.401 Chirality : 0.040 0.151 1632 Planarity : 0.003 0.036 1914 Dihedral : 22.711 167.340 2250 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.17 % Allowed : 13.43 % Favored : 83.40 % 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: 1.76 (0.24), residues: 1274 helix: 2.12 (0.17), residues: 904 sheet: -0.94 (0.89), residues: 44 loop : -1.33 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 697 TYR 0.014 0.001 TYR B 26 PHE 0.030 0.001 PHE A 406 TRP 0.014 0.001 TRP A 235 HIS 0.003 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (11646) covalent geometry : angle 1.04232 / 0.40 (15622) hydrogen bonds : bond 0.03786 / 2.55 ( 694) hydrogen bonds : angle 3.43376 / 2.52 ( 2046) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.419 Fit side-chains REVERT: A 268 GLU cc_start: 0.8836 (pt0) cc_final: 0.8375 (pm20) REVERT: A 282 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8294 (tpp) REVERT: A 320 TYR cc_start: 0.7740 (t80) cc_final: 0.7195 (t80) REVERT: B 268 GLU cc_start: 0.8849 (pt0) cc_final: 0.8364 (pm20) REVERT: B 282 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8340 (tpp) REVERT: B 320 TYR cc_start: 0.7908 (t80) cc_final: 0.7375 (t80) REVERT: B 484 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7883 (tm-30) outliers start: 34 outliers final: 9 residues processed: 149 average time/residue: 0.5066 time to fit residues: 82.1504 Evaluate side-chains 143 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 507 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 120 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS A 666 HIS A 696 GLN B 25 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 HIS B 666 HIS B 696 GLN B 698 GLN B 714 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.124500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.087770 restraints weight = 16550.369| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.00 r_work: 0.3024 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 11646 Z= 0.226 Angle : 1.080 46.146 15622 Z= 0.425 Chirality : 0.043 0.161 1632 Planarity : 0.004 0.041 1914 Dihedral : 22.475 165.179 2250 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.54 % Allowed : 13.62 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.69 (0.24), residues: 1274 helix: 2.12 (0.17), residues: 892 sheet: -0.95 (0.89), residues: 44 loop : -1.39 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 33 TYR 0.018 0.002 TYR B 26 PHE 0.028 0.002 PHE B 406 TRP 0.016 0.002 TRP B 141 HIS 0.004 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 (11646) covalent geometry : angle 1.07975 / 0.43 (15622) hydrogen bonds : bond 0.04539 / 3.06 ( 694) hydrogen bonds : angle 3.58022 / 2.61 ( 2046) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.422 Fit side-chains REVERT: A 268 GLU cc_start: 0.8875 (pt0) cc_final: 0.8376 (pm20) REVERT: A 320 TYR cc_start: 0.8025 (t80) cc_final: 0.7524 (t80) REVERT: B 268 GLU cc_start: 0.8867 (pt0) cc_final: 0.8346 (pm20) REVERT: B 320 TYR cc_start: 0.7938 (t80) cc_final: 0.7390 (t80) REVERT: B 484 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7949 (tm-30) outliers start: 38 outliers final: 7 residues processed: 150 average time/residue: 0.5052 time to fit residues: 82.4073 Evaluate side-chains 138 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 507 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 50 optimal weight: 0.9990 chunk 94 optimal weight: 0.0040 chunk 16 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS A 696 GLN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN B 479 HIS B 696 GLN B 714 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.125972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.089480 restraints weight = 16400.439| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.99 r_work: 0.3054 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11646 Z= 0.154 Angle : 1.065 46.140 15622 Z= 0.414 Chirality : 0.041 0.151 1632 Planarity : 0.004 0.034 1914 Dihedral : 22.034 165.096 2250 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.61 % Allowed : 14.93 % Favored : 82.46 % 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: 1.76 (0.24), residues: 1274 helix: 2.10 (0.17), residues: 904 sheet: -0.95 (0.90), residues: 44 loop : -1.24 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 697 TYR 0.017 0.002 TYR B 26 PHE 0.015 0.001 PHE A 406 TRP 0.020 0.001 TRP A 141 HIS 0.003 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (11646) covalent geometry : angle 1.06489 / 0.41 (15622) hydrogen bonds : bond 0.04079 / 2.75 ( 694) hydrogen bonds : angle 3.50414 / 2.56 ( 2046) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.332 Fit side-chains REVERT: A 268 GLU cc_start: 0.8866 (pt0) cc_final: 0.8368 (pm20) REVERT: A 320 TYR cc_start: 0.7849 (t80) cc_final: 0.7284 (t80) REVERT: B 268 GLU cc_start: 0.8874 (pt0) cc_final: 0.8326 (pm20) REVERT: B 320 TYR cc_start: 0.7979 (t80) cc_final: 0.7475 (t80) outliers start: 28 outliers final: 10 residues processed: 140 average time/residue: 0.5220 time to fit residues: 79.4528 Evaluate side-chains 146 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 546 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 78 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS A 696 GLN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 HIS B 696 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.124117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.087561 restraints weight = 16387.103| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.98 r_work: 0.3019 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11646 Z= 0.225 Angle : 1.097 46.211 15622 Z= 0.438 Chirality : 0.043 0.157 1632 Planarity : 0.004 0.040 1914 Dihedral : 21.770 163.731 2250 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.96 % Allowed : 16.23 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.24), residues: 1274 helix: 2.11 (0.17), residues: 892 sheet: -0.96 (0.90), residues: 44 loop : -1.36 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.018 0.002 TYR B 26 PHE 0.033 0.001 PHE B 406 TRP 0.019 0.002 TRP A 141 HIS 0.004 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 (11646) covalent geometry : angle 1.09744 / 0.44 (15622) hydrogen bonds : bond 0.04508 / 3.04 ( 694) hydrogen bonds : angle 3.59585 / 2.62 ( 2046) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.429 Fit side-chains REVERT: A 268 GLU cc_start: 0.8870 (pt0) cc_final: 0.8392 (pm20) REVERT: A 320 TYR cc_start: 0.8060 (t80) cc_final: 0.7293 (t80) REVERT: A 325 LYS cc_start: 0.8622 (tppt) cc_final: 0.8278 (tppt) REVERT: B 268 GLU cc_start: 0.8868 (pt0) cc_final: 0.8355 (pm20) REVERT: B 320 TYR cc_start: 0.8014 (t80) cc_final: 0.7419 (t80) REVERT: B 325 LYS cc_start: 0.8626 (tppt) cc_final: 0.8404 (tppt) outliers start: 21 outliers final: 9 residues processed: 146 average time/residue: 0.5818 time to fit residues: 91.9796 Evaluate side-chains 145 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 546 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 105 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN B 479 HIS B 696 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.126504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.090300 restraints weight = 16268.898| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.98 r_work: 0.3077 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11646 Z= 0.131 Angle : 1.076 46.220 15622 Z= 0.420 Chirality : 0.041 0.148 1632 Planarity : 0.004 0.033 1914 Dihedral : 21.051 164.199 2250 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.40 % Allowed : 17.07 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.24), residues: 1274 helix: 2.13 (0.17), residues: 904 sheet: -0.99 (0.86), residues: 48 loop : -1.16 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.016 0.001 TYR A 188 PHE 0.035 0.001 PHE A 406 TRP 0.023 0.001 TRP B 141 HIS 0.003 0.001 HIS B 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (11646) covalent geometry : angle 1.07557 / 0.42 (15622) hydrogen bonds : bond 0.03901 / 2.63 ( 694) hydrogen bonds : angle 3.49400 / 2.55 ( 2046) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.534 Fit side-chains REVERT: A 268 GLU cc_start: 0.8841 (pt0) cc_final: 0.8375 (pm20) REVERT: A 320 TYR cc_start: 0.8027 (t80) cc_final: 0.6931 (t80) REVERT: A 325 LYS cc_start: 0.8535 (tppt) cc_final: 0.8002 (tppt) REVERT: B 268 GLU cc_start: 0.8824 (pt0) cc_final: 0.8301 (pm20) REVERT: B 282 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8315 (tpp) REVERT: B 320 TYR cc_start: 0.7990 (t80) cc_final: 0.7048 (t80) REVERT: B 325 LYS cc_start: 0.8535 (tppt) cc_final: 0.8043 (tppt) outliers start: 15 outliers final: 3 residues processed: 141 average time/residue: 0.5848 time to fit residues: 89.4004 Evaluate side-chains 139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 282 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 126 optimal weight: 0.5980 chunk 11 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 3 optimal weight: 0.0470 chunk 17 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 HIS B 696 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.126812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.090687 restraints weight = 16431.862| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.97 r_work: 0.3072 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11646 Z= 0.136 Angle : 1.081 46.230 15622 Z= 0.426 Chirality : 0.041 0.150 1632 Planarity : 0.004 0.034 1914 Dihedral : 20.398 164.196 2250 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.75 % Allowed : 17.82 % Favored : 81.44 % 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: 1.92 (0.24), residues: 1274 helix: 2.19 (0.17), residues: 904 sheet: -0.89 (0.87), residues: 48 loop : -1.11 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.016 0.001 TYR A 457 PHE 0.034 0.001 PHE B 406 TRP 0.019 0.001 TRP A 235 HIS 0.003 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (11646) covalent geometry : angle 1.08111 / 0.43 (15622) hydrogen bonds : bond 0.03850 / 2.60 ( 694) hydrogen bonds : angle 3.45645 / 2.52 ( 2046) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.499 Fit side-chains REVERT: A 268 GLU cc_start: 0.8847 (pt0) cc_final: 0.8351 (pm20) REVERT: A 282 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8312 (tpp) REVERT: A 320 TYR cc_start: 0.7866 (t80) cc_final: 0.7453 (t80) REVERT: B 268 GLU cc_start: 0.8841 (pt0) cc_final: 0.8302 (pm20) REVERT: B 282 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8319 (tpp) REVERT: B 325 LYS cc_start: 0.8496 (tppt) cc_final: 0.8038 (tppt) REVERT: B 703 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7545 (pm20) outliers start: 8 outliers final: 2 residues processed: 134 average time/residue: 0.5460 time to fit residues: 79.2366 Evaluate side-chains 132 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 703 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 124 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN B 479 HIS B 696 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.125791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.089301 restraints weight = 16394.790| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.98 r_work: 0.3055 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11646 Z= 0.169 Angle : 1.083 46.162 15622 Z= 0.426 Chirality : 0.042 0.153 1632 Planarity : 0.004 0.035 1914 Dihedral : 20.169 163.567 2250 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.03 % Allowed : 17.26 % Favored : 81.72 % 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: 1.86 (0.24), residues: 1274 helix: 2.15 (0.17), residues: 904 sheet: -0.91 (0.86), residues: 48 loop : -1.11 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.016 0.002 TYR A 457 PHE 0.040 0.001 PHE A 406 TRP 0.017 0.002 TRP A 235 HIS 0.003 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (11646) covalent geometry : angle 1.08347 / 0.43 (15622) hydrogen bonds : bond 0.04118 / 2.77 ( 694) hydrogen bonds : angle 3.50576 / 2.56 ( 2046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4197.26 seconds wall clock time: 72 minutes 5.86 seconds (4325.86 seconds total)