Starting phenix.real_space_refine on Fri Jul 3 09:58:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8tp4_41466/07_2026/8tp4_41466.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp4_41466/07_2026/8tp4_41466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tp4_41466/07_2026/8tp4_41466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp4_41466/07_2026/8tp4_41466.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8tp4_41466/07_2026/8tp4_41466.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8tp4_41466/07_2026/8tp4_41466.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tp4_41466/07_2026/8tp4_41466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp4_41466/07_2026/8tp4_41466.map" } resolution = 3.3 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= 0.002 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 8427 2.51 5 N 2299 2.21 5 O 2666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 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: 13472 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3821 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain breaks: 1 Chain: "H" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1008 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "L" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 835 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "A" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3808 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 19, 'TRANS': 460} Chain breaks: 1 Chain: "B" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3748 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 18, 'TRANS': 455} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.02, per 1000 atoms: 0.22 Number of scatterers: 13472 At special positions: 0 Unit cell: (103.5, 101.2, 170.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2666 8.00 N 2299 7.00 C 8427 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.02 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.04 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.04 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.04 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.06 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 501 " - " ASN A 21 " " NAG A 502 " - " ASN A 33 " " NAG A 503 " - " ASN A 289 " " NAG A 504 " - " ASN A 483 " " NAG B 501 " - " ASN B 21 " " NAG B 502 " - " ASN B 33 " " NAG B 503 " - " ASN B 289 " " NAG B 504 " - " ASN B 483 " " NAG C 501 " - " ASN C 21 " " NAG C 502 " - " ASN C 33 " " NAG C 503 " - " ASN C 289 " " NAG C 504 " - " ASN C 483 " " NAG D 1 " - " ASN C 169 " " NAG E 1 " - " ASN A 169 " " NAG F 1 " - " ASN B 169 " Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 509.6 milliseconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 40 sheets defined 22.5% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.928A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ARG C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 125 through 127 removed outlier: 3.840A pdb=" N TRP C 127 " --> pdb=" O LYS C 125a" (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 366 through 386 Processing helix chain 'C' and resid 403 through 456 removed outlier: 3.721A pdb=" N LEU C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 482 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.901A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 125 through 127 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 366 through 386 Processing helix chain 'A' and resid 403 through 456 Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 125 through 127 removed outlier: 3.912A pdb=" N TRP B 127 " --> pdb=" O LYS B 125a" (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 366 through 386 Processing helix chain 'B' and resid 403 through 454 removed outlier: 3.557A pdb=" N LEU B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 444 " --> pdb=" O HIS B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing sheet with id=AA1, first strand: chain 'C' and resid 342 through 343 removed outlier: 7.988A pdb=" N TRP C 343 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR C 17 " --> pdb=" O TRP C 343 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 342 through 343 removed outlier: 7.988A pdb=" N TRP C 343 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR C 17 " --> pdb=" O TRP C 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.422A pdb=" N GLU C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AA5, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AA6, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.178A pdb=" N LEU C 51 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 62 removed outlier: 6.105A pdb=" N LEU C 59 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.729A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.729A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.496A pdb=" N ALA C 138 " --> pdb=" O ASN C 144 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N ASN C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AB3, first strand: chain 'C' and resid 286 through 287 removed outlier: 3.812A pdb=" N GLY C 303 " --> pdb=" O GLU C 393 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.065A pdb=" N SER H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.736A pdb=" N HIS H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY H 96 " --> pdb=" O PHE H 100M" (cutoff:3.500A) removed outlier: 7.325A pdb=" N PHE H 100M" --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.692A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.692A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AC1, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AC2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.437A pdb=" N GLU A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AC4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.104A pdb=" N LEU A 51 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 59 through 62 removed outlier: 6.082A pdb=" N LEU A 59 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.633A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.633A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.434A pdb=" N ALA A 138 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N ASN A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AD2, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AD3, first strand: chain 'B' and resid 364 through 365 Processing sheet with id=AD4, first strand: chain 'B' and resid 24 through 26 removed outlier: 4.412A pdb=" N GLU B 24 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AD6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AD7, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.203A pdb=" N LEU B 51 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N CYS B 277 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 59 through 62 removed outlier: 6.134A pdb=" N LEU B 59 " --> pdb=" O MET B 88 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.749A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.749A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.461A pdb=" N ALA B 138 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N ASN B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 164 through 168 Processing sheet with id=AE4, first strand: chain 'B' and resid 286 through 287 542 hydrogen bonds defined for protein. 1440 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: 2.34 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2733 1.32 - 1.45: 4321 1.45 - 1.59: 6585 1.59 - 1.72: 17 1.72 - 1.86: 116 Bond restraints: 13772 Sorted by residual: bond pdb=" CA SER H 31 " pdb=" CB SER H 31 " ideal model delta sigma weight residual 1.528 1.432 0.095 1.35e-02 5.49e+03 4.99e+01 bond pdb=" CB ASN C 433 " pdb=" CG ASN C 433 " ideal model delta sigma weight residual 1.516 1.369 0.147 2.50e-02 1.60e+03 3.45e+01 bond pdb=" CB LEU L 107 " pdb=" CG LEU L 107 " ideal model delta sigma weight residual 1.530 1.647 -0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" CB PHE H 55 " pdb=" CG PHE H 55 " ideal model delta sigma weight residual 1.502 1.369 0.133 2.30e-02 1.89e+03 3.35e+01 bond pdb=" CB ASN A 433 " pdb=" CG ASN A 433 " ideal model delta sigma weight residual 1.516 1.393 0.123 2.50e-02 1.60e+03 2.43e+01 ... (remaining 13767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 17506 3.45 - 6.89: 1039 6.89 - 10.34: 82 10.34 - 13.78: 10 13.78 - 17.23: 2 Bond angle restraints: 18639 Sorted by residual: angle pdb=" N LEU L 30 " pdb=" CA LEU L 30 " pdb=" C LEU L 30 " ideal model delta sigma weight residual 114.04 99.24 14.80 1.24e+00 6.50e-01 1.42e+02 angle pdb=" C HIS C 184 " pdb=" N PRO C 185 " pdb=" CA PRO C 185 " ideal model delta sigma weight residual 119.92 129.41 -9.49 1.07e+00 8.73e-01 7.87e+01 angle pdb=" C HIS C 354 " pdb=" CA HIS C 354 " pdb=" CB HIS C 354 " ideal model delta sigma weight residual 109.38 92.15 17.23 2.03e+00 2.43e-01 7.20e+01 angle pdb=" CA PHE C 118 " pdb=" CB PHE C 118 " pdb=" CG PHE C 118 " ideal model delta sigma weight residual 113.80 122.02 -8.22 1.00e+00 1.00e+00 6.76e+01 angle pdb=" C PRO C 57 " pdb=" N PRO C 58 " pdb=" CA PRO C 58 " ideal model delta sigma weight residual 120.52 128.65 -8.13 9.90e-01 1.02e+00 6.75e+01 ... (remaining 18634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7764 17.96 - 35.91: 229 35.91 - 53.87: 47 53.87 - 71.82: 22 71.82 - 89.78: 10 Dihedral angle restraints: 8072 sinusoidal: 3284 harmonic: 4788 Sorted by residual: dihedral pdb=" C HIS C 354 " pdb=" N HIS C 354 " pdb=" CA HIS C 354 " pdb=" CB HIS C 354 " ideal model delta harmonic sigma weight residual -122.60 -99.23 -23.37 0 2.50e+00 1.60e-01 8.74e+01 dihedral pdb=" CB CYS B 473 " pdb=" SG CYS B 473 " pdb=" SG CYS B 477 " pdb=" CB CYS B 477 " ideal model delta sinusoidal sigma weight residual -86.00 -15.99 -70.01 1 1.00e+01 1.00e-02 6.32e+01 dihedral pdb=" C HIS C 18 " pdb=" N HIS C 18 " pdb=" CA HIS C 18 " pdb=" CB HIS C 18 " ideal model delta harmonic sigma weight residual -122.60 -106.17 -16.43 0 2.50e+00 1.60e-01 4.32e+01 ... (remaining 8069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.209: 1987 0.209 - 0.417: 54 0.417 - 0.626: 5 0.626 - 0.835: 0 0.835 - 1.043: 2 Chirality restraints: 2048 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.21e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.36e+01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 169 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.72e+01 ... (remaining 2045 not shown) Planarity restraints: 2416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 504 " 0.322 2.00e-02 2.50e+03 2.77e-01 9.60e+02 pdb=" C7 NAG A 504 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG A 504 " 0.015 2.00e-02 2.50e+03 pdb=" N2 NAG A 504 " -0.478 2.00e-02 2.50e+03 pdb=" O7 NAG A 504 " 0.214 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 503 " 0.302 2.00e-02 2.50e+03 2.62e-01 8.59e+02 pdb=" C7 NAG C 503 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG C 503 " 0.150 2.00e-02 2.50e+03 pdb=" N2 NAG C 503 " -0.468 2.00e-02 2.50e+03 pdb=" O7 NAG C 503 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 504 " -0.303 2.00e-02 2.50e+03 2.55e-01 8.14e+02 pdb=" C7 NAG B 504 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B 504 " -0.189 2.00e-02 2.50e+03 pdb=" N2 NAG B 504 " 0.437 2.00e-02 2.50e+03 pdb=" O7 NAG B 504 " -0.023 2.00e-02 2.50e+03 ... (remaining 2413 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2487 2.76 - 3.29: 12321 3.29 - 3.83: 22345 3.83 - 4.36: 28523 4.36 - 4.90: 46480 Nonbonded interactions: 112156 Sorted by model distance: nonbonded pdb=" O CYS B 477 " pdb=" N SER B 480 " model vdw 2.221 3.120 nonbonded pdb=" O HIS C 355 " pdb=" O SER C 361 " model vdw 2.281 3.040 nonbonded pdb=" N ASP B 457 " pdb=" O ASP B 457 " model vdw 2.294 2.496 nonbonded pdb=" N LEU L 30 " pdb=" N GLY L 30A" model vdw 2.313 2.560 nonbonded pdb=" N GLN B 454 " pdb=" O GLN B 454 " model vdw 2.346 2.496 ... (remaining 112151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 487 or resid 501 through 504)) selection = (chain 'B' and (resid 11 through 334 or resid 337 through 504)) selection = (chain 'C' and (resid 11 through 334 or resid 337 through 487 or resid 501 throu \ gh 504)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.750 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 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 : 0.020 0.147 13810 Z= 1.106 Angle : 1.796 23.320 18733 Z= 1.194 Chirality : 0.099 1.043 2048 Planarity : 0.017 0.277 2401 Dihedral : 10.145 89.776 4962 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.46 % 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: 0.69 (0.19), residues: 1662 helix: 0.66 (0.26), residues: 329 sheet: 1.71 (0.25), residues: 370 loop : -0.07 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 229 TYR 0.054 0.008 TYR C 17 PHE 0.041 0.006 PHE C 118 TRP 0.033 0.006 TRP B 153 HIS 0.022 0.003 HIS C 354 Details of bonding type rmsd/Z covalent geometry : bond 0.02011 / 1.11 (13772) covalent geometry : angle 1.76578 / 1.19 (18639) SS BOND : bond 0.00964 / 0.63 ( 20) SS BOND : angle 2.64515 / 1.84 ( 40) hydrogen bonds : bond 0.14161 / 9.77 ( 505) hydrogen bonds : angle 7.52109 / 5.19 ( 1440) link_BETA1-4 : bond 0.00252 / 0.13 ( 3) link_BETA1-4 : angle 4.37959 / 3.18 ( 9) link_NAG-ASN : bond 0.01464 / 1.07 ( 15) link_NAG-ASN : angle 6.41538 / 4.02 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 456 ARG cc_start: 0.7268 (mtt180) cc_final: 0.6815 (mtp-110) REVERT: A 268 MET cc_start: 0.8576 (ttm) cc_final: 0.8366 (ttm) REVERT: A 279 THR cc_start: 0.8324 (t) cc_final: 0.8122 (t) REVERT: B 367 LYS cc_start: 0.8567 (mmtt) cc_final: 0.8078 (mmtm) REVERT: B 371 GLN cc_start: 0.7963 (tp40) cc_final: 0.7561 (tp40) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.1302 time to fit residues: 55.4047 Evaluate side-chains 162 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 18 HIS C 183 HIS C 244 ASN H 102 HIS L 37 GLN A 129 GLN A 354 HIS B 18 HIS B 471 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.129550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.109117 restraints weight = 19789.529| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.05 r_work: 0.3143 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13810 Z= 0.166 Angle : 0.703 13.889 18733 Z= 0.360 Chirality : 0.046 0.484 2048 Planarity : 0.004 0.047 2401 Dihedral : 4.968 26.056 1802 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.78 % Allowed : 6.58 % Favored : 91.64 % 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: 0.77 (0.20), residues: 1662 helix: 2.16 (0.28), residues: 329 sheet: 1.40 (0.26), residues: 352 loop : -0.41 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 66 TYR 0.014 0.002 TYR B 17 PHE 0.023 0.002 PHE B 118 TRP 0.013 0.001 TRP A 343 HIS 0.011 0.001 HIS B 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (13772) covalent geometry : angle 0.66699 / 0.35 (18639) SS BOND : bond 0.00319 / 0.19 ( 20) SS BOND : angle 1.28095 / 0.99 ( 40) hydrogen bonds : bond 0.05356 / 3.59 ( 505) hydrogen bonds : angle 5.61628 / 3.90 ( 1440) link_BETA1-4 : bond 0.00296 / 0.14 ( 3) link_BETA1-4 : angle 1.96434 / 1.31 ( 9) link_NAG-ASN : bond 0.00507 / 0.32 ( 15) link_NAG-ASN : angle 4.39674 / 2.81 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 VAL cc_start: 0.8682 (t) cc_final: 0.8186 (m) REVERT: C 340 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7888 (pp20) REVERT: C 388 MET cc_start: 0.8272 (mmm) cc_final: 0.8068 (mmm) REVERT: C 485 THR cc_start: 0.8095 (m) cc_final: 0.7680 (p) REVERT: A 279 THR cc_start: 0.8507 (t) cc_final: 0.8288 (m) REVERT: A 348 ASP cc_start: 0.7101 (p0) cc_final: 0.6512 (p0) REVERT: B 144 ASN cc_start: 0.8308 (m-40) cc_final: 0.8075 (m-40) outliers start: 26 outliers final: 19 residues processed: 223 average time/residue: 0.1245 time to fit residues: 39.2321 Evaluate side-chains 164 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 343 TRP Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 427 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 17 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.0970 chunk 68 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100EHIS L 37 GLN A 244 ASN B 471 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.124572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.103573 restraints weight = 20275.336| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.04 r_work: 0.3045 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 13810 Z= 0.222 Angle : 0.660 11.657 18733 Z= 0.340 Chirality : 0.046 0.311 2048 Planarity : 0.004 0.037 2401 Dihedral : 4.891 25.429 1802 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.40 % Allowed : 7.95 % Favored : 89.65 % 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: 0.36 (0.20), residues: 1662 helix: 2.09 (0.27), residues: 336 sheet: 0.79 (0.27), residues: 359 loop : -0.66 (0.18), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 76 TYR 0.026 0.002 TYR L 49 PHE 0.024 0.002 PHE A 439 TRP 0.030 0.002 TRP A 343 HIS 0.008 0.002 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 (13772) covalent geometry : angle 0.63394 / 0.33 (18639) SS BOND : bond 0.00400 / 0.24 ( 20) SS BOND : angle 1.35764 / 1.08 ( 40) hydrogen bonds : bond 0.04980 / 3.33 ( 505) hydrogen bonds : angle 5.29721 / 3.67 ( 1440) link_BETA1-4 : bond 0.00357 / 0.18 ( 3) link_BETA1-4 : angle 1.69544 / 1.33 ( 9) link_NAG-ASN : bond 0.00376 / 0.22 ( 15) link_NAG-ASN : angle 3.57306 / 2.27 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 340 GLU cc_start: 0.8540 (mm-30) cc_final: 0.7884 (pp20) REVERT: C 485 THR cc_start: 0.8338 (m) cc_final: 0.8110 (p) REVERT: H 66 ARG cc_start: 0.7691 (mtp85) cc_final: 0.7367 (mtp180) REVERT: L 37 GLN cc_start: 0.8114 (tt0) cc_final: 0.7685 (tt0) REVERT: L 91 TYR cc_start: 0.8886 (t80) cc_final: 0.8653 (t80) REVERT: A 279 THR cc_start: 0.8593 (t) cc_final: 0.8083 (m) REVERT: A 348 ASP cc_start: 0.7490 (p0) cc_final: 0.7023 (p0) REVERT: A 462 LEU cc_start: 0.9025 (mp) cc_final: 0.8807 (mt) REVERT: B 144 ASN cc_start: 0.8564 (m-40) cc_final: 0.8292 (m-40) outliers start: 35 outliers final: 27 residues processed: 192 average time/residue: 0.1102 time to fit residues: 31.0644 Evaluate side-chains 181 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 458 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 26 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN B 471 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.122810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.102221 restraints weight = 20192.518| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.10 r_work: 0.3027 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 13810 Z= 0.202 Angle : 0.615 9.774 18733 Z= 0.314 Chirality : 0.046 0.398 2048 Planarity : 0.004 0.040 2401 Dihedral : 4.759 24.998 1802 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.54 % Allowed : 9.66 % 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: 0.26 (0.20), residues: 1662 helix: 2.28 (0.27), residues: 336 sheet: 0.63 (0.26), residues: 377 loop : -0.83 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 76 TYR 0.024 0.002 TYR L 49 PHE 0.020 0.002 PHE A 439 TRP 0.022 0.001 TRP A 343 HIS 0.008 0.002 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (13772) covalent geometry : angle 0.59247 / 0.31 (18639) SS BOND : bond 0.00326 / 0.20 ( 20) SS BOND : angle 1.26678 / 1.05 ( 40) hydrogen bonds : bond 0.04613 / 3.07 ( 505) hydrogen bonds : angle 5.17419 / 3.58 ( 1440) link_BETA1-4 : bond 0.00473 / 0.23 ( 3) link_BETA1-4 : angle 1.71506 / 1.25 ( 9) link_NAG-ASN : bond 0.00401 / 0.27 ( 15) link_NAG-ASN : angle 3.19361 / 2.02 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 340 GLU cc_start: 0.8534 (mm-30) cc_final: 0.7834 (pp20) REVERT: H 66 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7304 (mtp-110) REVERT: L 37 GLN cc_start: 0.8028 (tt0) cc_final: 0.7362 (tt0) REVERT: A 56 ILE cc_start: 0.8008 (mt) cc_final: 0.7801 (pt) REVERT: A 348 ASP cc_start: 0.7672 (p0) cc_final: 0.7250 (p0) REVERT: A 462 LEU cc_start: 0.8986 (mp) cc_final: 0.8767 (mt) REVERT: B 144 ASN cc_start: 0.8611 (m-40) cc_final: 0.8312 (m-40) REVERT: B 435 ARG cc_start: 0.8261 (mtp85) cc_final: 0.7957 (mtp85) outliers start: 37 outliers final: 26 residues processed: 193 average time/residue: 0.1229 time to fit residues: 34.4770 Evaluate side-chains 178 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 471 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 64 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 157 optimal weight: 0.0980 chunk 93 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 298 HIS ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.123872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.103327 restraints weight = 20030.062| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.09 r_work: 0.3064 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13810 Z= 0.119 Angle : 0.553 8.693 18733 Z= 0.282 Chirality : 0.043 0.388 2048 Planarity : 0.003 0.039 2401 Dihedral : 4.505 32.629 1802 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.06 % Allowed : 11.03 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.46 (0.20), residues: 1662 helix: 2.64 (0.28), residues: 336 sheet: 0.77 (0.27), residues: 375 loop : -0.78 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 76 TYR 0.027 0.001 TYR L 49 PHE 0.014 0.001 PHE A 439 TRP 0.013 0.001 TRP A 343 HIS 0.012 0.001 HIS B 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13772) covalent geometry : angle 0.53001 / 0.28 (18639) SS BOND : bond 0.00245 / 0.15 ( 20) SS BOND : angle 1.51524 / 1.34 ( 40) hydrogen bonds : bond 0.04142 / 2.75 ( 505) hydrogen bonds : angle 4.94417 / 3.44 ( 1440) link_BETA1-4 : bond 0.00242 / 0.12 ( 3) link_BETA1-4 : angle 1.43153 / 0.95 ( 9) link_NAG-ASN : bond 0.00670 / 0.46 ( 15) link_NAG-ASN : angle 2.94174 / 1.89 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: C 340 GLU cc_start: 0.8577 (mm-30) cc_final: 0.7870 (pp20) REVERT: H 66 ARG cc_start: 0.7693 (mtp85) cc_final: 0.7209 (mtp-110) REVERT: H 100 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8307 (mt-10) REVERT: A 239 MET cc_start: 0.8171 (mmt) cc_final: 0.7896 (mmt) REVERT: A 268 MET cc_start: 0.8729 (ttm) cc_final: 0.8461 (ttm) REVERT: A 462 LEU cc_start: 0.8908 (mp) cc_final: 0.8684 (mt) REVERT: A 476 GLU cc_start: 0.7397 (tp30) cc_final: 0.7101 (tp30) REVERT: B 144 ASN cc_start: 0.8611 (m-40) cc_final: 0.8319 (m-40) REVERT: B 188 GLU cc_start: 0.8007 (mp0) cc_final: 0.7774 (mp0) outliers start: 30 outliers final: 22 residues processed: 180 average time/residue: 0.1207 time to fit residues: 32.0065 Evaluate side-chains 169 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 471 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 HIS A 117 HIS A 355 HIS ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.120245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.099077 restraints weight = 20267.010| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.06 r_work: 0.2980 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 13810 Z= 0.308 Angle : 0.685 9.113 18733 Z= 0.349 Chirality : 0.048 0.426 2048 Planarity : 0.004 0.047 2401 Dihedral : 4.910 24.529 1802 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.95 % Allowed : 12.13 % Favored : 84.92 % 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: -0.02 (0.20), residues: 1662 helix: 2.24 (0.27), residues: 334 sheet: 0.26 (0.26), residues: 377 loop : -1.00 (0.18), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 76 TYR 0.021 0.002 TYR L 49 PHE 0.027 0.002 PHE B 439 TRP 0.020 0.002 TRP A 343 HIS 0.009 0.002 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00746 / 0.31 (13772) covalent geometry : angle 0.66462 / 0.34 (18639) SS BOND : bond 0.00434 / 0.28 ( 20) SS BOND : angle 1.26458 / 0.99 ( 40) hydrogen bonds : bond 0.05009 / 3.34 ( 505) hydrogen bonds : angle 5.27512 / 3.65 ( 1440) link_BETA1-4 : bond 0.00236 / 0.12 ( 3) link_BETA1-4 : angle 1.98585 / 1.47 ( 9) link_NAG-ASN : bond 0.00638 / 0.44 ( 15) link_NAG-ASN : angle 3.19533 / 2.08 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 340 GLU cc_start: 0.8591 (mm-30) cc_final: 0.7805 (pp20) REVERT: H 36 TRP cc_start: 0.8373 (m100) cc_final: 0.8006 (m100) REVERT: L 4 LEU cc_start: 0.7899 (mt) cc_final: 0.7673 (mp) REVERT: L 27 SER cc_start: 0.8867 (p) cc_final: 0.8595 (t) REVERT: A 239 MET cc_start: 0.8691 (mmt) cc_final: 0.8116 (mmt) REVERT: A 348 ASP cc_start: 0.7789 (p0) cc_final: 0.7295 (p0) outliers start: 43 outliers final: 35 residues processed: 185 average time/residue: 0.1172 time to fit residues: 32.2273 Evaluate side-chains 185 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 355 HIS Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 481 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 156 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.0010 chunk 117 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.117879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.097702 restraints weight = 19911.991| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.94 r_work: 0.3064 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13810 Z= 0.126 Angle : 0.544 8.621 18733 Z= 0.277 Chirality : 0.043 0.369 2048 Planarity : 0.003 0.039 2401 Dihedral : 4.463 22.168 1802 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.06 % Allowed : 13.50 % Favored : 84.44 % 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: 0.23 (0.20), residues: 1662 helix: 2.51 (0.28), residues: 340 sheet: 0.55 (0.27), residues: 367 loop : -0.93 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 76 TYR 0.028 0.001 TYR L 49 PHE 0.013 0.001 PHE A 439 TRP 0.011 0.001 TRP A 343 HIS 0.005 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (13772) covalent geometry : angle 0.52478 / 0.27 (18639) SS BOND : bond 0.00288 / 0.19 ( 20) SS BOND : angle 0.95221 / 0.77 ( 40) hydrogen bonds : bond 0.04105 / 2.72 ( 505) hydrogen bonds : angle 4.95544 / 3.45 ( 1440) link_BETA1-4 : bond 0.00354 / 0.18 ( 3) link_BETA1-4 : angle 1.49938 / 0.97 ( 9) link_NAG-ASN : bond 0.00560 / 0.39 ( 15) link_NAG-ASN : angle 2.77948 / 1.79 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 275 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7383 (mp0) REVERT: C 340 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7842 (pp20) REVERT: H 36 TRP cc_start: 0.8221 (m100) cc_final: 0.7795 (m100) REVERT: H 100 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8332 (mt-10) REVERT: L 27 SER cc_start: 0.8976 (p) cc_final: 0.8633 (t) REVERT: A 239 MET cc_start: 0.8448 (mmt) cc_final: 0.7948 (mmt) REVERT: A 340 GLU cc_start: 0.8248 (mp0) cc_final: 0.7322 (pp20) REVERT: A 348 ASP cc_start: 0.7762 (p0) cc_final: 0.7317 (p0) REVERT: A 476 GLU cc_start: 0.7406 (tp30) cc_final: 0.7141 (tp30) outliers start: 30 outliers final: 23 residues processed: 172 average time/residue: 0.1197 time to fit residues: 30.4605 Evaluate side-chains 173 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 471 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 106 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 0.0020 chunk 76 optimal weight: 0.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.117681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.097602 restraints weight = 19763.799| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.92 r_work: 0.3065 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13810 Z= 0.132 Angle : 0.538 8.403 18733 Z= 0.274 Chirality : 0.043 0.370 2048 Planarity : 0.003 0.035 2401 Dihedral : 4.376 21.764 1802 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.99 % Allowed : 13.50 % 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: 0.25 (0.20), residues: 1662 helix: 2.56 (0.27), residues: 340 sheet: 0.51 (0.27), residues: 371 loop : -0.91 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 76 TYR 0.026 0.001 TYR L 49 PHE 0.015 0.001 PHE B 439 TRP 0.010 0.001 TRP A 343 HIS 0.008 0.001 HIS B 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (13772) covalent geometry : angle 0.52012 / 0.27 (18639) SS BOND : bond 0.00272 / 0.18 ( 20) SS BOND : angle 0.94336 / 0.76 ( 40) hydrogen bonds : bond 0.04098 / 2.72 ( 505) hydrogen bonds : angle 4.91809 / 3.42 ( 1440) link_BETA1-4 : bond 0.00266 / 0.13 ( 3) link_BETA1-4 : angle 1.52917 / 1.03 ( 9) link_NAG-ASN : bond 0.00533 / 0.38 ( 15) link_NAG-ASN : angle 2.71810 / 1.76 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 275 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7396 (mp0) REVERT: C 340 GLU cc_start: 0.8540 (mm-30) cc_final: 0.7835 (pp20) REVERT: C 363 TYR cc_start: 0.8318 (OUTLIER) cc_final: 0.5877 (t80) REVERT: H 36 TRP cc_start: 0.8222 (m100) cc_final: 0.7799 (m100) REVERT: H 46 GLU cc_start: 0.8359 (tt0) cc_final: 0.8081 (pt0) REVERT: L 27 SER cc_start: 0.8918 (p) cc_final: 0.8601 (t) REVERT: L 37 GLN cc_start: 0.8408 (tt0) cc_final: 0.8202 (tt0) REVERT: A 239 MET cc_start: 0.8419 (mmt) cc_final: 0.7892 (mmt) REVERT: A 340 GLU cc_start: 0.8267 (mp0) cc_final: 0.7364 (pp20) REVERT: A 348 ASP cc_start: 0.7768 (p0) cc_final: 0.7241 (p0) outliers start: 29 outliers final: 27 residues processed: 171 average time/residue: 0.1174 time to fit residues: 29.8191 Evaluate side-chains 178 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 471 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 6 optimal weight: 0.0570 chunk 125 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 87 optimal weight: 0.4980 chunk 63 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.118203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.098122 restraints weight = 19932.662| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.93 r_work: 0.3060 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13810 Z= 0.119 Angle : 0.530 8.145 18733 Z= 0.270 Chirality : 0.043 0.358 2048 Planarity : 0.003 0.033 2401 Dihedral : 4.298 21.494 1802 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.06 % Allowed : 13.57 % Favored : 84.37 % 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 (0.20), residues: 1662 helix: 2.64 (0.27), residues: 340 sheet: 0.51 (0.27), residues: 377 loop : -0.89 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 76 TYR 0.026 0.001 TYR L 49 PHE 0.014 0.001 PHE B 439 TRP 0.009 0.001 TRP A 343 HIS 0.016 0.001 HIS B 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (13772) covalent geometry : angle 0.51274 / 0.27 (18639) SS BOND : bond 0.00264 / 0.17 ( 20) SS BOND : angle 0.95467 / 0.78 ( 40) hydrogen bonds : bond 0.03997 / 2.65 ( 505) hydrogen bonds : angle 4.86433 / 3.38 ( 1440) link_BETA1-4 : bond 0.00328 / 0.16 ( 3) link_BETA1-4 : angle 1.51682 / 1.00 ( 9) link_NAG-ASN : bond 0.00525 / 0.37 ( 15) link_NAG-ASN : angle 2.61050 / 1.69 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 340 GLU cc_start: 0.8554 (mm-30) cc_final: 0.7854 (pp20) REVERT: C 363 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.5936 (t80) REVERT: H 36 TRP cc_start: 0.8200 (m100) cc_final: 0.7780 (m100) REVERT: H 46 GLU cc_start: 0.8362 (tt0) cc_final: 0.8111 (pt0) REVERT: L 27 SER cc_start: 0.8957 (p) cc_final: 0.8643 (t) REVERT: A 239 MET cc_start: 0.8360 (mmt) cc_final: 0.7841 (mmt) REVERT: A 340 GLU cc_start: 0.8268 (mp0) cc_final: 0.7348 (pp20) REVERT: A 348 ASP cc_start: 0.7759 (p0) cc_final: 0.7320 (p0) REVERT: B 26 VAL cc_start: 0.9070 (t) cc_final: 0.8805 (m) outliers start: 30 outliers final: 25 residues processed: 176 average time/residue: 0.1209 time to fit residues: 31.3621 Evaluate side-chains 172 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 459 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 30 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.115923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.095704 restraints weight = 20066.026| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.95 r_work: 0.3046 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13810 Z= 0.168 Angle : 0.561 8.094 18733 Z= 0.287 Chirality : 0.044 0.374 2048 Planarity : 0.004 0.047 2401 Dihedral : 4.405 21.811 1802 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.99 % Allowed : 13.85 % Favored : 84.17 % 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: 0.22 (0.20), residues: 1662 helix: 2.55 (0.27), residues: 340 sheet: 0.43 (0.27), residues: 377 loop : -0.92 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 93 TYR 0.025 0.002 TYR L 49 PHE 0.017 0.002 PHE B 439 TRP 0.010 0.001 TRP A 343 HIS 0.008 0.001 HIS B 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (13772) covalent geometry : angle 0.54383 / 0.28 (18639) SS BOND : bond 0.00321 / 0.22 ( 20) SS BOND : angle 1.02733 / 0.81 ( 40) hydrogen bonds : bond 0.04229 / 2.81 ( 505) hydrogen bonds : angle 4.93532 / 3.43 ( 1440) link_BETA1-4 : bond 0.00259 / 0.13 ( 3) link_BETA1-4 : angle 1.60946 / 1.13 ( 9) link_NAG-ASN : bond 0.00504 / 0.36 ( 15) link_NAG-ASN : angle 2.64524 / 1.72 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: C 340 GLU cc_start: 0.8551 (mm-30) cc_final: 0.7837 (pp20) REVERT: H 36 TRP cc_start: 0.8239 (m100) cc_final: 0.7843 (m100) REVERT: L 27 SER cc_start: 0.8931 (p) cc_final: 0.8605 (t) REVERT: L 32 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8092 (mm-30) REVERT: A 239 MET cc_start: 0.8513 (mmt) cc_final: 0.7951 (mmt) REVERT: A 340 GLU cc_start: 0.8361 (mp0) cc_final: 0.7393 (pp20) REVERT: A 348 ASP cc_start: 0.7668 (p0) cc_final: 0.7263 (p0) REVERT: B 239 MET cc_start: 0.8273 (mmm) cc_final: 0.8038 (mmt) outliers start: 29 outliers final: 26 residues processed: 167 average time/residue: 0.1177 time to fit residues: 29.1349 Evaluate side-chains 168 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 355 HIS Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 459 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 70 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 454 GLN H 10 GLN ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.116718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.096693 restraints weight = 20011.822| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.93 r_work: 0.3037 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13810 Z= 0.161 Angle : 0.566 10.663 18733 Z= 0.287 Chirality : 0.045 0.569 2048 Planarity : 0.004 0.052 2401 Dihedral : 4.430 21.850 1802 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.19 % Allowed : 13.85 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.20), residues: 1662 helix: 2.55 (0.27), residues: 340 sheet: 0.43 (0.27), residues: 377 loop : -0.95 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 93 TYR 0.025 0.002 TYR L 49 PHE 0.017 0.002 PHE B 439 TRP 0.011 0.001 TRP A 343 HIS 0.007 0.001 HIS B 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (13772) covalent geometry : angle 0.54838 / 0.28 (18639) SS BOND : bond 0.00287 / 0.19 ( 20) SS BOND : angle 0.97857 / 0.78 ( 40) hydrogen bonds : bond 0.04209 / 2.80 ( 505) hydrogen bonds : angle 4.94257 / 3.43 ( 1440) link_BETA1-4 : bond 0.00244 / 0.12 ( 3) link_BETA1-4 : angle 1.57471 / 1.08 ( 9) link_NAG-ASN : bond 0.00548 / 0.40 ( 15) link_NAG-ASN : angle 2.75814 / 1.82 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3178.49 seconds wall clock time: 55 minutes 35.33 seconds (3335.33 seconds total)