Starting phenix.real_space_refine on Sat Aug 23 17:09:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tp4_41466/08_2025/8tp4_41466.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp4_41466/08_2025/8tp4_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_41466/08_2025/8tp4_41466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp4_41466/08_2025/8tp4_41466.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tp4_41466/08_2025/8tp4_41466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp4_41466/08_2025/8tp4_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-2.0-5787/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 12 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.88, per 1000 atoms: 0.21 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: 1.37 Conformation dependent library (CDL) restraints added in 675.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.66 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: 2.89 Time building geometry restraints manager: 1.78 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: 8107 17.96 - 35.91: 254 35.91 - 53.87: 53 53.87 - 71.82: 26 71.82 - 89.78: 10 Dihedral angle restraints: 8450 sinusoidal: 3662 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 8447 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.570 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 10.273 89.776 5340 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 aren 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 covalent geometry : bond 0.02011 (13772) covalent geometry : angle 1.76578 (18639) SS BOND : bond 0.00964 ( 20) SS BOND : angle 2.64515 ( 40) hydrogen bonds : bond 0.14161 ( 505) hydrogen bonds : angle 7.52109 ( 1440) link_BETA1-4 : bond 0.00252 ( 3) link_BETA1-4 : angle 4.37959 ( 9) link_NAG-ASN : bond 0.01464 ( 15) link_NAG-ASN : angle 6.41538 ( 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 : 0.542 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: 0.1614 time to fit residues: 67.2331 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 : 0.645 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 18 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.129553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.108753 restraints weight = 19776.386| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.12 r_work: 0.3134 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13810 Z= 0.167 Angle : 0.714 15.257 18733 Z= 0.367 Chirality : 0.046 0.392 2048 Planarity : 0.004 0.047 2401 Dihedral : 6.356 48.299 2180 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.58 % Allowed : 6.92 % Favored : 91.50 % 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 aren not related in a simple way. whole: 0.78 (0.20), residues: 1662 helix: 2.15 (0.28), residues: 327 sheet: 1.41 (0.26), residues: 354 loop : -0.39 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 66 TYR 0.012 0.002 TYR C 363 PHE 0.022 0.002 PHE A 118 TRP 0.013 0.001 TRP A 343 HIS 0.010 0.001 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00365 (13772) covalent geometry : angle 0.67467 (18639) SS BOND : bond 0.00353 ( 20) SS BOND : angle 1.29804 ( 40) hydrogen bonds : bond 0.05524 ( 505) hydrogen bonds : angle 5.66174 ( 1440) link_BETA1-4 : bond 0.00261 ( 3) link_BETA1-4 : angle 2.22098 ( 9) link_NAG-ASN : bond 0.00510 ( 15) link_NAG-ASN : angle 4.60420 ( 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 228 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 VAL cc_start: 0.8697 (t) cc_final: 0.8203 (m) REVERT: C 340 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7886 (pp20) REVERT: C 388 MET cc_start: 0.8268 (mmm) cc_final: 0.8042 (mmm) REVERT: C 485 THR cc_start: 0.8143 (m) cc_final: 0.7701 (p) REVERT: A 268 MET cc_start: 0.8794 (ttm) cc_final: 0.8583 (ttm) REVERT: A 279 THR cc_start: 0.8473 (t) cc_final: 0.8254 (m) REVERT: A 348 ASP cc_start: 0.7108 (p0) cc_final: 0.6614 (p0) REVERT: A 357 ASN cc_start: 0.5737 (p0) cc_final: 0.5394 (p0) outliers start: 23 outliers final: 17 residues processed: 219 average time/residue: 0.1304 time to fit residues: 39.9002 Evaluate side-chains 165 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 264 SER Chi-restraints excluded: chain C residue 300 LEU 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 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: 0.6980 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 21 optimal weight: 0.0170 chunk 83 optimal weight: 3.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 ASN H 100EHIS B 92 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 = 0.3531 r_free = 0.3531 target = 0.128116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107089 restraints weight = 20096.787| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.04 r_work: 0.3104 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3063 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= 0.143 Angle : 0.590 11.019 18733 Z= 0.301 Chirality : 0.044 0.210 2048 Planarity : 0.004 0.034 2401 Dihedral : 5.774 53.486 2180 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.33 % Allowed : 7.68 % Favored : 89.99 % 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 aren not related in a simple way. whole: 0.63 (0.20), residues: 1662 helix: 2.35 (0.27), residues: 338 sheet: 1.06 (0.26), residues: 360 loop : -0.56 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 76 TYR 0.026 0.001 TYR L 49 PHE 0.018 0.002 PHE A 439 TRP 0.021 0.001 TRP A 343 HIS 0.007 0.001 HIS H 102 Details of bonding type rmsd covalent geometry : bond 0.00326 (13772) covalent geometry : angle 0.56201 (18639) SS BOND : bond 0.00674 ( 20) SS BOND : angle 1.16175 ( 40) hydrogen bonds : bond 0.04549 ( 505) hydrogen bonds : angle 5.13477 ( 1440) link_BETA1-4 : bond 0.00214 ( 3) link_BETA1-4 : angle 1.75651 ( 9) link_NAG-ASN : bond 0.00506 ( 15) link_NAG-ASN : angle 3.50452 ( 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 209 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: C 26 VAL cc_start: 0.8728 (t) cc_final: 0.8181 (m) REVERT: C 340 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7898 (pp20) REVERT: C 485 THR cc_start: 0.8262 (m) cc_final: 0.8029 (p) REVERT: H 12 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.8080 (mmm160) REVERT: H 17 SER cc_start: 0.7119 (p) cc_final: 0.6873 (t) REVERT: L 37 GLN cc_start: 0.8079 (tt0) cc_final: 0.7426 (tt0) REVERT: L 91 TYR cc_start: 0.8814 (t80) cc_final: 0.8526 (t80) REVERT: A 268 MET cc_start: 0.8782 (ttm) cc_final: 0.8543 (ttm) REVERT: A 279 THR cc_start: 0.8559 (t) cc_final: 0.8173 (t) REVERT: A 348 ASP cc_start: 0.7400 (p0) cc_final: 0.6931 (p0) REVERT: A 462 LEU cc_start: 0.8952 (mp) cc_final: 0.8724 (mt) REVERT: B 144 ASN cc_start: 0.8450 (m-40) cc_final: 0.8182 (m-40) outliers start: 34 outliers final: 25 residues processed: 197 average time/residue: 0.1169 time to fit residues: 33.6272 Evaluate side-chains 173 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 160 ASN 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 347 VAL Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 413 MET 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 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 343 TRP 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 26 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 0.0770 chunk 122 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 10 GLN L 37 GLN A 18 HIS A 355 HIS B 471 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103220 restraints weight = 20281.149| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.03 r_work: 0.3052 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13810 Z= 0.211 Angle : 0.635 10.283 18733 Z= 0.325 Chirality : 0.046 0.366 2048 Planarity : 0.004 0.038 2401 Dihedral : 5.984 52.474 2180 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.40 % Allowed : 9.25 % Favored : 88.35 % 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 aren not related in a simple way. whole: 0.38 (0.20), residues: 1662 helix: 2.38 (0.27), residues: 336 sheet: 0.68 (0.27), residues: 374 loop : -0.74 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 66 TYR 0.018 0.002 TYR L 49 PHE 0.023 0.002 PHE B 439 TRP 0.028 0.001 TRP A 343 HIS 0.008 0.002 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00505 (13772) covalent geometry : angle 0.60913 (18639) SS BOND : bond 0.00661 ( 20) SS BOND : angle 1.66595 ( 40) hydrogen bonds : bond 0.04677 ( 505) hydrogen bonds : angle 5.15589 ( 1440) link_BETA1-4 : bond 0.00214 ( 3) link_BETA1-4 : angle 1.89722 ( 9) link_NAG-ASN : bond 0.00298 ( 15) link_NAG-ASN : angle 3.31451 ( 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 194 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 340 GLU cc_start: 0.8514 (mm-30) cc_final: 0.7845 (pp20) REVERT: H 66 ARG cc_start: 0.7470 (mtp85) cc_final: 0.7050 (mtp85) REVERT: L 91 TYR cc_start: 0.8850 (t80) cc_final: 0.8583 (t80) REVERT: A 348 ASP cc_start: 0.7654 (p0) cc_final: 0.7201 (p0) REVERT: A 476 GLU cc_start: 0.7290 (tp30) cc_final: 0.7072 (tp30) REVERT: B 144 ASN cc_start: 0.8600 (m-40) cc_final: 0.8309 (m-40) outliers start: 35 outliers final: 24 residues processed: 181 average time/residue: 0.1093 time to fit residues: 29.1539 Evaluate side-chains 167 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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 H residue 25 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 51 ILE 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 203 SER 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 Chi-restraints excluded: chain B residue 459 VAL 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: 5.9990 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 152 optimal weight: 0.3980 chunk 121 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 HIS C 298 HIS H 3 GLN H 10 GLN A 18 HIS B 471 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.123988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.103654 restraints weight = 20133.694| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.05 r_work: 0.3060 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13810 Z= 0.148 Angle : 0.576 9.933 18733 Z= 0.293 Chirality : 0.044 0.335 2048 Planarity : 0.004 0.038 2401 Dihedral : 5.881 54.492 2180 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.12 % Allowed : 10.42 % Favored : 87.46 % 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 aren not related in a simple way. whole: 0.39 (0.20), residues: 1662 helix: 2.59 (0.27), residues: 336 sheet: 0.61 (0.27), residues: 367 loop : -0.77 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 76 TYR 0.027 0.001 TYR L 49 PHE 0.017 0.002 PHE A 439 TRP 0.018 0.001 TRP A 343 HIS 0.009 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00344 (13772) covalent geometry : angle 0.55215 (18639) SS BOND : bond 0.00408 ( 20) SS BOND : angle 1.34827 ( 40) hydrogen bonds : bond 0.04272 ( 505) hydrogen bonds : angle 4.99802 ( 1440) link_BETA1-4 : bond 0.00402 ( 3) link_BETA1-4 : angle 1.88731 ( 9) link_NAG-ASN : bond 0.00620 ( 15) link_NAG-ASN : angle 3.12191 ( 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 185 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: C 340 GLU cc_start: 0.8523 (mm-30) cc_final: 0.7862 (pp20) REVERT: L 37 GLN cc_start: 0.8407 (tt0) cc_final: 0.8044 (tt0) REVERT: A 476 GLU cc_start: 0.7270 (tp30) cc_final: 0.6986 (tp30) REVERT: B 144 ASN cc_start: 0.8596 (m-40) cc_final: 0.8304 (m-40) outliers start: 31 outliers final: 22 residues processed: 173 average time/residue: 0.1108 time to fit residues: 27.9717 Evaluate side-chains 165 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 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 H residue 31 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 279 THR 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 369 SER 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 459 VAL 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: 1.9990 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 10 GLN A 18 HIS A 244 ASN ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.101060 restraints weight = 20202.991| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.02 r_work: 0.3008 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 13810 Z= 0.247 Angle : 0.648 9.651 18733 Z= 0.331 Chirality : 0.046 0.336 2048 Planarity : 0.004 0.043 2401 Dihedral : 6.225 58.665 2180 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.37 % Favored : 96.57 % Rotamer: Outliers : 2.60 % Allowed : 10.83 % Favored : 86.57 % 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 aren not related in a simple way. whole: 0.13 (0.20), residues: 1662 helix: 2.40 (0.27), residues: 334 sheet: 0.39 (0.27), residues: 373 loop : -0.92 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 66 TYR 0.026 0.002 TYR L 49 PHE 0.024 0.002 PHE B 439 TRP 0.023 0.002 TRP A 343 HIS 0.015 0.002 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00595 (13772) covalent geometry : angle 0.62496 (18639) SS BOND : bond 0.00357 ( 20) SS BOND : angle 1.46648 ( 40) hydrogen bonds : bond 0.04721 ( 505) hydrogen bonds : angle 5.17013 ( 1440) link_BETA1-4 : bond 0.00144 ( 3) link_BETA1-4 : angle 2.19135 ( 9) link_NAG-ASN : bond 0.00660 ( 15) link_NAG-ASN : angle 3.15728 ( 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 193 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: C 151 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8435 (mtt) REVERT: C 340 GLU cc_start: 0.8571 (mm-30) cc_final: 0.7829 (pp20) REVERT: H 36 TRP cc_start: 0.8323 (m100) cc_final: 0.8044 (m100) REVERT: L 4 LEU cc_start: 0.7781 (mt) cc_final: 0.7549 (mp) REVERT: L 27 SER cc_start: 0.8976 (p) cc_final: 0.8589 (t) REVERT: A 348 ASP cc_start: 0.7718 (p0) cc_final: 0.7131 (p0) REVERT: A 476 GLU cc_start: 0.7299 (tp30) cc_final: 0.6966 (tp30) outliers start: 38 outliers final: 34 residues processed: 182 average time/residue: 0.1130 time to fit residues: 30.4910 Evaluate side-chains 184 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 264 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 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 22 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 203 SER Chi-restraints excluded: chain A residue 279 THR 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 268 MET Chi-restraints excluded: chain B residue 300 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 Chi-restraints excluded: chain B residue 459 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 156 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 148 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 161 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 10 GLN A 18 HIS B 471 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.097169 restraints weight = 19991.891| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.97 r_work: 0.3040 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13810 Z= 0.157 Angle : 0.574 9.375 18733 Z= 0.293 Chirality : 0.043 0.313 2048 Planarity : 0.004 0.037 2401 Dihedral : 5.986 57.312 2180 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 2.33 % Allowed : 12.54 % Favored : 85.13 % 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 aren not related in a simple way. whole: 0.22 (0.20), residues: 1662 helix: 2.60 (0.27), residues: 334 sheet: 0.45 (0.27), residues: 371 loop : -0.91 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 76 TYR 0.026 0.001 TYR L 49 PHE 0.017 0.002 PHE B 439 TRP 0.015 0.001 TRP A 343 HIS 0.019 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00368 (13772) covalent geometry : angle 0.55316 (18639) SS BOND : bond 0.00271 ( 20) SS BOND : angle 1.14860 ( 40) hydrogen bonds : bond 0.04317 ( 505) hydrogen bonds : angle 5.02091 ( 1440) link_BETA1-4 : bond 0.00292 ( 3) link_BETA1-4 : angle 1.91753 ( 9) link_NAG-ASN : bond 0.00601 ( 15) link_NAG-ASN : angle 2.95521 ( 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 186 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: C 151 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8340 (mtt) REVERT: C 275 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7342 (mp0) REVERT: C 340 GLU cc_start: 0.8554 (mm-30) cc_final: 0.7828 (pp20) REVERT: H 36 TRP cc_start: 0.8262 (m100) cc_final: 0.7925 (m100) REVERT: L 27 SER cc_start: 0.8972 (p) cc_final: 0.8605 (t) REVERT: L 30 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7953 (mm) REVERT: L 37 GLN cc_start: 0.8429 (tt0) cc_final: 0.8141 (tt0) REVERT: A 348 ASP cc_start: 0.7700 (p0) cc_final: 0.7184 (p0) REVERT: A 476 GLU cc_start: 0.7362 (tp30) cc_final: 0.7006 (tp30) REVERT: B 346 MET cc_start: 0.8653 (ttm) cc_final: 0.8430 (mtp) outliers start: 34 outliers final: 24 residues processed: 175 average time/residue: 0.1167 time to fit residues: 29.9940 Evaluate side-chains 170 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 208 THR 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 4 LEU 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 80 MET Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL 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 279 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 427 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 106 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 10 GLN L 34 HIS ** 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 = 0.3364 r_free = 0.3364 target = 0.111021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.090871 restraints weight = 20339.426| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.93 r_work: 0.2943 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 13810 Z= 0.265 Angle : 0.657 9.160 18733 Z= 0.336 Chirality : 0.047 0.339 2048 Planarity : 0.004 0.037 2401 Dihedral : 6.282 55.143 2180 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Rotamer: Outliers : 2.54 % Allowed : 12.47 % Favored : 84.99 % 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 aren not related in a simple way. whole: -0.10 (0.20), residues: 1662 helix: 2.20 (0.27), residues: 340 sheet: 0.15 (0.26), residues: 379 loop : -1.05 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 76 TYR 0.028 0.002 TYR L 49 PHE 0.025 0.002 PHE B 439 TRP 0.019 0.002 TRP A 343 HIS 0.008 0.002 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00643 (13772) covalent geometry : angle 0.63578 (18639) SS BOND : bond 0.00377 ( 20) SS BOND : angle 1.40236 ( 40) hydrogen bonds : bond 0.04808 ( 505) hydrogen bonds : angle 5.22914 ( 1440) link_BETA1-4 : bond 0.00200 ( 3) link_BETA1-4 : angle 2.23867 ( 9) link_NAG-ASN : bond 0.00570 ( 15) link_NAG-ASN : angle 3.07389 ( 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 193 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 275 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7377 (mp0) REVERT: C 340 GLU cc_start: 0.8454 (mm-30) cc_final: 0.7771 (pp20) REVERT: H 36 TRP cc_start: 0.8336 (m100) cc_final: 0.7951 (m100) REVERT: L 27 SER cc_start: 0.8926 (p) cc_final: 0.8613 (t) REVERT: A 340 GLU cc_start: 0.8282 (mp0) cc_final: 0.7433 (pp20) REVERT: A 348 ASP cc_start: 0.7630 (p0) cc_final: 0.7183 (p0) REVERT: A 476 GLU cc_start: 0.7410 (tp30) cc_final: 0.7042 (tp30) REVERT: B 56 ILE cc_start: 0.9019 (mt) cc_final: 0.8777 (pt) REVERT: B 144 ASN cc_start: 0.8695 (m-40) cc_final: 0.8477 (m-40) outliers start: 37 outliers final: 33 residues processed: 181 average time/residue: 0.0938 time to fit residues: 25.3710 Evaluate side-chains 183 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 300 LEU 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 4 LEU 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 51 ILE 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 58 VAL Chi-restraints excluded: chain L residue 97 VAL 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 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 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 427 LEU 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: 0.9980 chunk 125 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 150 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 10 GLN ** B 298 HIS ** 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 = 0.3384 r_free = 0.3384 target = 0.112489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.092076 restraints weight = 20439.007| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.98 r_work: 0.2987 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13810 Z= 0.124 Angle : 0.558 8.826 18733 Z= 0.285 Chirality : 0.042 0.293 2048 Planarity : 0.003 0.034 2401 Dihedral : 5.974 55.122 2180 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.41 % Favored : 97.53 % Rotamer: Outliers : 1.92 % Allowed : 13.37 % Favored : 84.72 % 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 aren not related in a simple way. whole: 0.13 (0.20), residues: 1662 helix: 2.52 (0.27), residues: 340 sheet: 0.31 (0.27), residues: 379 loop : -0.97 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 76 TYR 0.028 0.001 TYR L 49 PHE 0.014 0.001 PHE A 439 TRP 0.011 0.001 TRP A 343 HIS 0.024 0.001 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00284 (13772) covalent geometry : angle 0.53715 (18639) SS BOND : bond 0.00297 ( 20) SS BOND : angle 1.46628 ( 40) hydrogen bonds : bond 0.04116 ( 505) hydrogen bonds : angle 5.00732 ( 1440) link_BETA1-4 : bond 0.00233 ( 3) link_BETA1-4 : angle 1.77599 ( 9) link_NAG-ASN : bond 0.00562 ( 15) link_NAG-ASN : angle 2.79186 ( 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 180 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 151 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8382 (mtt) REVERT: C 275 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7401 (mp0) REVERT: C 340 GLU cc_start: 0.8482 (mm-30) cc_final: 0.7826 (pp20) REVERT: H 36 TRP cc_start: 0.8239 (m100) cc_final: 0.7813 (m100) REVERT: L 27 SER cc_start: 0.8856 (p) cc_final: 0.8548 (t) REVERT: L 32 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8179 (mm-30) REVERT: A 340 GLU cc_start: 0.8288 (mp0) cc_final: 0.7380 (pp20) REVERT: A 348 ASP cc_start: 0.7654 (p0) cc_final: 0.7300 (p0) REVERT: A 476 GLU cc_start: 0.7383 (tp30) cc_final: 0.7021 (tp30) REVERT: B 26 VAL cc_start: 0.9072 (t) cc_final: 0.8809 (m) REVERT: B 56 ILE cc_start: 0.9022 (mt) cc_final: 0.8796 (pt) REVERT: B 144 ASN cc_start: 0.8671 (m-40) cc_final: 0.8460 (m-40) outliers start: 28 outliers final: 23 residues processed: 170 average time/residue: 0.1015 time to fit residues: 25.7131 Evaluate side-chains 172 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 208 THR 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 4 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 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 203 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 30 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 10 GLN ** B 298 HIS ** 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 = 0.3460 r_free = 0.3460 target = 0.123312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.102507 restraints weight = 20043.630| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.00 r_work: 0.3047 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13810 Z= 0.149 Angle : 0.564 8.935 18733 Z= 0.288 Chirality : 0.043 0.289 2048 Planarity : 0.003 0.032 2401 Dihedral : 5.920 55.235 2180 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 1.92 % Allowed : 13.50 % Favored : 84.58 % 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 aren not related in a simple way. whole: 0.14 (0.20), residues: 1662 helix: 2.54 (0.27), residues: 342 sheet: 0.30 (0.27), residues: 379 loop : -0.97 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 76 TYR 0.028 0.002 TYR L 49 PHE 0.016 0.002 PHE B 439 TRP 0.012 0.001 TRP A 343 HIS 0.017 0.001 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00350 (13772) covalent geometry : angle 0.54434 (18639) SS BOND : bond 0.00258 ( 20) SS BOND : angle 1.38832 ( 40) hydrogen bonds : bond 0.04160 ( 505) hydrogen bonds : angle 4.99226 ( 1440) link_BETA1-4 : bond 0.00252 ( 3) link_BETA1-4 : angle 1.88779 ( 9) link_NAG-ASN : bond 0.00536 ( 15) link_NAG-ASN : angle 2.71326 ( 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 177 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 151 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8298 (mtt) REVERT: C 275 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7429 (mp0) REVERT: C 340 GLU cc_start: 0.8561 (mm-30) cc_final: 0.7853 (pp20) REVERT: H 36 TRP cc_start: 0.8261 (m100) cc_final: 0.7829 (m100) REVERT: L 27 SER cc_start: 0.8891 (p) cc_final: 0.8579 (t) REVERT: L 32 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8177 (mm-30) REVERT: A 239 MET cc_start: 0.8408 (mmt) cc_final: 0.8180 (mmt) REVERT: A 340 GLU cc_start: 0.8241 (mp0) cc_final: 0.7371 (pp20) REVERT: A 476 GLU cc_start: 0.7412 (tp30) cc_final: 0.7046 (tp30) REVERT: B 26 VAL cc_start: 0.9090 (t) cc_final: 0.8831 (m) REVERT: B 56 ILE cc_start: 0.9060 (mt) cc_final: 0.8831 (pt) REVERT: B 144 ASN cc_start: 0.8682 (m-40) cc_final: 0.8477 (m-40) outliers start: 28 outliers final: 24 residues processed: 168 average time/residue: 0.0928 time to fit residues: 23.4578 Evaluate side-chains 168 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 151 MET 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 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 L residue 22 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 31 GLU Chi-restraints excluded: chain A residue 203 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 70 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 10 GLN ** B 298 HIS ** 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 = 0.3455 r_free = 0.3455 target = 0.116483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.096438 restraints weight = 20051.797| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.93 r_work: 0.3034 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13810 Z= 0.184 Angle : 0.580 9.286 18733 Z= 0.296 Chirality : 0.044 0.291 2048 Planarity : 0.004 0.032 2401 Dihedral : 5.995 59.220 2180 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 2.19 % Allowed : 13.30 % Favored : 84.51 % 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 aren not related in a simple way. whole: 0.08 (0.20), residues: 1662 helix: 2.48 (0.27), residues: 342 sheet: 0.23 (0.27), residues: 379 loop : -0.98 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 66 TYR 0.026 0.002 TYR L 49 PHE 0.018 0.002 PHE B 439 TRP 0.013 0.001 TRP A 343 HIS 0.020 0.002 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00439 (13772) covalent geometry : angle 0.56103 (18639) SS BOND : bond 0.00290 ( 20) SS BOND : angle 1.39010 ( 40) hydrogen bonds : bond 0.04300 ( 505) hydrogen bonds : angle 5.03638 ( 1440) link_BETA1-4 : bond 0.00214 ( 3) link_BETA1-4 : angle 1.93631 ( 9) link_NAG-ASN : bond 0.00514 ( 15) link_NAG-ASN : angle 2.70422 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3066.18 seconds wall clock time: 53 minutes 27.77 seconds (3207.77 seconds total)