Starting phenix.real_space_refine on Thu May 15 19:45:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tp4_41466/05_2025/8tp4_41466.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp4_41466/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tp4_41466/05_2025/8tp4_41466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp4_41466/05_2025/8tp4_41466.map" model { file = "/net/cci-nas-00/data/ceres_data/8tp4_41466/05_2025/8tp4_41466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp4_41466/05_2025/8tp4_41466.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.42, per 1000 atoms: 0.63 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: 3.39 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 2.13 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: 5.36 Time building geometry restraints manager: 3.94 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 487 or resid 501 throu \ gh 504)) selection = (chain 'C' and (resid 11 through 334 or resid 337 through 487 or resid 501 throu \ gh 504)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 34.250 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.460 ------------------------------------------------------------------------------- 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 : 2.95 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (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 TRP 0.033 0.006 TRP B 153 HIS 0.022 0.003 HIS C 354 PHE 0.041 0.006 PHE C 118 TYR 0.054 0.008 TYR C 17 ARG 0.008 0.001 ARG C 229 Details of bonding type rmsd link_NAG-ASN : bond 0.01464 ( 15) link_NAG-ASN : angle 6.41538 ( 45) link_BETA1-4 : bond 0.00252 ( 3) link_BETA1-4 : angle 4.37959 ( 9) hydrogen bonds : bond 0.14161 ( 505) hydrogen bonds : angle 7.52109 ( 1440) SS BOND : bond 0.00964 ( 20) SS BOND : angle 2.64515 ( 40) covalent geometry : bond 0.02011 (13772) covalent geometry : angle 1.76578 (18639) *********************** 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 : 1.511 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: 0.3243 time to fit residues: 135.1532 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 : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 0.8980 chunk 126 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 151 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.129518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109087 restraints weight = 19713.505| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.05 r_work: 0.3142 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13810 Z= 0.167 Angle : 0.692 11.768 18733 Z= 0.359 Chirality : 0.046 0.429 2048 Planarity : 0.004 0.043 2401 Dihedral : 6.245 47.291 2180 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.78 % Allowed : 6.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1662 helix: 2.13 (0.28), residues: 329 sheet: 1.43 (0.26), residues: 359 loop : -0.37 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 127 HIS 0.012 0.001 HIS B 471 PHE 0.023 0.002 PHE B 118 TYR 0.013 0.002 TYR B 17 ARG 0.006 0.001 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00976 ( 15) link_NAG-ASN : angle 4.37343 ( 45) link_BETA1-4 : bond 0.00401 ( 3) link_BETA1-4 : angle 2.09466 ( 9) hydrogen bonds : bond 0.05445 ( 505) hydrogen bonds : angle 5.61537 ( 1440) SS BOND : bond 0.00611 ( 20) SS BOND : angle 1.36215 ( 40) covalent geometry : bond 0.00362 (13772) covalent geometry : angle 0.65525 (18639) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 VAL cc_start: 0.8696 (t) cc_final: 0.8205 (m) REVERT: C 340 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7890 (pp20) REVERT: C 388 MET cc_start: 0.8250 (mmm) cc_final: 0.8050 (mmm) REVERT: C 485 THR cc_start: 0.8093 (m) cc_final: 0.7684 (p) REVERT: A 268 MET cc_start: 0.8779 (ttm) cc_final: 0.8515 (ttm) REVERT: A 279 THR cc_start: 0.8492 (t) cc_final: 0.8289 (m) REVERT: A 348 ASP cc_start: 0.7095 (p0) cc_final: 0.6617 (p0) REVERT: A 357 ASN cc_start: 0.5804 (p0) cc_final: 0.5520 (p0) REVERT: B 144 ASN cc_start: 0.8302 (m-40) cc_final: 0.8069 (m-40) outliers start: 26 outliers final: 20 residues processed: 223 average time/residue: 0.3174 time to fit residues: 99.9641 Evaluate side-chains 167 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 1.542 ------------------------------------------------------------------------------- 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 347 VAL Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 343 TRP Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 427 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 164 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.128099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107100 restraints weight = 19967.338| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.02 r_work: 0.3106 rms_B_bonded: 2.41 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: 0.8358 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 13810 Z= 0.146 Angle : 0.593 10.854 18733 Z= 0.304 Chirality : 0.044 0.238 2048 Planarity : 0.004 0.034 2401 Dihedral : 5.747 52.946 2180 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.19 % Allowed : 7.88 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1662 helix: 2.35 (0.27), residues: 336 sheet: 1.08 (0.26), residues: 360 loop : -0.53 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 343 HIS 0.008 0.001 HIS H 102 PHE 0.019 0.002 PHE A 439 TYR 0.027 0.001 TYR L 49 ARG 0.010 0.001 ARG H 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 15) link_NAG-ASN : angle 3.47579 ( 45) link_BETA1-4 : bond 0.00263 ( 3) link_BETA1-4 : angle 1.76836 ( 9) hydrogen bonds : bond 0.04575 ( 505) hydrogen bonds : angle 5.13365 ( 1440) SS BOND : bond 0.00299 ( 20) SS BOND : angle 1.13164 ( 40) covalent geometry : bond 0.00335 (13772) covalent geometry : angle 0.56571 (18639) *********************** 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 212 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 VAL cc_start: 0.8740 (t) cc_final: 0.8197 (m) REVERT: C 340 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7884 (pp20) REVERT: C 485 THR cc_start: 0.8291 (m) cc_final: 0.8080 (p) REVERT: H 12 ARG cc_start: 0.8343 (mmm-85) cc_final: 0.8086 (mmm160) REVERT: H 17 SER cc_start: 0.7140 (p) cc_final: 0.6873 (t) REVERT: H 66 ARG cc_start: 0.7540 (mtp85) cc_final: 0.7333 (mtp180) REVERT: L 37 GLN cc_start: 0.8133 (tt0) cc_final: 0.7470 (tt0) REVERT: L 91 TYR cc_start: 0.8819 (t80) cc_final: 0.8539 (t80) REVERT: A 268 MET cc_start: 0.8778 (ttm) cc_final: 0.8529 (ttm) REVERT: A 279 THR cc_start: 0.8556 (t) cc_final: 0.8182 (t) REVERT: A 348 ASP cc_start: 0.7402 (p0) cc_final: 0.6929 (p0) REVERT: A 462 LEU cc_start: 0.8950 (mp) cc_final: 0.8731 (mt) REVERT: B 144 ASN cc_start: 0.8461 (m-40) cc_final: 0.8193 (m-40) REVERT: B 435 ARG cc_start: 0.8209 (mtp85) cc_final: 0.7856 (mtp85) outliers start: 32 outliers final: 23 residues processed: 199 average time/residue: 0.2504 time to fit residues: 72.6676 Evaluate side-chains 175 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU 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 395 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 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 Chi-restraints excluded: chain B residue 459 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 78 optimal weight: 0.0970 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 3 GLN H 10 GLN L 37 GLN A 18 HIS A 355 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 = 0.3473 r_free = 0.3473 target = 0.123423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.102737 restraints weight = 20054.978| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.10 r_work: 0.3035 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13810 Z= 0.209 Angle : 0.631 10.227 18733 Z= 0.323 Chirality : 0.045 0.247 2048 Planarity : 0.004 0.038 2401 Dihedral : 5.928 51.316 2180 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.60 % Allowed : 9.18 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.20), residues: 1662 helix: 2.37 (0.27), residues: 336 sheet: 0.73 (0.26), residues: 379 loop : -0.72 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 343 HIS 0.008 0.002 HIS A 18 PHE 0.022 0.002 PHE B 439 TYR 0.018 0.002 TYR L 49 ARG 0.004 0.001 ARG C 405 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 15) link_NAG-ASN : angle 3.30857 ( 45) link_BETA1-4 : bond 0.00282 ( 3) link_BETA1-4 : angle 1.94416 ( 9) hydrogen bonds : bond 0.04673 ( 505) hydrogen bonds : angle 5.14298 ( 1440) SS BOND : bond 0.00352 ( 20) SS BOND : angle 1.54309 ( 40) covalent geometry : bond 0.00499 (13772) covalent geometry : angle 0.60562 (18639) *********************** 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 201 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 340 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7848 (pp20) REVERT: H 12 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.8175 (mmm160) REVERT: L 91 TYR cc_start: 0.8856 (t80) cc_final: 0.8582 (t80) REVERT: A 348 ASP cc_start: 0.7640 (p0) cc_final: 0.7216 (p0) REVERT: A 476 GLU cc_start: 0.7267 (tp30) cc_final: 0.7038 (tp30) REVERT: B 144 ASN cc_start: 0.8592 (m-40) cc_final: 0.8305 (m-40) outliers start: 38 outliers final: 26 residues processed: 186 average time/residue: 0.2474 time to fit residues: 67.9851 Evaluate side-chains 175 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 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 82 THR 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 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 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 90 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 123 optimal weight: 0.1980 chunk 159 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 298 HIS H 10 GLN A 18 HIS B 471 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.124875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104256 restraints weight = 19985.841| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.10 r_work: 0.3078 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13810 Z= 0.126 Angle : 0.556 9.559 18733 Z= 0.282 Chirality : 0.043 0.318 2048 Planarity : 0.003 0.038 2401 Dihedral : 5.787 54.880 2180 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.33 % Allowed : 10.01 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1662 helix: 2.67 (0.27), residues: 336 sheet: 0.87 (0.27), residues: 359 loop : -0.74 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 343 HIS 0.009 0.001 HIS A 18 PHE 0.015 0.001 PHE A 439 TYR 0.027 0.001 TYR L 49 ARG 0.004 0.000 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00563 ( 15) link_NAG-ASN : angle 3.02840 ( 45) link_BETA1-4 : bond 0.00222 ( 3) link_BETA1-4 : angle 1.66013 ( 9) hydrogen bonds : bond 0.04156 ( 505) hydrogen bonds : angle 4.93206 ( 1440) SS BOND : bond 0.00274 ( 20) SS BOND : angle 1.28410 ( 40) covalent geometry : bond 0.00287 (13772) covalent geometry : angle 0.53231 (18639) *********************** 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 190 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 340 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7841 (pp20) REVERT: A 476 GLU cc_start: 0.7298 (tp30) cc_final: 0.7010 (tp30) REVERT: B 144 ASN cc_start: 0.8593 (m-40) cc_final: 0.8303 (m-40) REVERT: B 188 GLU cc_start: 0.8013 (mp0) cc_final: 0.7788 (mp0) outliers start: 34 outliers final: 26 residues processed: 179 average time/residue: 0.2552 time to fit residues: 67.0980 Evaluate side-chains 168 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 100 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 343 TRP 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 20 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 10 GLN A 117 HIS A 244 ASN A 355 HIS ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.118882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.097836 restraints weight = 20633.351| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.07 r_work: 0.2955 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.109 13810 Z= 0.403 Angle : 0.795 10.159 18733 Z= 0.407 Chirality : 0.052 0.378 2048 Planarity : 0.005 0.048 2401 Dihedral : 6.766 59.605 2180 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.88 % Allowed : 11.38 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 1662 helix: 1.96 (0.27), residues: 336 sheet: 0.19 (0.26), residues: 375 loop : -1.13 (0.18), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 343 HIS 0.024 0.003 HIS B 471 PHE 0.032 0.003 PHE C 439 TYR 0.021 0.003 TYR C 470 ARG 0.011 0.001 ARG C 405 Details of bonding type rmsd link_NAG-ASN : bond 0.00706 ( 15) link_NAG-ASN : angle 3.52335 ( 45) link_BETA1-4 : bond 0.00463 ( 3) link_BETA1-4 : angle 2.55224 ( 9) hydrogen bonds : bond 0.05531 ( 505) hydrogen bonds : angle 5.50268 ( 1440) SS BOND : bond 0.00538 ( 20) SS BOND : angle 1.68940 ( 40) covalent geometry : bond 0.00970 (13772) covalent geometry : angle 0.77163 (18639) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 340 GLU cc_start: 0.8596 (mm-30) cc_final: 0.7803 (pp20) REVERT: H 36 TRP cc_start: 0.8446 (m100) cc_final: 0.8228 (m100) REVERT: L 27 SER cc_start: 0.8923 (p) cc_final: 0.8665 (t) REVERT: A 340 GLU cc_start: 0.8435 (mp0) cc_final: 0.7600 (pp20) REVERT: A 348 ASP cc_start: 0.7787 (p0) cc_final: 0.7201 (p0) REVERT: A 476 GLU cc_start: 0.7422 (tp30) cc_final: 0.7088 (tp30) REVERT: B 144 ASN cc_start: 0.8758 (m-40) cc_final: 0.8556 (m-40) outliers start: 42 outliers final: 32 residues processed: 184 average time/residue: 0.2737 time to fit residues: 72.8989 Evaluate side-chains 177 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 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 H residue 51 ILE Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 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 46 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 355 HIS Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 458 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 49 optimal weight: 10.0000 chunk 162 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 HIS ** 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 = 0.3458 r_free = 0.3458 target = 0.123374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102582 restraints weight = 20090.582| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.03 r_work: 0.3033 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13810 Z= 0.136 Angle : 0.578 9.690 18733 Z= 0.294 Chirality : 0.043 0.312 2048 Planarity : 0.004 0.040 2401 Dihedral : 6.128 56.298 2180 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 2.19 % Allowed : 12.41 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1662 helix: 2.34 (0.27), residues: 340 sheet: 0.42 (0.27), residues: 369 loop : -1.02 (0.18), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 343 HIS 0.007 0.001 HIS A 18 PHE 0.014 0.001 PHE B 439 TYR 0.028 0.001 TYR L 49 ARG 0.008 0.000 ARG A 262a Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 15) link_NAG-ASN : angle 3.06581 ( 45) link_BETA1-4 : bond 0.00312 ( 3) link_BETA1-4 : angle 1.78162 ( 9) hydrogen bonds : bond 0.04318 ( 505) hydrogen bonds : angle 5.09853 ( 1440) SS BOND : bond 0.00346 ( 20) SS BOND : angle 1.30801 ( 40) covalent geometry : bond 0.00314 (13772) covalent geometry : angle 0.55518 (18639) *********************** 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 187 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 340 GLU cc_start: 0.8604 (mm-30) cc_final: 0.7852 (pp20) REVERT: H 36 TRP cc_start: 0.8293 (m100) cc_final: 0.7978 (m100) REVERT: L 27 SER cc_start: 0.9031 (p) cc_final: 0.8710 (t) REVERT: A 340 GLU cc_start: 0.8312 (mp0) cc_final: 0.7403 (pp20) REVERT: A 348 ASP cc_start: 0.7737 (p0) cc_final: 0.7294 (p0) REVERT: A 476 GLU cc_start: 0.7389 (tp30) cc_final: 0.7040 (tp30) outliers start: 32 outliers final: 25 residues processed: 176 average time/residue: 0.2491 time to fit residues: 64.2792 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 : 1.471 ------------------------------------------------------------------------------- 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 25 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 82 THR 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 402 LEU Chi-restraints excluded: chain A residue 427 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 147 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 98 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 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 = 0.3461 r_free = 0.3461 target = 0.123486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.102662 restraints weight = 20087.851| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.01 r_work: 0.3048 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13810 Z= 0.145 Angle : 0.572 12.487 18733 Z= 0.290 Chirality : 0.043 0.297 2048 Planarity : 0.004 0.052 2401 Dihedral : 5.925 55.973 2180 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.81 % Rotamer: Outliers : 1.99 % Allowed : 12.68 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.20), residues: 1662 helix: 2.49 (0.27), residues: 342 sheet: 0.44 (0.27), residues: 375 loop : -0.99 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 343 HIS 0.011 0.001 HIS A 18 PHE 0.017 0.002 PHE B 439 TYR 0.027 0.001 TYR L 49 ARG 0.010 0.000 ARG B 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 15) link_NAG-ASN : angle 2.89334 ( 45) link_BETA1-4 : bond 0.00212 ( 3) link_BETA1-4 : angle 1.88081 ( 9) hydrogen bonds : bond 0.04240 ( 505) hydrogen bonds : angle 4.99693 ( 1440) SS BOND : bond 0.00257 ( 20) SS BOND : angle 1.26493 ( 40) covalent geometry : bond 0.00339 (13772) covalent geometry : angle 0.55068 (18639) *********************** 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 182 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 275 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7376 (mp0) REVERT: C 340 GLU cc_start: 0.8568 (mm-30) cc_final: 0.7844 (pp20) REVERT: H 36 TRP cc_start: 0.8277 (m100) cc_final: 0.7853 (m100) REVERT: H 46 GLU cc_start: 0.8332 (tt0) cc_final: 0.8121 (pt0) REVERT: L 27 SER cc_start: 0.8933 (p) cc_final: 0.8606 (t) REVERT: L 37 GLN cc_start: 0.8431 (tt0) cc_final: 0.8157 (tt0) REVERT: A 340 GLU cc_start: 0.8374 (mp0) cc_final: 0.7406 (pp20) REVERT: A 348 ASP cc_start: 0.7711 (p0) cc_final: 0.7283 (p0) REVERT: A 476 GLU cc_start: 0.7413 (tp30) cc_final: 0.7057 (tp30) outliers start: 29 outliers final: 23 residues processed: 173 average time/residue: 0.2638 time to fit residues: 66.8740 Evaluate side-chains 172 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 1.653 ------------------------------------------------------------------------------- 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 H residue 74 SER Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 203 SER 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 471 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 355 HIS ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 HIS A 18 HIS ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.102911 restraints weight = 19922.909| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.01 r_work: 0.3049 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13810 Z= 0.157 Angle : 0.571 8.905 18733 Z= 0.291 Chirality : 0.043 0.295 2048 Planarity : 0.004 0.050 2401 Dihedral : 5.918 55.508 2180 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.99 % Allowed : 13.09 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.20), residues: 1662 helix: 2.52 (0.27), residues: 342 sheet: 0.46 (0.27), residues: 369 loop : -1.00 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 343 HIS 0.010 0.001 HIS A 18 PHE 0.017 0.002 PHE B 439 TYR 0.026 0.001 TYR L 49 ARG 0.006 0.000 ARG A 262a Details of bonding type rmsd link_NAG-ASN : bond 0.00570 ( 15) link_NAG-ASN : angle 2.83979 ( 45) link_BETA1-4 : bond 0.00201 ( 3) link_BETA1-4 : angle 1.84892 ( 9) hydrogen bonds : bond 0.04244 ( 505) hydrogen bonds : angle 4.99886 ( 1440) SS BOND : bond 0.00273 ( 20) SS BOND : angle 1.51035 ( 40) covalent geometry : bond 0.00371 (13772) covalent geometry : angle 0.54915 (18639) *********************** 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 179 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 275 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7396 (mp0) REVERT: C 340 GLU cc_start: 0.8548 (mm-30) cc_final: 0.7838 (pp20) REVERT: H 36 TRP cc_start: 0.8268 (m100) cc_final: 0.7838 (m100) REVERT: L 27 SER cc_start: 0.8959 (p) cc_final: 0.8594 (t) REVERT: A 340 GLU cc_start: 0.8400 (mp0) cc_final: 0.7422 (pp20) REVERT: A 348 ASP cc_start: 0.7707 (p0) cc_final: 0.7292 (p0) REVERT: A 476 GLU cc_start: 0.7414 (tp30) cc_final: 0.7047 (tp30) outliers start: 29 outliers final: 26 residues processed: 171 average time/residue: 0.2525 time to fit residues: 63.5081 Evaluate side-chains 174 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.507 ------------------------------------------------------------------------------- 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 355 HIS 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 H residue 74 SER Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 203 SER 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 471 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 20 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.0070 chunk 10 optimal weight: 0.0980 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 110 optimal weight: 0.0030 chunk 14 optimal weight: 0.7980 overall best weight: 0.3808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 355 HIS ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 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 = 0.3482 r_free = 0.3482 target = 0.124846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104104 restraints weight = 19957.053| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.02 r_work: 0.3075 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13810 Z= 0.103 Angle : 0.534 8.457 18733 Z= 0.273 Chirality : 0.042 0.275 2048 Planarity : 0.003 0.032 2401 Dihedral : 5.731 55.412 2180 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.59 % Favored : 97.35 % Rotamer: Outliers : 1.64 % Allowed : 13.50 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1662 helix: 2.65 (0.27), residues: 342 sheet: 0.54 (0.28), residues: 375 loop : -0.95 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 421 HIS 0.010 0.001 HIS A 18 PHE 0.012 0.001 PHE B 439 TYR 0.027 0.001 TYR L 49 ARG 0.006 0.000 ARG A 262a Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 15) link_NAG-ASN : angle 2.69272 ( 45) link_BETA1-4 : bond 0.00217 ( 3) link_BETA1-4 : angle 1.75939 ( 9) hydrogen bonds : bond 0.03943 ( 505) hydrogen bonds : angle 4.86481 ( 1440) SS BOND : bond 0.00373 ( 20) SS BOND : angle 0.96801 ( 40) covalent geometry : bond 0.00220 (13772) covalent geometry : angle 0.51495 (18639) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 275 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7438 (mp0) REVERT: C 340 GLU cc_start: 0.8556 (mm-30) cc_final: 0.7847 (pp20) REVERT: H 36 TRP cc_start: 0.8210 (m100) cc_final: 0.7799 (m100) REVERT: L 27 SER cc_start: 0.8939 (p) cc_final: 0.8580 (t) REVERT: L 32 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8101 (mm-30) REVERT: A 340 GLU cc_start: 0.8404 (mp0) cc_final: 0.7390 (pp20) REVERT: A 348 ASP cc_start: 0.7700 (p0) cc_final: 0.7290 (p0) REVERT: A 476 GLU cc_start: 0.7423 (tp30) cc_final: 0.7057 (tp30) REVERT: B 274 LEU cc_start: 0.8182 (tp) cc_final: 0.7907 (tp) outliers start: 24 outliers final: 19 residues processed: 166 average time/residue: 0.2461 time to fit residues: 60.1150 Evaluate side-chains 164 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 203 SER 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 471 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 71 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 59 optimal weight: 0.0980 chunk 82 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.102630 restraints weight = 20237.939| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.00 r_work: 0.3037 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4285 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= 0.161 Angle : 0.556 8.402 18733 Z= 0.284 Chirality : 0.043 0.280 2048 Planarity : 0.003 0.032 2401 Dihedral : 5.782 55.403 2180 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 1.37 % Allowed : 13.71 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1662 helix: 2.57 (0.27), residues: 342 sheet: 0.50 (0.27), residues: 375 loop : -0.98 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 343 HIS 0.010 0.001 HIS B 471 PHE 0.017 0.002 PHE B 439 TYR 0.025 0.001 TYR L 49 ARG 0.006 0.000 ARG A 262a Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 15) link_NAG-ASN : angle 2.67350 ( 45) link_BETA1-4 : bond 0.00250 ( 3) link_BETA1-4 : angle 1.83377 ( 9) hydrogen bonds : bond 0.04149 ( 505) hydrogen bonds : angle 4.91555 ( 1440) SS BOND : bond 0.00334 ( 20) SS BOND : angle 1.06708 ( 40) covalent geometry : bond 0.00381 (13772) covalent geometry : angle 0.53754 (18639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6346.28 seconds wall clock time: 111 minutes 3.69 seconds (6663.69 seconds total)