Starting phenix.real_space_refine on Sat Sep 12 09:19:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6y5e_10695/09_2026/6y5e_10695.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5e_10695/09_2026/6y5e_10695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6y5e_10695/09_2026/6y5e_10695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5e_10695/09_2026/6y5e_10695.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6y5e_10695/09_2026/6y5e_10695.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6y5e_10695/09_2026/6y5e_10695.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y5e_10695/09_2026/6y5e_10695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5e_10695/09_2026/6y5e_10695.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 306 5.49 5 S 27 5.16 5 C 8699 2.51 5 N 2815 2.21 5 O 3444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15292 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3119 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "J" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3154 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "K" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2980 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-1': 2, 'PTD:plan-2': 2} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "K" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'PTD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14165 SG CYS K 396 77.673 20.971 33.960 0.00 21.29 S ATOM 14171 SG CYS K 397 79.534 19.817 37.046 0.00 21.76 S ATOM 14230 SG CYS K 404 81.302 21.908 34.439 0.00600.00 S Time building chain proxies: 3.61, per 1000 atoms: 0.24 Number of scatterers: 15292 At special positions: 0 Unit cell: (121.26, 126.42, 122.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 27 16.00 P 306 15.00 O 3444 8.00 N 2815 7.00 C 8699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 546.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 390 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 404 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 396 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 397 " Number of angles added : 3 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 14 sheets defined 64.6% alpha, 7.9% beta 153 base pairs and 281 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'B' and resid 25 through 30 removed outlier: 3.521A pdb=" N GLN B 28 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.037A pdb=" N VAL B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 47 through 74 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 106 through 125 Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 removed outlier: 3.507A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 4.076A pdb=" N VAL F 61 " --> pdb=" O GLY F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 28 through 35 Processing helix chain 'G' and resid 36 through 40 removed outlier: 3.679A pdb=" N ASN G 39 " --> pdb=" O ARG G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 74 Processing helix chain 'G' and resid 80 through 91 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 50 removed outlier: 3.511A pdb=" N GLN H 48 " --> pdb=" O LYS H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 106 through 123 Processing helix chain 'K' and resid 162 through 175 Processing helix chain 'K' and resid 176 through 178 No H-bonds generated for 'chain 'K' and resid 176 through 178' Processing helix chain 'K' and resid 179 through 200 Processing helix chain 'K' and resid 260 through 264 removed outlier: 3.998A pdb=" N GLN K 264 " --> pdb=" O PRO K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 289 removed outlier: 3.569A pdb=" N ASN K 289 " --> pdb=" O LYS K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 335 Processing helix chain 'K' and resid 345 through 353 Processing helix chain 'K' and resid 379 through 388 Processing helix chain 'K' and resid 399 through 403 Processing helix chain 'K' and resid 405 through 424 Processing helix chain 'K' and resid 434 through 449 Processing helix chain 'K' and resid 451 through 458 removed outlier: 3.756A pdb=" N ASP K 456 " --> pdb=" O SER K 453 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG K 457 " --> pdb=" O GLN K 454 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LYS K 458 " --> pdb=" O TRP K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 478 Processing helix chain 'K' and resid 497 through 513 Processing helix chain 'K' and resid 514 through 515 No H-bonds generated for 'chain 'K' and resid 514 through 515' Processing helix chain 'K' and resid 516 through 520 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.998A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.048A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.861A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.012A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB2, first strand: chain 'K' and resid 207 through 208 removed outlier: 7.221A pdb=" N LEU K 322 " --> pdb=" O PRO K 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 207 through 208 Processing sheet with id=AB4, first strand: chain 'K' and resid 266 through 267 Processing sheet with id=AB5, first strand: chain 'K' and resid 364 through 366 569 hydrogen bonds defined for protein. 1626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 391 hydrogen bonds 782 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 281 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2598 1.32 - 1.45: 5560 1.45 - 1.57: 7372 1.57 - 1.69: 612 1.69 - 1.82: 44 Bond restraints: 16186 Sorted by residual: bond pdb=" C4 PTD C 201 " pdb=" C5 PTD C 201 " ideal model delta sigma weight residual 1.501 1.615 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" CD ARG E 64 " pdb=" NE ARG E 64 " ideal model delta sigma weight residual 1.458 1.378 0.080 1.40e-02 5.10e+03 3.25e+01 bond pdb=" CD ARG F 36 " pdb=" NE ARG F 36 " ideal model delta sigma weight residual 1.458 1.385 0.073 1.40e-02 5.10e+03 2.71e+01 bond pdb=" CD ARG A 64 " pdb=" NE ARG A 64 " ideal model delta sigma weight residual 1.458 1.390 0.068 1.40e-02 5.10e+03 2.37e+01 bond pdb=" CD ARG B 93 " pdb=" NE ARG B 93 " ideal model delta sigma weight residual 1.458 1.391 0.067 1.40e-02 5.10e+03 2.32e+01 ... (remaining 16181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 21409 2.12 - 4.23: 1578 4.23 - 6.35: 107 6.35 - 8.46: 26 8.46 - 10.58: 3 Bond angle restraints: 23123 Sorted by residual: angle pdb=" N GLY G 38 " pdb=" CA GLY G 38 " pdb=" C GLY G 38 " ideal model delta sigma weight residual 115.30 104.72 10.58 1.39e+00 5.18e-01 5.79e+01 angle pdb=" C3' DT J 60 " pdb=" O3' DT J 60 " pdb=" P DT J 61 " ideal model delta sigma weight residual 119.70 127.93 -8.23 1.20e+00 6.94e-01 4.71e+01 angle pdb=" C LEU G 117 " pdb=" N PRO G 118 " pdb=" CA PRO G 118 " ideal model delta sigma weight residual 119.85 126.73 -6.88 1.01e+00 9.80e-01 4.64e+01 angle pdb=" C3' DT I 150 " pdb=" O3' DT I 150 " pdb=" P DG I 151 " ideal model delta sigma weight residual 119.70 127.84 -8.14 1.20e+00 6.94e-01 4.60e+01 angle pdb=" N GLY C 38 " pdb=" CA GLY C 38 " pdb=" C GLY C 38 " ideal model delta sigma weight residual 115.30 105.98 9.32 1.39e+00 5.18e-01 4.50e+01 ... (remaining 23118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.13: 7531 34.13 - 68.25: 1419 68.25 - 102.38: 31 102.38 - 136.50: 0 136.50 - 170.63: 5 Dihedral angle restraints: 8986 sinusoidal: 5726 harmonic: 3260 Sorted by residual: dihedral pdb=" CA SER K 305 " pdb=" C SER K 305 " pdb=" N PRO K 306 " pdb=" CA PRO K 306 " ideal model delta harmonic sigma weight residual 180.00 153.69 26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" C4' DC I 81 " pdb=" C3' DC I 81 " pdb=" O3' DC I 81 " pdb=" P DC I 82 " ideal model delta sinusoidal sigma weight residual 220.00 49.37 170.63 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I 150 " pdb=" C3' DT I 150 " pdb=" O3' DT I 150 " pdb=" P DG I 151 " ideal model delta sinusoidal sigma weight residual 220.00 51.04 168.96 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 8983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1865 0.067 - 0.134: 616 0.134 - 0.202: 98 0.202 - 0.269: 18 0.269 - 0.336: 3 Chirality restraints: 2600 Sorted by residual: chirality pdb=" CA LYS G 37 " pdb=" N LYS G 37 " pdb=" C LYS G 37 " pdb=" CB LYS G 37 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA CYS K 397 " pdb=" N CYS K 397 " pdb=" C CYS K 397 " pdb=" CB CYS K 397 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA LYS B 32 " pdb=" N LYS B 32 " pdb=" C LYS B 32 " pdb=" CB LYS B 32 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 2597 not shown) Planarity restraints: 1867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 55 " -0.070 2.00e-02 2.50e+03 3.81e-02 2.91e+01 pdb=" CG TYR E 55 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR E 55 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR E 55 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR E 55 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR E 55 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR E 55 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 55 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 37 " 0.027 2.00e-02 2.50e+03 5.38e-02 2.90e+01 pdb=" C LYS G 37 " -0.093 2.00e-02 2.50e+03 pdb=" O LYS G 37 " 0.036 2.00e-02 2.50e+03 pdb=" N GLY G 38 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 358 " 0.067 2.00e-02 2.50e+03 3.56e-02 2.54e+01 pdb=" CG TYR K 358 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR K 358 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR K 358 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR K 358 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR K 358 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR K 358 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR K 358 " 0.049 2.00e-02 2.50e+03 ... (remaining 1864 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 5967 2.92 - 3.42: 13487 3.42 - 3.91: 29568 3.91 - 4.41: 35830 4.41 - 4.90: 46908 Nonbonded interactions: 131760 Sorted by model distance: nonbonded pdb=" N GLY G 38 " pdb=" N ASN G 39 " model vdw 2.429 2.560 nonbonded pdb=" O PHE K 491 " pdb=" NZ LYS K 501 " model vdw 2.455 3.120 nonbonded pdb=" N GLY C 38 " pdb=" N ASN C 39 " model vdw 2.468 2.560 nonbonded pdb=" O ASN G 39 " pdb=" C TYR G 40 " model vdw 2.488 3.270 nonbonded pdb=" N ALA K 273 " pdb=" OE1 GLU K 373 " model vdw 2.493 3.120 ... (remaining 131755 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 39 through 201) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 103) } ncs_group { reference = (chain 'C' and resid 12 through 118) selection = (chain 'G' and resid 12 through 118) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 33 through 301) } 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=0.00 max=1.00 mean=0.93 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.360 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.015 0.171 16206 Z= 0.965 Angle : 1.157 10.579 23126 Z= 0.860 Chirality : 0.067 0.336 2600 Planarity : 0.010 0.054 1867 Dihedral : 25.715 170.629 6878 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.91 % Favored : 98.00 % Rotamer: Outliers : 0.21 % Allowed : 0.31 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.23), residues: 1102 helix: 0.67 (0.18), residues: 690 sheet: -0.43 (0.63), residues: 54 loop : 0.14 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG K 166 TYR 0.070 0.011 TYR E 55 PHE 0.045 0.009 PHE K 265 TRP 0.030 0.009 TRP K 343 HIS 0.008 0.002 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.01414 / 0.81 (16186) covalent geometry : angle 1.15696 / 0.86 (23123) hydrogen bonds : bond 0.16021 / 10.83 ( 950) hydrogen bonds : angle 5.63875 / 4.14 ( 2408) metal coordination : bond 0.02180 / 1.45 ( 4) metal coordination : angle 2.66466 / 1.94 ( 3) Misc. bond : bond 0.16888 / 11.47 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 249 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9245 (p) cc_final: 0.8999 (p) REVERT: C 93 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7182 (mt-10) REVERT: G 16 LYS cc_start: 0.7726 (ttmt) cc_final: 0.7497 (tttt) REVERT: G 111 ASN cc_start: 0.8498 (t0) cc_final: 0.8279 (p0) REVERT: H 35 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8267 (mttt) REVERT: K 229 MET cc_start: 0.6850 (ttm) cc_final: 0.6514 (mmm) REVERT: K 233 GLU cc_start: 0.8056 (tt0) cc_final: 0.7589 (tm-30) REVERT: K 325 GLU cc_start: 0.7556 (tt0) cc_final: 0.7162 (tm-30) REVERT: K 359 LEU cc_start: 0.8157 (mt) cc_final: 0.7746 (mt) outliers start: 2 outliers final: 0 residues processed: 249 average time/residue: 0.1167 time to fit residues: 43.7987 Evaluate side-chains 180 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 10.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS B 26 ASN D 64 ASN K 260 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.096115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.065370 restraints weight = 43887.268| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.20 r_work: 0.2936 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16206 Z= 0.259 Angle : 0.825 11.716 23126 Z= 0.447 Chirality : 0.050 0.339 2600 Planarity : 0.005 0.047 1867 Dihedral : 29.990 178.029 4600 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.27 % Favored : 98.64 % Rotamer: Outliers : 1.35 % Allowed : 8.02 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.24), residues: 1102 helix: 1.97 (0.19), residues: 695 sheet: -1.01 (0.59), residues: 55 loop : -0.10 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 36 TYR 0.023 0.002 TYR K 415 PHE 0.018 0.002 PHE K 519 TRP 0.015 0.002 TRP K 330 HIS 0.006 0.001 HIS K 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.26 (16186) covalent geometry : angle 0.82530 / 0.45 (23123) hydrogen bonds : bond 0.06584 / 4.49 ( 950) hydrogen bonds : angle 3.72646 / 2.73 ( 2408) metal coordination : bond 0.01314 / 0.85 ( 4) metal coordination : angle 1.08187 / 0.77 ( 3) Misc. bond : bond 0.01346 / 0.91 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 LYS cc_start: 0.6563 (tppp) cc_final: 0.6333 (ttpt) REVERT: C 77 THR cc_start: 0.8486 (p) cc_final: 0.8079 (t) REVERT: E 60 GLU cc_start: 0.8843 (pm20) cc_final: 0.8620 (pm20) REVERT: E 130 ARG cc_start: 0.8980 (ttm170) cc_final: 0.8733 (tpp80) REVERT: F 60 LYS cc_start: 0.9273 (tttm) cc_final: 0.9007 (ttmt) REVERT: G 16 LYS cc_start: 0.7751 (ttmt) cc_final: 0.7458 (tttt) REVERT: G 75 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8810 (mmtm) REVERT: G 111 ASN cc_start: 0.8843 (t0) cc_final: 0.8341 (p0) REVERT: H 35 LYS cc_start: 0.8532 (mmmt) cc_final: 0.7988 (mttt) REVERT: K 359 LEU cc_start: 0.8878 (mt) cc_final: 0.8643 (mt) REVERT: K 375 TRP cc_start: 0.8102 (m100) cc_final: 0.7380 (m100) outliers start: 13 outliers final: 10 residues processed: 203 average time/residue: 0.1209 time to fit residues: 36.0463 Evaluate side-chains 182 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 72 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 30.0000 chunk 6 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 128 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 chunk 101 optimal weight: 50.0000 chunk 62 optimal weight: 0.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.094753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.064021 restraints weight = 44436.904| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.17 r_work: 0.2897 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 16206 Z= 0.241 Angle : 0.712 11.312 23126 Z= 0.396 Chirality : 0.046 0.296 2600 Planarity : 0.005 0.038 1867 Dihedral : 30.140 179.145 4600 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.27 % Favored : 98.64 % Rotamer: Outliers : 2.29 % Allowed : 7.92 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.25), residues: 1102 helix: 2.35 (0.19), residues: 695 sheet: -0.70 (0.63), residues: 53 loop : -0.17 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 36 TYR 0.013 0.002 TYR F 52 PHE 0.012 0.002 PHE K 471 TRP 0.004 0.001 TRP K 343 HIS 0.011 0.001 HIS K 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.24 (16186) covalent geometry : angle 0.71179 / 0.40 (23123) hydrogen bonds : bond 0.05832 / 3.98 ( 950) hydrogen bonds : angle 3.44437 / 2.52 ( 2408) metal coordination : bond 0.01436 / 0.93 ( 4) metal coordination : angle 1.43685 / 1.04 ( 3) Misc. bond : bond 0.00928 / 0.58 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8351 (pm20) cc_final: 0.8067 (pm20) REVERT: C 14 LYS cc_start: 0.6907 (tppp) cc_final: 0.6703 (ttpt) REVERT: C 77 THR cc_start: 0.9089 (p) cc_final: 0.8805 (t) REVERT: C 91 ASP cc_start: 0.8584 (t0) cc_final: 0.8325 (t70) REVERT: D 69 ASP cc_start: 0.9080 (t0) cc_final: 0.8853 (t0) REVERT: D 106 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8302 (tt0) REVERT: E 59 THR cc_start: 0.9373 (OUTLIER) cc_final: 0.8992 (t) REVERT: E 60 GLU cc_start: 0.8805 (pm20) cc_final: 0.8471 (pm20) REVERT: E 130 ARG cc_start: 0.9042 (ttm170) cc_final: 0.8763 (tpp80) REVERT: F 60 LYS cc_start: 0.9210 (tttm) cc_final: 0.8894 (ttmt) REVERT: F 89 TYR cc_start: 0.8909 (m-80) cc_final: 0.8701 (m-80) REVERT: G 111 ASN cc_start: 0.8846 (t0) cc_final: 0.8393 (p0) REVERT: H 35 LYS cc_start: 0.8616 (mmmt) cc_final: 0.8049 (mttt) REVERT: H 85 ASN cc_start: 0.9310 (m-40) cc_final: 0.9101 (m110) REVERT: H 87 ARG cc_start: 0.8959 (mmt-90) cc_final: 0.8720 (mmt-90) REVERT: K 359 LEU cc_start: 0.8966 (mt) cc_final: 0.8706 (mt) REVERT: K 375 TRP cc_start: 0.8354 (m100) cc_final: 0.7638 (m100) outliers start: 22 outliers final: 13 residues processed: 194 average time/residue: 0.1216 time to fit residues: 34.7162 Evaluate side-chains 179 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain K residue 404 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 91 optimal weight: 20.0000 chunk 73 optimal weight: 50.0000 chunk 5 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.095777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.064577 restraints weight = 44372.140| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.23 r_work: 0.2921 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16206 Z= 0.152 Angle : 0.639 8.398 23126 Z= 0.364 Chirality : 0.043 0.277 2600 Planarity : 0.004 0.037 1867 Dihedral : 29.887 179.852 4600 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.27 % Favored : 98.64 % Rotamer: Outliers : 1.56 % Allowed : 9.90 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.25), residues: 1102 helix: 2.57 (0.19), residues: 695 sheet: -0.70 (0.63), residues: 53 loop : -0.15 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 80 TYR 0.011 0.001 TYR H 41 PHE 0.011 0.001 PHE K 471 TRP 0.010 0.001 TRP K 343 HIS 0.003 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (16186) covalent geometry : angle 0.63928 / 0.36 (23123) hydrogen bonds : bond 0.04891 / 3.34 ( 950) hydrogen bonds : angle 3.19857 / 2.33 ( 2408) metal coordination : bond 0.01241 / 0.79 ( 4) metal coordination : angle 1.50393 / 1.18 ( 3) Misc. bond : bond 0.00455 / 0.31 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8396 (pm20) cc_final: 0.8039 (pm20) REVERT: B 85 MET cc_start: 0.9370 (mmm) cc_final: 0.9041 (mmp) REVERT: B 89 TYR cc_start: 0.8754 (m-80) cc_final: 0.8416 (m-80) REVERT: C 77 THR cc_start: 0.9110 (p) cc_final: 0.8858 (t) REVERT: C 91 ASP cc_start: 0.8637 (t0) cc_final: 0.8235 (t70) REVERT: D 69 ASP cc_start: 0.9050 (t0) cc_final: 0.8795 (t0) REVERT: D 106 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8200 (tt0) REVERT: E 59 THR cc_start: 0.9386 (OUTLIER) cc_final: 0.9033 (t) REVERT: E 60 GLU cc_start: 0.8766 (pm20) cc_final: 0.8363 (pm20) REVERT: E 126 GLN cc_start: 0.9326 (mt0) cc_final: 0.9052 (mt0) REVERT: E 130 ARG cc_start: 0.9063 (ttm170) cc_final: 0.8774 (tpp80) REVERT: F 60 LYS cc_start: 0.9155 (tttm) cc_final: 0.8813 (ttmt) REVERT: G 111 ASN cc_start: 0.8857 (t0) cc_final: 0.8404 (p0) REVERT: H 35 LYS cc_start: 0.8638 (mmmt) cc_final: 0.8101 (mttt) REVERT: K 359 LEU cc_start: 0.8960 (mt) cc_final: 0.8711 (mt) REVERT: K 375 TRP cc_start: 0.8367 (m100) cc_final: 0.7666 (m100) outliers start: 15 outliers final: 9 residues processed: 193 average time/residue: 0.1179 time to fit residues: 33.5179 Evaluate side-chains 181 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain K residue 404 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 112 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 115 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 89 optimal weight: 30.0000 chunk 134 optimal weight: 9.9990 chunk 9 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.095121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.063827 restraints weight = 44149.451| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.24 r_work: 0.2898 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16206 Z= 0.184 Angle : 0.658 11.119 23126 Z= 0.368 Chirality : 0.044 0.285 2600 Planarity : 0.004 0.035 1867 Dihedral : 29.862 178.922 4600 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.81 % Favored : 98.09 % Rotamer: Outliers : 1.88 % Allowed : 10.00 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.25), residues: 1102 helix: 2.55 (0.19), residues: 698 sheet: -0.36 (0.65), residues: 53 loop : -0.15 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 80 TYR 0.010 0.001 TYR H 41 PHE 0.011 0.001 PHE E 68 TRP 0.017 0.002 TRP K 343 HIS 0.018 0.001 HIS K 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (16186) covalent geometry : angle 0.65783 / 0.37 (23123) hydrogen bonds : bond 0.05007 / 3.41 ( 950) hydrogen bonds : angle 3.19992 / 2.32 ( 2408) metal coordination : bond 0.01130 / 0.72 ( 4) metal coordination : angle 1.70874 / 1.32 ( 3) Misc. bond : bond 0.00308 / 0.21 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8498 (pm20) cc_final: 0.8095 (pm20) REVERT: D 69 ASP cc_start: 0.9067 (t0) cc_final: 0.8821 (t0) REVERT: D 106 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8254 (tt0) REVERT: E 59 THR cc_start: 0.9418 (OUTLIER) cc_final: 0.9110 (t) REVERT: E 60 GLU cc_start: 0.8681 (pm20) cc_final: 0.8318 (pm20) REVERT: E 126 GLN cc_start: 0.9389 (mt0) cc_final: 0.9167 (mt0) REVERT: E 130 ARG cc_start: 0.9078 (ttm170) cc_final: 0.8783 (tpp80) REVERT: F 60 LYS cc_start: 0.9204 (tttm) cc_final: 0.8857 (ttmt) REVERT: G 111 ASN cc_start: 0.8868 (t0) cc_final: 0.8450 (p0) REVERT: H 35 LYS cc_start: 0.8695 (mmmt) cc_final: 0.8140 (mttt) REVERT: K 359 LEU cc_start: 0.8986 (mt) cc_final: 0.8722 (mt) REVERT: K 375 TRP cc_start: 0.8397 (m100) cc_final: 0.7662 (m100) outliers start: 18 outliers final: 12 residues processed: 189 average time/residue: 0.1160 time to fit residues: 32.6016 Evaluate side-chains 182 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain K residue 404 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 20 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 133 optimal weight: 30.0000 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 115 optimal weight: 40.0000 chunk 69 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 40.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.095917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.065141 restraints weight = 44190.893| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.22 r_work: 0.2930 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 16206 Z= 0.140 Angle : 0.615 9.719 23126 Z= 0.354 Chirality : 0.042 0.278 2600 Planarity : 0.004 0.032 1867 Dihedral : 29.637 178.591 4600 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.72 % Favored : 98.19 % Rotamer: Outliers : 1.77 % Allowed : 10.73 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.25), residues: 1102 helix: 2.63 (0.19), residues: 699 sheet: -0.26 (0.66), residues: 53 loop : -0.16 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 80 TYR 0.027 0.001 TYR K 470 PHE 0.010 0.001 PHE K 471 TRP 0.024 0.002 TRP K 343 HIS 0.012 0.001 HIS K 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (16186) covalent geometry : angle 0.61456 / 0.35 (23123) hydrogen bonds : bond 0.04551 / 3.10 ( 950) hydrogen bonds : angle 3.07225 / 2.23 ( 2408) metal coordination : bond 0.00944 / 0.59 ( 4) metal coordination : angle 1.77543 / 1.34 ( 3) Misc. bond : bond 0.00415 / 0.32 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8471 (pm20) cc_final: 0.8019 (pm20) REVERT: C 37 LYS cc_start: 0.6650 (tppt) cc_final: 0.6422 (mmtm) REVERT: C 91 ASP cc_start: 0.8493 (t0) cc_final: 0.8132 (t70) REVERT: D 69 ASP cc_start: 0.9051 (t0) cc_final: 0.8844 (t0) REVERT: D 94 GLU cc_start: 0.8597 (mp0) cc_final: 0.7755 (mp0) REVERT: D 106 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8235 (tt0) REVERT: E 59 THR cc_start: 0.9409 (OUTLIER) cc_final: 0.9120 (t) REVERT: E 60 GLU cc_start: 0.8655 (pm20) cc_final: 0.8264 (pm20) REVERT: E 126 GLN cc_start: 0.9344 (mt0) cc_final: 0.9114 (mt0) REVERT: E 130 ARG cc_start: 0.9094 (ttm170) cc_final: 0.8783 (tpp80) REVERT: F 85 MET cc_start: 0.9176 (mmm) cc_final: 0.8953 (mmm) REVERT: G 111 ASN cc_start: 0.8856 (t0) cc_final: 0.8428 (p0) REVERT: H 35 LYS cc_start: 0.8723 (mmmt) cc_final: 0.8160 (mttt) REVERT: K 359 LEU cc_start: 0.8988 (mt) cc_final: 0.8707 (mt) REVERT: K 375 TRP cc_start: 0.8420 (m100) cc_final: 0.7651 (m100) outliers start: 17 outliers final: 12 residues processed: 197 average time/residue: 0.1242 time to fit residues: 36.2639 Evaluate side-chains 190 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 72 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 115 optimal weight: 30.0000 chunk 82 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 40.0000 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 64 ASN F 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.094579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.063025 restraints weight = 43616.868| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.23 r_work: 0.2882 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16206 Z= 0.203 Angle : 0.648 9.645 23126 Z= 0.365 Chirality : 0.044 0.290 2600 Planarity : 0.004 0.032 1867 Dihedral : 29.770 179.706 4600 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.91 % Favored : 98.00 % Rotamer: Outliers : 2.08 % Allowed : 10.73 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.25), residues: 1102 helix: 2.59 (0.19), residues: 701 sheet: -0.17 (0.67), residues: 53 loop : -0.16 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 30 TYR 0.019 0.002 TYR K 470 PHE 0.011 0.001 PHE E 68 TRP 0.061 0.005 TRP K 343 HIS 0.008 0.001 HIS K 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 (16186) covalent geometry : angle 0.64744 / 0.36 (23123) hydrogen bonds : bond 0.05092 / 3.46 ( 950) hydrogen bonds : angle 3.16079 / 2.29 ( 2408) metal coordination : bond 0.00988 / 0.61 ( 4) metal coordination : angle 1.77423 / 1.34 ( 3) Misc. bond : bond 0.00279 / 0.23 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8523 (pm20) cc_final: 0.8104 (pm20) REVERT: C 91 ASP cc_start: 0.8530 (t0) cc_final: 0.8218 (t70) REVERT: D 69 ASP cc_start: 0.9133 (t0) cc_final: 0.8897 (t0) REVERT: D 102 LEU cc_start: 0.9527 (mt) cc_final: 0.9286 (mm) REVERT: D 106 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8307 (tp30) REVERT: E 59 THR cc_start: 0.9426 (OUTLIER) cc_final: 0.9199 (t) REVERT: E 60 GLU cc_start: 0.8557 (pm20) cc_final: 0.8172 (pm20) REVERT: E 126 GLN cc_start: 0.9393 (mt0) cc_final: 0.9168 (mt0) REVERT: E 130 ARG cc_start: 0.9098 (ttm170) cc_final: 0.8798 (tpp80) REVERT: G 111 ASN cc_start: 0.8872 (t0) cc_final: 0.8468 (p0) REVERT: H 35 LYS cc_start: 0.8744 (mmmt) cc_final: 0.8183 (mttt) REVERT: H 106 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8377 (mt-10) REVERT: K 359 LEU cc_start: 0.9032 (mt) cc_final: 0.8776 (mt) REVERT: K 375 TRP cc_start: 0.8427 (m100) cc_final: 0.7657 (m100) outliers start: 20 outliers final: 17 residues processed: 176 average time/residue: 0.1163 time to fit residues: 30.5183 Evaluate side-chains 180 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain K residue 404 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 46 optimal weight: 0.0870 chunk 81 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 134 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 106 optimal weight: 0.0020 chunk 137 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 overall best weight: 1.1970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 94 GLN H 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.095265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.064405 restraints weight = 44215.633| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.22 r_work: 0.2914 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16206 Z= 0.143 Angle : 0.618 10.373 23126 Z= 0.352 Chirality : 0.042 0.279 2600 Planarity : 0.003 0.030 1867 Dihedral : 29.614 178.154 4600 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.63 % Favored : 98.28 % Rotamer: Outliers : 1.56 % Allowed : 11.77 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.25), residues: 1102 helix: 2.65 (0.19), residues: 701 sheet: -0.01 (0.69), residues: 53 loop : -0.20 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 100 TYR 0.015 0.001 TYR D 84 PHE 0.009 0.001 PHE E 68 TRP 0.035 0.003 TRP K 343 HIS 0.006 0.001 HIS K 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (16186) covalent geometry : angle 0.61734 / 0.35 (23123) hydrogen bonds : bond 0.04505 / 3.06 ( 950) hydrogen bonds : angle 3.03280 / 2.20 ( 2408) metal coordination : bond 0.00868 / 0.54 ( 4) metal coordination : angle 1.80459 / 1.33 ( 3) Misc. bond : bond 0.00269 / 0.16 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8494 (pm20) cc_final: 0.8052 (pm20) REVERT: C 91 ASP cc_start: 0.8487 (t0) cc_final: 0.8123 (t70) REVERT: D 69 ASP cc_start: 0.9107 (t0) cc_final: 0.8873 (t0) REVERT: D 94 GLU cc_start: 0.8575 (mp0) cc_final: 0.7714 (mp0) REVERT: E 57 LYS cc_start: 0.9072 (ttmt) cc_final: 0.8866 (ttpp) REVERT: E 130 ARG cc_start: 0.9106 (ttm170) cc_final: 0.8791 (tpp80) REVERT: G 111 ASN cc_start: 0.8868 (t0) cc_final: 0.8397 (p0) REVERT: H 35 LYS cc_start: 0.8752 (mmmt) cc_final: 0.8176 (mttt) REVERT: K 359 LEU cc_start: 0.9034 (mt) cc_final: 0.8784 (mt) REVERT: K 375 TRP cc_start: 0.8445 (m100) cc_final: 0.7716 (m100) outliers start: 15 outliers final: 12 residues processed: 189 average time/residue: 0.1237 time to fit residues: 34.3376 Evaluate side-chains 178 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain K residue 404 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 135 optimal weight: 0.5980 chunk 80 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.094991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.063795 restraints weight = 43950.775| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.23 r_work: 0.2895 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16206 Z= 0.172 Angle : 0.633 10.315 23126 Z= 0.357 Chirality : 0.042 0.278 2600 Planarity : 0.004 0.029 1867 Dihedral : 29.621 178.414 4600 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.81 % Favored : 98.09 % Rotamer: Outliers : 1.56 % Allowed : 12.19 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.25), residues: 1102 helix: 2.59 (0.19), residues: 701 sheet: 0.06 (0.69), residues: 53 loop : -0.25 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 130 TYR 0.016 0.001 TYR D 84 PHE 0.009 0.001 PHE E 68 TRP 0.028 0.002 TRP K 343 HIS 0.005 0.001 HIS K 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (16186) covalent geometry : angle 0.63309 / 0.36 (23123) hydrogen bonds : bond 0.04724 / 3.22 ( 950) hydrogen bonds : angle 3.08562 / 2.23 ( 2408) metal coordination : bond 0.00836 / 0.52 ( 4) metal coordination : angle 1.77903 / 1.30 ( 3) Misc. bond : bond 0.00228 / 0.13 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8519 (pm20) cc_final: 0.8092 (pm20) REVERT: D 69 ASP cc_start: 0.9104 (t0) cc_final: 0.8876 (t0) REVERT: D 106 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8344 (tt0) REVERT: E 57 LYS cc_start: 0.9132 (ttmt) cc_final: 0.8914 (ttpp) REVERT: E 130 ARG cc_start: 0.9109 (ttm170) cc_final: 0.8798 (tpp80) REVERT: G 39 ASN cc_start: 0.7510 (m110) cc_final: 0.7227 (m-40) REVERT: G 111 ASN cc_start: 0.8862 (t0) cc_final: 0.8421 (p0) REVERT: H 35 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8191 (mttt) REVERT: K 359 LEU cc_start: 0.9058 (mt) cc_final: 0.8807 (mt) REVERT: K 375 TRP cc_start: 0.8482 (m100) cc_final: 0.7826 (m100) outliers start: 15 outliers final: 15 residues processed: 182 average time/residue: 0.1233 time to fit residues: 32.7482 Evaluate side-chains 182 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain K residue 404 CYS Chi-restraints excluded: chain K residue 518 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 19 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 75 optimal weight: 20.0000 chunk 1 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.095714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.064408 restraints weight = 44392.943| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.27 r_work: 0.2914 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16206 Z= 0.143 Angle : 0.624 11.109 23126 Z= 0.353 Chirality : 0.042 0.280 2600 Planarity : 0.003 0.030 1867 Dihedral : 29.496 179.221 4600 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.63 % Favored : 98.28 % Rotamer: Outliers : 1.56 % Allowed : 12.71 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.25), residues: 1102 helix: 2.61 (0.20), residues: 701 sheet: 0.08 (0.69), residues: 53 loop : -0.20 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 80 TYR 0.019 0.001 TYR K 215 PHE 0.009 0.001 PHE E 68 TRP 0.023 0.002 TRP K 343 HIS 0.005 0.001 HIS K 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (16186) covalent geometry : angle 0.62385 / 0.35 (23123) hydrogen bonds : bond 0.04406 / 3.00 ( 950) hydrogen bonds : angle 3.02963 / 2.18 ( 2408) metal coordination : bond 0.00766 / 0.47 ( 4) metal coordination : angle 1.77231 / 1.27 ( 3) Misc. bond : bond 0.00125 / 0.09 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8510 (pm20) cc_final: 0.8132 (pm20) REVERT: C 37 LYS cc_start: 0.6653 (OUTLIER) cc_final: 0.6154 (tttm) REVERT: C 91 ASP cc_start: 0.8582 (t0) cc_final: 0.8323 (t70) REVERT: D 69 ASP cc_start: 0.9085 (t0) cc_final: 0.8860 (t0) REVERT: D 94 GLU cc_start: 0.8563 (mp0) cc_final: 0.7733 (mp0) REVERT: D 106 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8310 (tt0) REVERT: E 57 LYS cc_start: 0.9111 (ttmt) cc_final: 0.8792 (ttpp) REVERT: E 60 GLU cc_start: 0.8318 (pm20) cc_final: 0.7972 (pm20) REVERT: E 130 ARG cc_start: 0.9101 (ttm170) cc_final: 0.8794 (tpp80) REVERT: G 111 ASN cc_start: 0.8827 (t0) cc_final: 0.8397 (p0) REVERT: H 35 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8222 (mttt) REVERT: K 359 LEU cc_start: 0.9075 (mt) cc_final: 0.8842 (mt) REVERT: K 375 TRP cc_start: 0.8511 (m100) cc_final: 0.7874 (m100) outliers start: 15 outliers final: 13 residues processed: 182 average time/residue: 0.1333 time to fit residues: 35.0246 Evaluate side-chains 182 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 123 LYS Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain K residue 404 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 108 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 136 optimal weight: 40.0000 chunk 129 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 26 optimal weight: 0.0060 chunk 58 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 overall best weight: 3.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.093900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.062397 restraints weight = 44148.463| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.23 r_work: 0.2855 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16206 Z= 0.251 Angle : 0.707 10.316 23126 Z= 0.384 Chirality : 0.045 0.279 2600 Planarity : 0.004 0.040 1867 Dihedral : 29.822 178.204 4600 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.00 % Favored : 97.91 % Rotamer: Outliers : 1.98 % Allowed : 11.98 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.25), residues: 1102 helix: 2.45 (0.19), residues: 701 sheet: 0.17 (0.70), residues: 53 loop : -0.30 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 30 TYR 0.017 0.001 TYR D 84 PHE 0.011 0.001 PHE E 68 TRP 0.024 0.002 TRP K 343 HIS 0.005 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.25 (16186) covalent geometry : angle 0.70713 / 0.38 (23123) hydrogen bonds : bond 0.05459 / 3.70 ( 950) hydrogen bonds : angle 3.25111 / 2.34 ( 2408) metal coordination : bond 0.00801 / 0.48 ( 4) metal coordination : angle 1.89416 / 1.35 ( 3) Misc. bond : bond 0.00105 / 0.09 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3375.51 seconds wall clock time: 58 minutes 20.16 seconds (3500.16 seconds total)