Starting phenix.real_space_refine on Thu Sep 18 07:24:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5e_10695/09_2025/6y5e_10695.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5e_10695/09_2025/6y5e_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6y5e_10695/09_2025/6y5e_10695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5e_10695/09_2025/6y5e_10695.map" model { file = "/net/cci-nas-00/data/ceres_data/6y5e_10695/09_2025/6y5e_10695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5e_10695/09_2025/6y5e_10695.cif" } 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-2.0-5805/lib/python3.9/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: 3.44, per 1000 atoms: 0.22 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 490.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.36 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: 3.77 Time building geometry restraints manager: 1.71 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: 21422 2.12 - 4.23: 1557 4.23 - 6.35: 115 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=" 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=" 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 angle pdb=" C HIS D 50 " pdb=" N PRO D 51 " pdb=" CA PRO D 51 " ideal model delta sigma weight residual 119.47 127.16 -7.69 1.16e+00 7.43e-01 4.40e+01 angle pdb=" C ASN K 449 " pdb=" N PRO K 450 " pdb=" CA PRO K 450 " ideal model delta sigma weight residual 119.64 126.30 -6.66 1.01e+00 9.80e-01 4.34e+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: 1874 0.067 - 0.134: 626 0.134 - 0.202: 84 0.202 - 0.269: 13 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: 2.690 Set stop_for_unknowns flag: 0.010 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.630 Find NCS groups from input model: 0.130 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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= 0.907 Angle : 1.162 10.579 23126 Z= 0.780 Chirality : 0.066 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 aren 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 covalent geometry : bond 0.01438 (16186) covalent geometry : angle 1.16215 (23123) hydrogen bonds : bond 0.16021 ( 950) hydrogen bonds : angle 5.63875 ( 2408) metal coordination : bond 0.02180 ( 4) metal coordination : angle 2.66466 ( 3) Misc. bond : bond 0.16888 ( 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 : 0.492 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: 0.7498 (tttt) REVERT: G 111 ASN cc_start: 0.8498 (t0) cc_final: 0.8277 (p0) REVERT: H 35 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8268 (mttt) REVERT: K 229 MET cc_start: 0.6850 (ttm) cc_final: 0.6515 (mmm) REVERT: K 233 GLU cc_start: 0.8056 (tt0) cc_final: 0.7590 (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: 0.1339 time to fit residues: 49.5494 Evaluate side-chains 179 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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: 1.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 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: 0.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS B 26 ASN D 64 ASN F 94 GLN K 260 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.098166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.067976 restraints weight = 44117.326| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.18 r_work: 0.3003 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 16206 Z= 0.186 Angle : 0.642 11.539 23126 Z= 0.371 Chirality : 0.038 0.163 2600 Planarity : 0.004 0.039 1867 Dihedral : 29.404 176.998 4600 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.82 % Favored : 99.09 % Rotamer: Outliers : 1.46 % Allowed : 7.40 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.25), residues: 1102 helix: 2.34 (0.19), residues: 694 sheet: -0.75 (0.59), residues: 53 loop : 0.07 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 93 TYR 0.020 0.002 TYR K 415 PHE 0.018 0.002 PHE K 471 TRP 0.009 0.002 TRP K 330 HIS 0.005 0.001 HIS K 192 Details of bonding type rmsd covalent geometry : bond 0.00414 (16186) covalent geometry : angle 0.64146 (23123) hydrogen bonds : bond 0.05246 ( 950) hydrogen bonds : angle 3.36203 ( 2408) metal coordination : bond 0.01367 ( 4) metal coordination : angle 1.67540 ( 3) Misc. bond : bond 0.00194 ( 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 232 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 THR cc_start: 0.8363 (p) cc_final: 0.8003 (t) REVERT: D 69 ASP cc_start: 0.8879 (t0) cc_final: 0.8671 (t0) REVERT: E 59 THR cc_start: 0.9286 (OUTLIER) cc_final: 0.8891 (t) REVERT: E 60 GLU cc_start: 0.8828 (pm20) cc_final: 0.8576 (pm20) REVERT: F 60 LYS cc_start: 0.9211 (tttm) cc_final: 0.8925 (ttmt) REVERT: F 89 TYR cc_start: 0.8882 (m-80) cc_final: 0.8551 (m-80) REVERT: G 16 LYS cc_start: 0.7756 (ttmt) cc_final: 0.7458 (tttt) REVERT: G 111 ASN cc_start: 0.8834 (t0) cc_final: 0.8356 (p0) REVERT: H 35 LYS cc_start: 0.8505 (mmmt) cc_final: 0.8024 (mttt) REVERT: K 325 GLU cc_start: 0.8399 (tt0) cc_final: 0.8171 (tt0) REVERT: K 359 LEU cc_start: 0.8913 (mt) cc_final: 0.8701 (mt) REVERT: K 375 TRP cc_start: 0.8125 (m100) cc_final: 0.7533 (m100) outliers start: 14 outliers final: 7 residues processed: 227 average time/residue: 0.1384 time to fit residues: 45.7987 Evaluate side-chains 186 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 178 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 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 C residue 63 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 GLN 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: 10.0000 chunk 6 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 ASN D 110 HIS H 85 ASN H 110 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.092981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.061581 restraints weight = 44657.105| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.29 r_work: 0.2833 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 16206 Z= 0.372 Angle : 0.697 7.885 23126 Z= 0.397 Chirality : 0.044 0.221 2600 Planarity : 0.005 0.046 1867 Dihedral : 29.988 175.441 4600 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.54 % Favored : 98.28 % Rotamer: Outliers : 2.40 % Allowed : 8.33 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.25), residues: 1102 helix: 2.29 (0.19), residues: 700 sheet: -0.38 (0.63), residues: 53 loop : -0.18 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 117 TYR 0.012 0.002 TYR H 41 PHE 0.013 0.002 PHE K 519 TRP 0.007 0.001 TRP K 343 HIS 0.009 0.002 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00840 (16186) covalent geometry : angle 0.69647 (23123) hydrogen bonds : bond 0.05709 ( 950) hydrogen bonds : angle 3.43680 ( 2408) metal coordination : bond 0.01296 ( 4) metal coordination : angle 1.96740 ( 3) Misc. bond : bond 0.00425 ( 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 201 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8590 (pm20) cc_final: 0.8359 (pm20) REVERT: C 91 ASP cc_start: 0.8661 (t0) cc_final: 0.8455 (t70) REVERT: D 69 ASP cc_start: 0.9100 (t0) cc_final: 0.8848 (t0) REVERT: E 59 THR cc_start: 0.9420 (OUTLIER) cc_final: 0.9113 (t) REVERT: E 60 GLU cc_start: 0.8673 (pm20) cc_final: 0.8290 (pm20) REVERT: F 60 LYS cc_start: 0.9267 (tttm) cc_final: 0.8916 (ttmt) REVERT: G 111 ASN cc_start: 0.8867 (t0) cc_final: 0.8477 (p0) REVERT: H 35 LYS cc_start: 0.8684 (mmmt) cc_final: 0.8126 (mttt) REVERT: K 359 LEU cc_start: 0.9023 (mt) cc_final: 0.8810 (mt) REVERT: K 375 TRP cc_start: 0.8415 (m100) cc_final: 0.7742 (m100) outliers start: 23 outliers final: 17 residues processed: 189 average time/residue: 0.1492 time to fit residues: 39.9936 Evaluate side-chains 175 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain G residue 96 LYS 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 H residue 72 GLU Chi-restraints excluded: chain K residue 404 CYS Chi-restraints excluded: chain K residue 429 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 91 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 85 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 = 0.3804 r_free = 0.3804 target = 0.095028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.063799 restraints weight = 44098.238| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.24 r_work: 0.2896 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16206 Z= 0.166 Angle : 0.576 7.291 23126 Z= 0.337 Chirality : 0.036 0.189 2600 Planarity : 0.004 0.034 1867 Dihedral : 29.393 176.006 4600 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.36 % Favored : 98.55 % Rotamer: Outliers : 1.46 % Allowed : 10.21 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.25), residues: 1102 helix: 2.57 (0.19), residues: 700 sheet: 0.26 (0.67), residues: 51 loop : -0.18 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 80 TYR 0.020 0.001 TYR K 470 PHE 0.010 0.001 PHE E 68 TRP 0.003 0.001 TRP K 343 HIS 0.003 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00364 (16186) covalent geometry : angle 0.57597 (23123) hydrogen bonds : bond 0.04247 ( 950) hydrogen bonds : angle 3.06317 ( 2408) metal coordination : bond 0.01010 ( 4) metal coordination : angle 1.78912 ( 3) Misc. bond : bond 0.00180 ( 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 200 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.448 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: 0.8518 (pm20) cc_final: 0.8227 (pm20) REVERT: C 42 GLU cc_start: 0.8479 (mp0) cc_final: 0.8216 (mp0) REVERT: C 91 ASP cc_start: 0.8740 (t0) cc_final: 0.8422 (t70) REVERT: E 57 LYS cc_start: 0.9075 (ttmt) cc_final: 0.8863 (ttpp) REVERT: E 59 THR cc_start: 0.9412 (OUTLIER) cc_final: 0.9189 (t) REVERT: E 60 GLU cc_start: 0.8580 (pm20) cc_final: 0.8169 (pm20) REVERT: E 126 GLN cc_start: 0.9385 (mt0) cc_final: 0.9064 (mt0) REVERT: F 60 LYS cc_start: 0.9207 (tttm) cc_final: 0.8854 (ttmt) REVERT: G 111 ASN cc_start: 0.8877 (t0) cc_final: 0.8446 (p0) REVERT: H 35 LYS cc_start: 0.8681 (mmmt) cc_final: 0.8093 (mttt) REVERT: K 359 LEU cc_start: 0.9029 (mt) cc_final: 0.8790 (mt) REVERT: K 375 TRP cc_start: 0.8462 (m100) cc_final: 0.7744 (m100) outliers start: 14 outliers final: 10 residues processed: 191 average time/residue: 0.1435 time to fit residues: 39.6120 Evaluate side-chains 176 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 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 E residue 59 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 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: 6.9990 chunk 6 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 134 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.093099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.061651 restraints weight = 44593.792| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.29 r_work: 0.2838 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 16206 Z= 0.332 Angle : 0.648 11.132 23126 Z= 0.370 Chirality : 0.041 0.200 2600 Planarity : 0.004 0.037 1867 Dihedral : 29.645 174.572 4600 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.81 % Favored : 98.09 % Rotamer: Outliers : 2.08 % Allowed : 10.62 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.25), residues: 1102 helix: 2.47 (0.19), residues: 700 sheet: 0.45 (0.69), residues: 50 loop : -0.32 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 36 TYR 0.011 0.002 TYR K 214 PHE 0.011 0.001 PHE K 265 TRP 0.002 0.001 TRP K 375 HIS 0.003 0.001 HIS K 381 Details of bonding type rmsd covalent geometry : bond 0.00751 (16186) covalent geometry : angle 0.64763 (23123) hydrogen bonds : bond 0.05059 ( 950) hydrogen bonds : angle 3.25855 ( 2408) metal coordination : bond 0.00967 ( 4) metal coordination : angle 2.14995 ( 3) Misc. bond : bond 0.00328 ( 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 184 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8562 (pm20) cc_final: 0.8212 (pm20) REVERT: D 109 LYS cc_start: 0.9043 (mtpp) cc_final: 0.8774 (tttp) REVERT: E 59 THR cc_start: 0.9376 (OUTLIER) cc_final: 0.9132 (t) REVERT: E 60 GLU cc_start: 0.8521 (pm20) cc_final: 0.8098 (pm20) REVERT: E 116 LYS cc_start: 0.9009 (ttmm) cc_final: 0.8795 (mtpp) REVERT: E 126 GLN cc_start: 0.9383 (mt0) cc_final: 0.9180 (mt0) REVERT: F 60 LYS cc_start: 0.9204 (tttm) cc_final: 0.8840 (ttmt) REVERT: G 39 ASN cc_start: 0.8123 (m110) cc_final: 0.7508 (m110) REVERT: G 111 ASN cc_start: 0.8898 (t0) cc_final: 0.8416 (p0) REVERT: H 35 LYS cc_start: 0.8711 (mmmt) cc_final: 0.8059 (mttt) REVERT: H 106 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8351 (mt-10) outliers start: 20 outliers final: 14 residues processed: 173 average time/residue: 0.1428 time to fit residues: 35.8260 Evaluate side-chains 170 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 83 LEU 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 H residue 72 GLU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain K residue 404 CYS Chi-restraints excluded: chain K residue 429 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 20 optimal weight: 0.8980 chunk 106 optimal weight: 30.0000 chunk 133 optimal weight: 30.0000 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 127 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.093668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.062535 restraints weight = 44334.631| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.23 r_work: 0.2857 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16206 Z= 0.247 Angle : 0.598 8.494 23126 Z= 0.347 Chirality : 0.038 0.220 2600 Planarity : 0.004 0.034 1867 Dihedral : 29.483 176.364 4600 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.72 % Favored : 98.19 % Rotamer: Outliers : 2.29 % Allowed : 10.83 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.25), residues: 1102 helix: 2.50 (0.19), residues: 702 sheet: 0.69 (0.71), residues: 50 loop : -0.35 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 80 TYR 0.011 0.001 TYR D 84 PHE 0.008 0.001 PHE E 68 TRP 0.005 0.001 TRP K 375 HIS 0.003 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00556 (16186) covalent geometry : angle 0.59708 (23123) hydrogen bonds : bond 0.04416 ( 950) hydrogen bonds : angle 3.12190 ( 2408) metal coordination : bond 0.00853 ( 4) metal coordination : angle 2.15918 ( 3) Misc. bond : bond 0.00149 ( 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 192 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8545 (pm20) cc_final: 0.8215 (pm20) REVERT: C 91 ASP cc_start: 0.8719 (t0) cc_final: 0.8328 (t70) REVERT: C 93 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7756 (pt0) REVERT: E 116 LYS cc_start: 0.9008 (ttmm) cc_final: 0.8794 (mtpp) REVERT: E 126 GLN cc_start: 0.9387 (mt0) cc_final: 0.9156 (mt0) REVERT: G 111 ASN cc_start: 0.8902 (t0) cc_final: 0.8441 (p0) REVERT: H 35 LYS cc_start: 0.8712 (mmmt) cc_final: 0.8089 (mttt) outliers start: 22 outliers final: 15 residues processed: 181 average time/residue: 0.1420 time to fit residues: 37.2888 Evaluate side-chains 173 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 88 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 40 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 115 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.095061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.064247 restraints weight = 43962.994| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.23 r_work: 0.2905 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16206 Z= 0.172 Angle : 0.563 9.178 23126 Z= 0.329 Chirality : 0.035 0.214 2600 Planarity : 0.003 0.033 1867 Dihedral : 29.051 179.914 4600 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.72 % Favored : 98.19 % Rotamer: Outliers : 1.04 % Allowed : 12.71 % 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 aren not related in a simple way. whole: 2.52 (0.25), residues: 1102 helix: 2.66 (0.19), residues: 701 sheet: 0.85 (0.69), residues: 51 loop : -0.29 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.011 0.001 TYR H 41 PHE 0.011 0.001 PHE E 68 TRP 0.012 0.001 TRP K 343 HIS 0.003 0.001 HIS K 381 Details of bonding type rmsd covalent geometry : bond 0.00380 (16186) covalent geometry : angle 0.56310 (23123) hydrogen bonds : bond 0.03870 ( 950) hydrogen bonds : angle 2.93754 ( 2408) metal coordination : bond 0.00701 ( 4) metal coordination : angle 1.69309 ( 3) Misc. bond : bond 0.00138 ( 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 189 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 179 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8481 (pm20) cc_final: 0.8133 (pm20) REVERT: D 94 GLU cc_start: 0.8519 (mp0) cc_final: 0.7822 (mp0) REVERT: D 106 GLU cc_start: 0.8398 (tt0) cc_final: 0.8192 (tp30) REVERT: E 116 LYS cc_start: 0.9011 (ttmm) cc_final: 0.8722 (mtpp) REVERT: E 126 GLN cc_start: 0.9354 (mt0) cc_final: 0.9110 (mt0) REVERT: G 74 ASN cc_start: 0.8855 (t0) cc_final: 0.8340 (t0) REVERT: G 111 ASN cc_start: 0.8864 (t0) cc_final: 0.8415 (p0) REVERT: H 35 LYS cc_start: 0.8744 (mmmt) cc_final: 0.8110 (mttt) REVERT: K 375 TRP cc_start: 0.8555 (m100) cc_final: 0.8131 (m100) outliers start: 10 outliers final: 8 residues processed: 182 average time/residue: 0.1373 time to fit residues: 36.6126 Evaluate side-chains 174 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 166 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 G residue 115 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain K residue 429 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 46 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 134 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 GLN G 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.093764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.062675 restraints weight = 44572.517| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.27 r_work: 0.2851 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16206 Z= 0.267 Angle : 0.607 9.833 23126 Z= 0.350 Chirality : 0.038 0.178 2600 Planarity : 0.004 0.033 1867 Dihedral : 29.346 179.335 4600 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.91 % Favored : 98.00 % Rotamer: Outliers : 1.67 % Allowed : 12.81 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.25), residues: 1102 helix: 2.51 (0.19), residues: 704 sheet: 0.99 (0.72), residues: 50 loop : -0.36 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 34 TYR 0.043 0.002 TYR K 415 PHE 0.010 0.001 PHE K 265 TRP 0.023 0.002 TRP K 343 HIS 0.003 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00604 (16186) covalent geometry : angle 0.60700 (23123) hydrogen bonds : bond 0.04515 ( 950) hydrogen bonds : angle 3.07385 ( 2408) metal coordination : bond 0.00690 ( 4) metal coordination : angle 1.90688 ( 3) Misc. bond : bond 0.00098 ( 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 170 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8549 (pm20) cc_final: 0.8208 (pm20) REVERT: C 37 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7165 (tttt) REVERT: C 93 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7734 (pt0) REVERT: E 126 GLN cc_start: 0.9394 (mt0) cc_final: 0.9120 (mt0) REVERT: G 74 ASN cc_start: 0.8928 (t0) cc_final: 0.8406 (t0) REVERT: G 111 ASN cc_start: 0.8864 (t0) cc_final: 0.8405 (p0) REVERT: H 35 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8086 (mttt) REVERT: H 106 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8297 (mt-10) outliers start: 16 outliers final: 12 residues processed: 159 average time/residue: 0.1379 time to fit residues: 32.0256 Evaluate side-chains 166 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 37 LYS Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 40 HIS 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 106 GLU Chi-restraints excluded: chain K residue 404 CYS Chi-restraints excluded: chain K residue 429 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 66 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 132 optimal weight: 40.0000 chunk 135 optimal weight: 0.4980 chunk 80 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 105 optimal weight: 30.0000 chunk 96 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.095233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.064217 restraints weight = 44477.197| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.26 r_work: 0.2892 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16206 Z= 0.173 Angle : 0.575 10.457 23126 Z= 0.333 Chirality : 0.035 0.161 2600 Planarity : 0.004 0.033 1867 Dihedral : 29.105 179.602 4600 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.81 % Favored : 98.09 % Rotamer: Outliers : 1.35 % Allowed : 13.12 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.25), residues: 1102 helix: 2.57 (0.19), residues: 702 sheet: 0.99 (0.72), residues: 50 loop : -0.30 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 100 TYR 0.035 0.002 TYR K 415 PHE 0.008 0.001 PHE K 443 TRP 0.062 0.004 TRP K 343 HIS 0.003 0.001 HIS K 192 Details of bonding type rmsd covalent geometry : bond 0.00385 (16186) covalent geometry : angle 0.57481 (23123) hydrogen bonds : bond 0.03902 ( 950) hydrogen bonds : angle 2.93718 ( 2408) metal coordination : bond 0.00648 ( 4) metal coordination : angle 1.62148 ( 3) Misc. bond : bond 0.00087 ( 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 178 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8492 (pm20) cc_final: 0.8128 (pm20) REVERT: C 37 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6786 (tttt) REVERT: C 91 ASP cc_start: 0.8640 (t0) cc_final: 0.8363 (t70) REVERT: D 43 TYR cc_start: 0.8538 (t80) cc_final: 0.8110 (t80) REVERT: D 94 GLU cc_start: 0.8516 (mp0) cc_final: 0.7784 (mp0) REVERT: D 106 GLU cc_start: 0.8422 (tt0) cc_final: 0.8189 (tp30) REVERT: D 109 LYS cc_start: 0.8991 (mtpp) cc_final: 0.8655 (tttp) REVERT: E 60 GLU cc_start: 0.8329 (pm20) cc_final: 0.7980 (pm20) REVERT: E 126 GLN cc_start: 0.9348 (mt0) cc_final: 0.9063 (mt0) REVERT: G 74 ASN cc_start: 0.8880 (t0) cc_final: 0.8360 (t0) REVERT: G 111 ASN cc_start: 0.8844 (t0) cc_final: 0.8362 (p0) REVERT: H 35 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8067 (mttt) REVERT: H 106 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8211 (mt-10) outliers start: 13 outliers final: 10 residues processed: 169 average time/residue: 0.1355 time to fit residues: 33.6663 Evaluate side-chains 171 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 88 SER 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 G residue 115 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 106 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 19 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 131 optimal weight: 0.0770 chunk 110 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 GLN F 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.096810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.066292 restraints weight = 44670.484| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.28 r_work: 0.2947 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16206 Z= 0.147 Angle : 0.572 10.867 23126 Z= 0.330 Chirality : 0.034 0.177 2600 Planarity : 0.004 0.032 1867 Dihedral : 28.770 179.379 4600 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.91 % Favored : 98.00 % Rotamer: Outliers : 0.83 % Allowed : 14.17 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.59 (0.25), residues: 1102 helix: 2.69 (0.19), residues: 698 sheet: 1.17 (0.72), residues: 51 loop : -0.22 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 100 TYR 0.027 0.001 TYR K 415 PHE 0.013 0.001 PHE K 230 TRP 0.078 0.005 TRP K 343 HIS 0.003 0.001 HIS K 192 Details of bonding type rmsd covalent geometry : bond 0.00319 (16186) covalent geometry : angle 0.57183 (23123) hydrogen bonds : bond 0.03634 ( 950) hydrogen bonds : angle 2.82797 ( 2408) metal coordination : bond 0.00688 ( 4) metal coordination : angle 1.07319 ( 3) Misc. bond : bond 0.00059 ( 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 189 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 181 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8423 (pm20) cc_final: 0.8022 (pm20) REVERT: B 89 TYR cc_start: 0.8751 (m-80) cc_final: 0.8500 (m-80) REVERT: C 37 LYS cc_start: 0.6978 (OUTLIER) cc_final: 0.6467 (tttm) REVERT: D 94 GLU cc_start: 0.8440 (mp0) cc_final: 0.7756 (mp0) REVERT: D 106 GLU cc_start: 0.8377 (tt0) cc_final: 0.8172 (tp30) REVERT: D 109 LYS cc_start: 0.8959 (mtpp) cc_final: 0.8646 (tttp) REVERT: E 60 GLU cc_start: 0.8289 (pm20) cc_final: 0.7968 (pm20) REVERT: E 126 GLN cc_start: 0.9305 (mt0) cc_final: 0.9031 (mt0) REVERT: F 28 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8703 (mp10) REVERT: F 61 VAL cc_start: 0.9115 (p) cc_final: 0.8735 (p) REVERT: F 89 TYR cc_start: 0.8787 (m-80) cc_final: 0.8570 (m-80) REVERT: G 74 ASN cc_start: 0.8793 (t0) cc_final: 0.8279 (t0) REVERT: G 111 ASN cc_start: 0.8772 (t0) cc_final: 0.8362 (p0) REVERT: H 35 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8045 (mttt) outliers start: 8 outliers final: 6 residues processed: 184 average time/residue: 0.1309 time to fit residues: 35.5248 Evaluate side-chains 176 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 169 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 G residue 115 VAL 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: 0.8980 chunk 93 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3809 r_free = 0.3809 target = 0.095674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.064846 restraints weight = 44352.353| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.27 r_work: 0.2910 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16206 Z= 0.178 Angle : 0.574 10.182 23126 Z= 0.331 Chirality : 0.035 0.175 2600 Planarity : 0.004 0.033 1867 Dihedral : 28.920 179.941 4600 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.18 % Favored : 97.73 % Rotamer: Outliers : 0.94 % Allowed : 14.48 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.25), residues: 1102 helix: 2.71 (0.19), residues: 698 sheet: 1.17 (0.71), residues: 51 loop : -0.24 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 100 TYR 0.025 0.002 TYR K 415 PHE 0.014 0.001 PHE K 253 TRP 0.048 0.003 TRP K 343 HIS 0.003 0.001 HIS K 381 Details of bonding type rmsd covalent geometry : bond 0.00396 (16186) covalent geometry : angle 0.57368 (23123) hydrogen bonds : bond 0.03890 ( 950) hydrogen bonds : angle 2.87527 ( 2408) metal coordination : bond 0.00583 ( 4) metal coordination : angle 1.09215 ( 3) Misc. bond : bond 0.00072 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4007.89 seconds wall clock time: 69 minutes 15.98 seconds (4155.98 seconds total)