Starting phenix.real_space_refine on Tue Dec 31 06:15:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5e_10695/12_2024/6y5e_10695.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5e_10695/12_2024/6y5e_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_10695/12_2024/6y5e_10695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5e_10695/12_2024/6y5e_10695.map" model { file = "/net/cci-nas-00/data/ceres_data/6y5e_10695/12_2024/6y5e_10695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5e_10695/12_2024/6y5e_10695.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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-2': 1, 'PTD:plan-1': 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-2': 1, 'PTD:plan-1': 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-2': 1, 'PTD:plan-1': 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-2': 2, 'PTD:plan-1': 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-2': 1, 'PTD:plan-1': 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-2': 1, 'PTD:plan-1': 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-2': 1, 'PTD:plan-1': 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: 9.00, per 1000 atoms: 0.59 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: 3.81 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 7.72 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: 8.01 Time building geometry restraints manager: 4.40 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 134 or resid 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 125 or resid 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 46.000 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.620 ------------------------------------------------------------------------------- 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 : 0.014 0.128 16186 Z= 0.909 Angle : 1.162 10.579 23123 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (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 TRP 0.030 0.009 TRP K 343 HIS 0.008 0.002 HIS H 110 PHE 0.045 0.009 PHE K 265 TYR 0.070 0.011 TYR E 55 ARG 0.019 0.002 ARG K 166 *********************** 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 : 1.753 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: 0.2950 time to fit residues: 109.5721 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 : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 125 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN F 94 GLN K 260 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 16186 Z= 0.224 Angle : 0.638 13.399 23123 Z= 0.369 Chirality : 0.037 0.157 2600 Planarity : 0.004 0.041 1867 Dihedral : 29.347 177.864 4600 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.64 % Favored : 99.27 % Rotamer: Outliers : 1.15 % Allowed : 7.81 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.25), residues: 1102 helix: 2.30 (0.19), residues: 695 sheet: -0.78 (0.59), residues: 53 loop : 0.10 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 330 HIS 0.005 0.001 HIS K 192 PHE 0.016 0.002 PHE K 471 TYR 0.023 0.002 TYR K 415 ARG 0.004 0.001 ARG A 50 *********************** 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 231 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 220 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 59 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8945 (t) REVERT: G 96 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8878 (ttmm) REVERT: H 35 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8425 (mttt) REVERT: K 233 GLU cc_start: 0.8557 (tt0) cc_final: 0.8252 (tm-30) REVERT: K 325 GLU cc_start: 0.7525 (tt0) cc_final: 0.7146 (tt0) REVERT: K 359 LEU cc_start: 0.7957 (mt) cc_final: 0.7653 (mt) REVERT: K 375 TRP cc_start: 0.6914 (m100) cc_final: 0.6551 (m100) outliers start: 11 outliers final: 6 residues processed: 225 average time/residue: 0.2954 time to fit residues: 95.4246 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 : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 113 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 G residue 96 LYS 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 69 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 104 optimal weight: 50.0000 chunk 85 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 125 optimal weight: 0.1980 chunk 135 optimal weight: 20.0000 chunk 111 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS C 74 ASN D 64 ASN D 110 HIS G 111 ASN H 85 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16186 Z= 0.282 Angle : 0.611 8.622 23123 Z= 0.354 Chirality : 0.038 0.186 2600 Planarity : 0.004 0.043 1867 Dihedral : 29.428 176.773 4600 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.63 % Favored : 98.28 % Rotamer: Outliers : 1.98 % Allowed : 8.44 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.25), residues: 1102 helix: 2.56 (0.19), residues: 698 sheet: -0.54 (0.64), residues: 53 loop : 0.07 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 330 HIS 0.006 0.001 HIS D 110 PHE 0.014 0.001 PHE E 68 TYR 0.012 0.001 TYR G 58 ARG 0.005 0.000 ARG H 80 *********************** 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 214 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 THR cc_start: 0.9062 (p) cc_final: 0.8807 (t) REVERT: G 96 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8966 (ttmm) REVERT: H 35 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8502 (mttt) REVERT: K 233 GLU cc_start: 0.8819 (tt0) cc_final: 0.8460 (tm-30) REVERT: K 359 LEU cc_start: 0.7932 (mt) cc_final: 0.7678 (mt) REVERT: K 375 TRP cc_start: 0.6983 (m100) cc_final: 0.6673 (m100) outliers start: 19 outliers final: 12 residues processed: 203 average time/residue: 0.3167 time to fit residues: 91.1782 Evaluate side-chains 184 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 97 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 96 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 65 optimal weight: 0.0570 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16186 Z= 0.265 Angle : 0.586 7.386 23123 Z= 0.341 Chirality : 0.037 0.213 2600 Planarity : 0.004 0.035 1867 Dihedral : 29.205 175.273 4600 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.45 % Favored : 98.46 % Rotamer: Outliers : 2.40 % Allowed : 9.90 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.25), residues: 1102 helix: 2.65 (0.19), residues: 698 sheet: 0.13 (0.71), residues: 53 loop : -0.08 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 343 HIS 0.003 0.001 HIS K 381 PHE 0.009 0.001 PHE E 68 TYR 0.014 0.001 TYR D 84 ARG 0.005 0.000 ARG F 36 *********************** 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 212 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8493 (mttt) REVERT: K 233 GLU cc_start: 0.8932 (tt0) cc_final: 0.8642 (tp30) REVERT: K 359 LEU cc_start: 0.7972 (mt) cc_final: 0.7751 (mt) REVERT: K 375 TRP cc_start: 0.6867 (m100) cc_final: 0.6584 (m100) outliers start: 23 outliers final: 14 residues processed: 198 average time/residue: 0.3072 time to fit residues: 87.7080 Evaluate side-chains 186 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 1.975 ------------------------------------------------------------------------------- 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 97 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain E residue 72 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16186 Z= 0.271 Angle : 0.582 7.851 23123 Z= 0.340 Chirality : 0.037 0.222 2600 Planarity : 0.004 0.034 1867 Dihedral : 29.153 175.133 4600 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.00 % Favored : 97.91 % Rotamer: Outliers : 1.88 % Allowed : 10.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.25), residues: 1102 helix: 2.62 (0.19), residues: 700 sheet: 0.64 (0.71), residues: 51 loop : -0.30 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 343 HIS 0.003 0.001 HIS K 381 PHE 0.009 0.001 PHE E 68 TYR 0.010 0.001 TYR D 84 ARG 0.006 0.000 ARG D 34 *********************** 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 202 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 57 LYS cc_start: 0.9395 (ttmt) cc_final: 0.9174 (ttpp) REVERT: G 39 ASN cc_start: 0.7508 (m110) cc_final: 0.7092 (m110) REVERT: H 35 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8459 (mttt) REVERT: K 233 GLU cc_start: 0.9045 (tt0) cc_final: 0.8740 (tp30) REVERT: K 359 LEU cc_start: 0.8019 (mt) cc_final: 0.7802 (mt) REVERT: K 375 TRP cc_start: 0.6741 (m100) cc_final: 0.6475 (m100) outliers start: 18 outliers final: 12 residues processed: 191 average time/residue: 0.3152 time to fit residues: 86.5247 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 : 1.340 ------------------------------------------------------------------------------- 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 97 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain E residue 72 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 133 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 0.004 0.040 16186 Z= 0.217 Angle : 0.564 8.933 23123 Z= 0.330 Chirality : 0.035 0.235 2600 Planarity : 0.004 0.033 1867 Dihedral : 28.986 179.391 4600 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.45 % Favored : 98.46 % Rotamer: Outliers : 1.67 % Allowed : 11.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.25), residues: 1102 helix: 2.69 (0.19), residues: 698 sheet: 0.95 (0.73), residues: 51 loop : -0.27 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP K 343 HIS 0.002 0.001 HIS K 381 PHE 0.010 0.001 PHE K 265 TYR 0.015 0.001 TYR D 84 ARG 0.004 0.000 ARG D 34 *********************** 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 200 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 94 GLU cc_start: 0.8041 (mp0) cc_final: 0.7607 (mp0) REVERT: E 57 LYS cc_start: 0.9370 (ttmt) cc_final: 0.9088 (ttpp) REVERT: F 60 LYS cc_start: 0.9280 (ttmt) cc_final: 0.9041 (tttp) REVERT: G 39 ASN cc_start: 0.7418 (m110) cc_final: 0.7116 (m-40) REVERT: H 35 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8456 (mttt) REVERT: K 233 GLU cc_start: 0.9077 (tt0) cc_final: 0.8756 (tp30) REVERT: K 359 LEU cc_start: 0.8012 (mt) cc_final: 0.7806 (mt) REVERT: K 375 TRP cc_start: 0.6754 (m100) cc_final: 0.6518 (m100) outliers start: 16 outliers final: 13 residues processed: 189 average time/residue: 0.2963 time to fit residues: 80.9259 Evaluate side-chains 185 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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 E residue 40 HIS Chi-restraints excluded: chain E residue 72 VAL 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 K residue 429 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 133 optimal weight: 30.0000 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 G 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 16186 Z= 0.467 Angle : 0.669 8.726 23123 Z= 0.380 Chirality : 0.042 0.184 2600 Planarity : 0.005 0.044 1867 Dihedral : 29.727 179.797 4600 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.27 % Favored : 97.64 % Rotamer: Outliers : 2.40 % Allowed : 11.04 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.25), residues: 1102 helix: 2.36 (0.19), residues: 701 sheet: 1.18 (0.74), residues: 51 loop : -0.45 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.005 TRP K 343 HIS 0.003 0.001 HIS K 381 PHE 0.011 0.002 PHE K 265 TYR 0.016 0.002 TYR D 84 ARG 0.007 0.001 ARG C 30 *********************** 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 191 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 93 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7669 (pt0) REVERT: E 57 LYS cc_start: 0.9385 (ttmt) cc_final: 0.9097 (ttpp) REVERT: E 87 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8669 (t) REVERT: G 39 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7314 (m-40) REVERT: G 74 ASN cc_start: 0.8954 (t0) cc_final: 0.8478 (t0) REVERT: H 106 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: K 233 GLU cc_start: 0.9081 (tt0) cc_final: 0.8767 (tp30) outliers start: 23 outliers final: 19 residues processed: 176 average time/residue: 0.3116 time to fit residues: 78.7851 Evaluate side-chains 175 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 81 THR 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 58 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 72 VAL 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 F residue 61 VAL Chi-restraints excluded: chain G residue 39 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 104 optimal weight: 40.0000 chunk 120 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 GLN H 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16186 Z= 0.191 Angle : 0.582 10.408 23123 Z= 0.336 Chirality : 0.035 0.247 2600 Planarity : 0.004 0.034 1867 Dihedral : 29.107 179.445 4600 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.45 % Favored : 98.46 % Rotamer: Outliers : 1.46 % Allowed : 12.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.25), residues: 1102 helix: 2.57 (0.19), residues: 697 sheet: 1.13 (0.74), residues: 51 loop : -0.38 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.005 TRP K 343 HIS 0.002 0.001 HIS K 381 PHE 0.008 0.001 PHE A 68 TYR 0.047 0.001 TYR K 415 ARG 0.005 0.000 ARG H 80 *********************** 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 185 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 94 GLU cc_start: 0.8078 (mp0) cc_final: 0.7632 (mp0) REVERT: F 60 LYS cc_start: 0.9262 (ttmt) cc_final: 0.9019 (tttp) REVERT: G 39 ASN cc_start: 0.7641 (m110) cc_final: 0.7182 (m-40) REVERT: G 74 ASN cc_start: 0.8792 (t0) cc_final: 0.8304 (t0) REVERT: H 35 LYS cc_start: 0.8887 (mmmt) cc_final: 0.8540 (mttt) REVERT: K 233 GLU cc_start: 0.9103 (tt0) cc_final: 0.8786 (tp30) outliers start: 14 outliers final: 12 residues processed: 176 average time/residue: 0.3018 time to fit residues: 77.1490 Evaluate side-chains 168 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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 C residue 63 ILE Chi-restraints excluded: chain E residue 72 VAL 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 352 LEU 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 127 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 126 GLN F 76 HIS F 94 GLN G 69 ASN H 85 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 16186 Z= 0.387 Angle : 0.649 10.719 23123 Z= 0.366 Chirality : 0.039 0.257 2600 Planarity : 0.004 0.056 1867 Dihedral : 29.337 178.601 4600 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.18 % Favored : 97.73 % Rotamer: Outliers : 1.77 % Allowed : 12.81 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.25), residues: 1102 helix: 2.49 (0.19), residues: 698 sheet: 1.27 (0.75), residues: 50 loop : -0.43 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP K 343 HIS 0.003 0.001 HIS K 381 PHE 0.013 0.001 PHE K 265 TYR 0.035 0.002 TYR K 415 ARG 0.008 0.001 ARG H 100 *********************** 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 171 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 74 ASN cc_start: 0.8906 (t0) cc_final: 0.8440 (t0) REVERT: H 35 LYS cc_start: 0.8952 (mmmt) cc_final: 0.8543 (mttt) REVERT: K 233 GLU cc_start: 0.9118 (tt0) cc_final: 0.8796 (tp30) outliers start: 17 outliers final: 16 residues processed: 161 average time/residue: 0.3039 time to fit residues: 71.0324 Evaluate side-chains 168 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 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 72 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 134 GLU 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 352 LEU 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 79 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 76 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16186 Z= 0.232 Angle : 0.592 11.475 23123 Z= 0.339 Chirality : 0.035 0.243 2600 Planarity : 0.004 0.033 1867 Dihedral : 29.097 179.414 4600 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.54 % Favored : 98.37 % Rotamer: Outliers : 1.46 % Allowed : 13.33 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.25), residues: 1102 helix: 2.56 (0.19), residues: 699 sheet: 1.29 (0.75), residues: 50 loop : -0.40 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP K 343 HIS 0.004 0.001 HIS F 76 PHE 0.011 0.001 PHE K 265 TYR 0.029 0.001 TYR K 415 ARG 0.008 0.000 ARG H 100 ********************** 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 172 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 60 LYS cc_start: 0.9279 (ttmt) cc_final: 0.9045 (tttp) REVERT: G 74 ASN cc_start: 0.8848 (t0) cc_final: 0.8376 (t0) REVERT: H 35 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8527 (mttt) REVERT: K 233 GLU cc_start: 0.9116 (tt0) cc_final: 0.8799 (tp30) outliers start: 14 outliers final: 13 residues processed: 163 average time/residue: 0.2935 time to fit residues: 69.7053 Evaluate side-chains 168 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 C residue 63 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 134 GLU 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 352 LEU 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 33 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 GLN E 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.095835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.065374 restraints weight = 44490.560| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.24 r_work: 0.2926 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16186 Z= 0.188 Angle : 0.578 11.188 23123 Z= 0.331 Chirality : 0.034 0.238 2600 Planarity : 0.004 0.032 1867 Dihedral : 28.854 179.856 4600 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.91 % Favored : 98.00 % Rotamer: Outliers : 1.25 % Allowed : 13.54 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.25), residues: 1102 helix: 2.68 (0.19), residues: 697 sheet: 1.42 (0.75), residues: 50 loop : -0.38 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP K 343 HIS 0.002 0.001 HIS K 192 PHE 0.012 0.001 PHE K 265 TYR 0.025 0.001 TYR K 415 ARG 0.008 0.000 ARG H 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2905.18 seconds wall clock time: 53 minutes 56.22 seconds (3236.22 seconds total)