Starting phenix.real_space_refine on Tue Feb 11 05:46:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a7o_15222/02_2025/8a7o_15222.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a7o_15222/02_2025/8a7o_15222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a7o_15222/02_2025/8a7o_15222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a7o_15222/02_2025/8a7o_15222.map" model { file = "/net/cci-nas-00/data/ceres_data/8a7o_15222/02_2025/8a7o_15222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a7o_15222/02_2025/8a7o_15222.cif" } resolution = 3.0 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2790 2.51 5 N 714 2.21 5 O 840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4362 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 727 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "B" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 727 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Restraints were copied for chains: C, E, D, F Time building chain proxies: 2.68, per 1000 atoms: 0.61 Number of scatterers: 4362 At special positions: 0 Unit cell: (122.84, 109.56, 34.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 840 8.00 N 714 7.00 C 2790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 500.9 milliseconds 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 46.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 12 removed outlier: 6.494A pdb=" N GLN A 8 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER C 11 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR A 10 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN C 8 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N SER E 11 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR C 10 " --> pdb=" O SER E 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 23 Processing sheet with id=AA4, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.222A pdb=" N TYR A 26 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR C 26 " --> pdb=" O VAL E 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 33 through 39 removed outlier: 6.868A pdb=" N ASP C 34 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP E 34 " --> pdb=" O SER C 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 42 through 46 removed outlier: 7.032A pdb=" N ILE C 46 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE E 46 " --> pdb=" O ARG C 45 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.660A pdb=" N VAL A 49 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL C 49 " --> pdb=" O GLU E 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 60 through 66 removed outlier: 6.346A pdb=" N SER A 61 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU C 64 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N TYR A 63 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR C 66 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 65 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N SER C 61 " --> pdb=" O PHE E 62 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU E 64 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR C 63 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N TYR E 66 " --> pdb=" O TYR C 63 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU C 65 " --> pdb=" O TYR E 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AB1, first strand: chain 'A' and resid 73 through 78 Processing sheet with id=AB2, first strand: chain 'A' and resid 81 through 88 removed outlier: 6.528A pdb=" N ARG A 81 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N HIS C 84 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASN A 83 " --> pdb=" O HIS C 84 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N THR C 86 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A 85 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N SER C 88 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 87 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG C 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N HIS E 84 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASN C 83 " --> pdb=" O HIS E 84 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N THR E 86 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C 85 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N SER E 88 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C 87 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 91 through 92 removed outlier: 6.559A pdb=" N LYS A 91 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS C 91 " --> pdb=" O ILE E 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 7 through 12 Processing sheet with id=AB5, first strand: chain 'B' and resid 15 through 17 Processing sheet with id=AB6, first strand: chain 'B' and resid 20 through 22 removed outlier: 6.947A pdb=" N ASN D 21 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN F 21 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 33 through 39 removed outlier: 6.919A pdb=" N ASP D 34 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP F 34 " --> pdb=" O SER D 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 42 through 44 Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 53 removed outlier: 9.168A pdb=" N LYS B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 10.212A pdb=" N HIS D 51 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU B 50 " --> pdb=" O HIS D 51 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ASP D 53 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER B 52 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N LYS D 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N HIS F 51 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU D 50 " --> pdb=" O HIS F 51 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ASP F 53 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER D 52 " --> pdb=" O ASP F 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 59 through 66 removed outlier: 7.096A pdb=" N TYR D 63 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU B 64 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU D 65 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR B 66 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TYR F 63 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU D 64 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU F 65 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR D 66 " --> pdb=" O LEU F 65 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AC3, first strand: chain 'B' and resid 73 through 78 Processing sheet with id=AC4, first strand: chain 'B' and resid 81 through 83 removed outlier: 6.639A pdb=" N VAL B 82 " --> pdb=" O ASN D 83 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL D 82 " --> pdb=" O ASN F 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 86 through 88 removed outlier: 6.475A pdb=" N LEU B 87 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU D 87 " --> pdb=" O SER F 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 91 through 92 removed outlier: 6.740A pdb=" N LYS B 91 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS D 91 " --> pdb=" O ILE F 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 86 hydrogen bonds defined for protein. 258 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1392 1.34 - 1.46: 977 1.46 - 1.58: 2089 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 4482 Sorted by residual: bond pdb=" C THR C 71 " pdb=" N PRO C 72 " ideal model delta sigma weight residual 1.333 1.342 -0.009 1.20e-02 6.94e+03 5.69e-01 bond pdb=" C ASN F 42 " pdb=" N GLY F 43 " ideal model delta sigma weight residual 1.322 1.332 -0.010 1.41e-02 5.03e+03 5.30e-01 bond pdb=" C TYR F 78 " pdb=" N ALA F 79 " ideal model delta sigma weight residual 1.333 1.342 -0.009 1.30e-02 5.92e+03 5.09e-01 bond pdb=" C THR A 71 " pdb=" N PRO A 72 " ideal model delta sigma weight residual 1.333 1.341 -0.008 1.20e-02 6.94e+03 5.00e-01 bond pdb=" C ASN D 42 " pdb=" N GLY D 43 " ideal model delta sigma weight residual 1.322 1.332 -0.010 1.41e-02 5.03e+03 4.77e-01 ... (remaining 4477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 5823 1.16 - 2.31: 190 2.31 - 3.47: 41 3.47 - 4.62: 15 4.62 - 5.78: 3 Bond angle restraints: 6072 Sorted by residual: angle pdb=" N LYS D 48 " pdb=" CA LYS D 48 " pdb=" C LYS D 48 " ideal model delta sigma weight residual 108.13 111.44 -3.31 1.72e+00 3.38e-01 3.69e+00 angle pdb=" N LYS F 48 " pdb=" CA LYS F 48 " pdb=" C LYS F 48 " ideal model delta sigma weight residual 108.13 111.41 -3.28 1.72e+00 3.38e-01 3.64e+00 angle pdb=" N LYS B 48 " pdb=" CA LYS B 48 " pdb=" C LYS B 48 " ideal model delta sigma weight residual 108.13 111.40 -3.27 1.72e+00 3.38e-01 3.61e+00 angle pdb=" C LYS F 19 " pdb=" N SER F 20 " pdb=" CA SER F 20 " ideal model delta sigma weight residual 121.62 118.42 3.20 1.83e+00 2.99e-01 3.07e+00 angle pdb=" C LYS B 19 " pdb=" N SER B 20 " pdb=" CA SER B 20 " ideal model delta sigma weight residual 121.62 118.46 3.16 1.83e+00 2.99e-01 2.98e+00 ... (remaining 6067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.02: 2469 13.02 - 26.03: 138 26.03 - 39.05: 24 39.05 - 52.07: 15 52.07 - 65.08: 18 Dihedral angle restraints: 2664 sinusoidal: 1086 harmonic: 1578 Sorted by residual: dihedral pdb=" CA ARG D 12 " pdb=" CB ARG D 12 " pdb=" CG ARG D 12 " pdb=" CD ARG D 12 " ideal model delta sinusoidal sigma weight residual 180.00 125.74 54.26 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CA ARG F 12 " pdb=" CB ARG F 12 " pdb=" CG ARG F 12 " pdb=" CD ARG F 12 " ideal model delta sinusoidal sigma weight residual 180.00 125.80 54.20 3 1.50e+01 4.44e-03 9.26e+00 dihedral pdb=" CA ARG B 12 " pdb=" CB ARG B 12 " pdb=" CG ARG B 12 " pdb=" CD ARG B 12 " ideal model delta sinusoidal sigma weight residual 180.00 125.83 54.17 3 1.50e+01 4.44e-03 9.26e+00 ... (remaining 2661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 303 0.026 - 0.052: 226 0.052 - 0.078: 53 0.078 - 0.104: 19 0.104 - 0.130: 41 Chirality restraints: 642 Sorted by residual: chirality pdb=" CA VAL E 49 " pdb=" N VAL E 49 " pdb=" C VAL E 49 " pdb=" CB VAL E 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA PRO F 14 " pdb=" N PRO F 14 " pdb=" C PRO F 14 " pdb=" CB PRO F 14 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 639 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 13 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO D 14 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 13 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO B 14 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 14 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 14 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 13 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO F 14 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 14 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 14 " 0.025 5.00e-02 4.00e+02 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 15 2.60 - 3.18: 3356 3.18 - 3.75: 5788 3.75 - 4.33: 8473 4.33 - 4.90: 13786 Nonbonded interactions: 31418 Sorted by model distance: nonbonded pdb=" SG CYS C 25 " pdb=" SG CYS C 80 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS E 25 " pdb=" SG CYS E 80 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS D 25 " pdb=" SG CYS D 80 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS F 25 " pdb=" SG CYS F 80 " model vdw 2.031 3.760 nonbonded pdb=" O LYS B 58 " pdb=" N LYS D 58 " model vdw 2.418 3.120 ... (remaining 31413 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.970 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 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:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.002 0.020 4482 Z= 0.158 Angle : 0.549 5.776 6072 Z= 0.316 Chirality : 0.045 0.130 642 Planarity : 0.004 0.044 780 Dihedral : 11.280 65.084 1638 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.59 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 60 HIS 0.004 0.001 HIS E 13 PHE 0.008 0.001 PHE B 22 TYR 0.006 0.001 TYR E 63 ARG 0.001 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.479 Fit side-chains REVERT: A 45 ARG cc_start: 0.7959 (mtt-85) cc_final: 0.6058 (tmm160) REVERT: B 12 ARG cc_start: 0.7181 (mtt180) cc_final: 0.6096 (tpm170) REVERT: B 34 ASP cc_start: 0.6576 (m-30) cc_final: 0.6303 (m-30) REVERT: B 91 LYS cc_start: 0.7899 (tttt) cc_final: 0.7432 (tttt) REVERT: C 50 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7810 (mt-10) REVERT: D 36 GLU cc_start: 0.7948 (tt0) cc_final: 0.7743 (tm-30) REVERT: D 91 LYS cc_start: 0.7892 (tttt) cc_final: 0.7435 (tttp) REVERT: E 6 MET cc_start: 0.8252 (mtp) cc_final: 0.7935 (mtm) REVERT: F 36 GLU cc_start: 0.8002 (tt0) cc_final: 0.7748 (tm-30) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 1.8520 time to fit residues: 153.6243 Evaluate side-chains 45 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 30.0000 chunk 36 optimal weight: 0.1980 chunk 20 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 overall best weight: 6.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 13 HIS A 31 HIS A 42 ASN B 13 HIS B 89 GLN C 8 GLN C 13 HIS C 31 HIS C 42 ASN D 89 GLN E 8 GLN E 13 HIS E 42 ASN F 89 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.086005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.071223 restraints weight = 11066.690| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.28 r_work: 0.3450 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4482 Z= 0.318 Angle : 0.629 6.299 6072 Z= 0.350 Chirality : 0.048 0.151 642 Planarity : 0.004 0.042 780 Dihedral : 4.982 17.724 576 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.61 % Allowed : 7.83 % Favored : 90.56 % 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: -3.57 (0.30), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.23), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 60 HIS 0.005 0.001 HIS A 13 PHE 0.016 0.002 PHE D 22 TYR 0.015 0.002 TYR E 67 ARG 0.003 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.541 Fit side-chains REVERT: A 45 ARG cc_start: 0.8605 (mtt-85) cc_final: 0.7010 (ppt170) REVERT: A 67 TYR cc_start: 0.8619 (m-80) cc_final: 0.8306 (m-80) REVERT: B 91 LYS cc_start: 0.7409 (tttt) cc_final: 0.6986 (tttt) REVERT: C 50 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8278 (mt-10) REVERT: D 12 ARG cc_start: 0.7439 (mtt180) cc_final: 0.7145 (mmt-90) REVERT: D 36 GLU cc_start: 0.8537 (tt0) cc_final: 0.8209 (tm-30) REVERT: D 91 LYS cc_start: 0.7262 (tttt) cc_final: 0.6798 (tttp) REVERT: E 6 MET cc_start: 0.8606 (mtp) cc_final: 0.8370 (mtm) REVERT: F 36 GLU cc_start: 0.8601 (tt0) cc_final: 0.8281 (tm-30) REVERT: F 44 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: F 47 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7717 (tm-30) REVERT: F 75 LYS cc_start: 0.7694 (mtpm) cc_final: 0.6666 (mmpt) REVERT: F 87 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8131 (mt) outliers start: 8 outliers final: 3 residues processed: 64 average time/residue: 1.9803 time to fit residues: 129.8953 Evaluate side-chains 51 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 87 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 40 optimal weight: 40.0000 chunk 8 optimal weight: 50.0000 chunk 22 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.084640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.069769 restraints weight = 11228.408| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.27 r_work: 0.3434 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4482 Z= 0.341 Angle : 0.636 4.622 6072 Z= 0.354 Chirality : 0.048 0.143 642 Planarity : 0.004 0.038 780 Dihedral : 5.136 17.202 576 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.61 % Allowed : 9.64 % Favored : 88.76 % 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: -3.57 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 60 HIS 0.005 0.001 HIS B 31 PHE 0.018 0.002 PHE D 22 TYR 0.013 0.002 TYR C 66 ARG 0.003 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.502 Fit side-chains REVERT: A 45 ARG cc_start: 0.8517 (mtt-85) cc_final: 0.6960 (ppt170) REVERT: A 67 TYR cc_start: 0.8663 (m-80) cc_final: 0.8398 (m-80) REVERT: B 36 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: C 50 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8253 (mt-10) REVERT: D 12 ARG cc_start: 0.7555 (mtt180) cc_final: 0.7275 (mmt-90) REVERT: D 36 GLU cc_start: 0.8577 (tt0) cc_final: 0.8350 (tt0) REVERT: E 6 MET cc_start: 0.8593 (mtp) cc_final: 0.8333 (mtm) REVERT: F 36 GLU cc_start: 0.8557 (tt0) cc_final: 0.8163 (tm-30) REVERT: F 44 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: F 47 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7500 (tm-30) REVERT: F 75 LYS cc_start: 0.7698 (mtpm) cc_final: 0.6691 (mmpt) outliers start: 8 outliers final: 2 residues processed: 56 average time/residue: 2.0142 time to fit residues: 115.6167 Evaluate side-chains 46 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 44 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 50.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.083779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.068914 restraints weight = 11196.713| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.25 r_work: 0.3402 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4482 Z= 0.410 Angle : 0.665 5.408 6072 Z= 0.371 Chirality : 0.049 0.144 642 Planarity : 0.004 0.035 780 Dihedral : 5.260 16.826 576 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.20 % Allowed : 10.44 % Favored : 88.35 % 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: -3.59 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 60 HIS 0.005 0.001 HIS F 31 PHE 0.018 0.002 PHE D 22 TYR 0.016 0.002 TYR E 67 ARG 0.002 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.538 Fit side-chains REVERT: B 36 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8435 (tt0) REVERT: C 50 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8287 (mt-10) REVERT: D 12 ARG cc_start: 0.7604 (mpt180) cc_final: 0.7234 (mmt-90) REVERT: D 36 GLU cc_start: 0.8593 (tt0) cc_final: 0.8382 (tt0) REVERT: E 6 MET cc_start: 0.8599 (mtp) cc_final: 0.8389 (mtm) REVERT: F 12 ARG cc_start: 0.5235 (pmt170) cc_final: 0.5011 (pmt170) REVERT: F 44 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: F 75 LYS cc_start: 0.7806 (mtpm) cc_final: 0.6796 (mmpt) outliers start: 6 outliers final: 2 residues processed: 47 average time/residue: 2.0977 time to fit residues: 101.0767 Evaluate side-chains 41 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 44 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 8 optimal weight: 50.0000 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 1 optimal weight: 0.0000 chunk 46 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 overall best weight: 5.5992 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.083861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.069249 restraints weight = 11584.944| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.28 r_work: 0.3435 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4482 Z= 0.275 Angle : 0.611 4.553 6072 Z= 0.337 Chirality : 0.046 0.137 642 Planarity : 0.003 0.032 780 Dihedral : 5.130 16.706 576 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 1.20 % Allowed : 11.04 % Favored : 87.75 % 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: -3.53 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 60 HIS 0.004 0.001 HIS B 31 PHE 0.019 0.002 PHE D 22 TYR 0.014 0.002 TYR E 67 ARG 0.002 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.511 Fit side-chains REVERT: A 45 ARG cc_start: 0.8465 (mtt-85) cc_final: 0.6936 (ppt170) REVERT: B 36 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8419 (tt0) REVERT: C 47 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7551 (tp30) REVERT: C 50 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8252 (mt-10) REVERT: D 12 ARG cc_start: 0.7594 (mpt180) cc_final: 0.7243 (mmt-90) REVERT: D 36 GLU cc_start: 0.8563 (tt0) cc_final: 0.8353 (tt0) REVERT: D 74 GLU cc_start: 0.8185 (pt0) cc_final: 0.7668 (pt0) REVERT: E 47 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7764 (tm-30) REVERT: F 44 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: F 47 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: F 75 LYS cc_start: 0.7611 (mtpm) cc_final: 0.6553 (mmpt) outliers start: 6 outliers final: 2 residues processed: 48 average time/residue: 1.9768 time to fit residues: 97.3236 Evaluate side-chains 45 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 47 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.084428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.069830 restraints weight = 11437.068| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.24 r_work: 0.3418 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 4482 Z= 0.368 Angle : 0.651 6.574 6072 Z= 0.361 Chirality : 0.048 0.140 642 Planarity : 0.004 0.033 780 Dihedral : 5.221 16.418 576 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.20 % Allowed : 11.24 % Favored : 87.55 % 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: -3.58 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 60 HIS 0.005 0.001 HIS F 31 PHE 0.018 0.002 PHE D 22 TYR 0.015 0.002 TYR E 67 ARG 0.002 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.464 Fit side-chains REVERT: B 36 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: C 50 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8269 (mt-10) REVERT: D 12 ARG cc_start: 0.7632 (mpt180) cc_final: 0.7336 (mmt-90) REVERT: D 74 GLU cc_start: 0.8148 (pt0) cc_final: 0.7624 (pt0) REVERT: E 47 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7944 (tm-30) REVERT: F 36 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8429 (tt0) REVERT: F 44 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: F 47 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: F 75 LYS cc_start: 0.7691 (mtpm) cc_final: 0.6609 (mmpt) outliers start: 6 outliers final: 2 residues processed: 46 average time/residue: 2.0568 time to fit residues: 96.9505 Evaluate side-chains 43 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 47 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.0270 chunk 33 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 8 optimal weight: 40.0000 chunk 26 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 24 optimal weight: 30.0000 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 overall best weight: 6.4046 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.084882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.070232 restraints weight = 11436.288| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.27 r_work: 0.3432 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4482 Z= 0.308 Angle : 0.634 5.276 6072 Z= 0.350 Chirality : 0.047 0.138 642 Planarity : 0.003 0.032 780 Dihedral : 5.168 16.244 576 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.41 % Allowed : 11.85 % Favored : 86.75 % 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: -3.59 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 60 HIS 0.005 0.001 HIS B 31 PHE 0.019 0.002 PHE D 22 TYR 0.015 0.002 TYR E 67 ARG 0.002 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.562 Fit side-chains REVERT: B 36 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: C 50 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8233 (mt-10) REVERT: D 74 GLU cc_start: 0.8123 (pt0) cc_final: 0.7633 (pt0) REVERT: E 47 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7946 (tm-30) REVERT: E 50 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8525 (mt-10) REVERT: F 44 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: F 47 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7386 (tm-30) REVERT: F 75 LYS cc_start: 0.7658 (mtpm) cc_final: 0.6605 (mmpt) outliers start: 7 outliers final: 2 residues processed: 46 average time/residue: 1.9673 time to fit residues: 93.0497 Evaluate side-chains 42 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 47 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 overall best weight: 5.9590 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.084839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.070261 restraints weight = 11330.649| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.26 r_work: 0.3434 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4482 Z= 0.289 Angle : 0.621 5.100 6072 Z= 0.342 Chirality : 0.047 0.136 642 Planarity : 0.003 0.031 780 Dihedral : 5.128 16.091 576 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.41 % Allowed : 12.85 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 60 HIS 0.004 0.001 HIS D 31 PHE 0.018 0.002 PHE D 22 TYR 0.015 0.002 TYR E 67 ARG 0.001 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.508 Fit side-chains REVERT: B 36 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8420 (tt0) REVERT: C 47 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7516 (tm-30) REVERT: C 50 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8243 (mt-10) REVERT: D 74 GLU cc_start: 0.8114 (pt0) cc_final: 0.7611 (pt0) REVERT: E 47 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7930 (tm-30) REVERT: E 50 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8509 (mt-10) REVERT: F 12 ARG cc_start: 0.5071 (pmt170) cc_final: 0.4307 (pmt-80) REVERT: F 36 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8399 (tt0) REVERT: F 44 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: F 47 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: F 74 GLU cc_start: 0.8383 (pt0) cc_final: 0.7906 (pt0) REVERT: F 75 LYS cc_start: 0.7692 (mtpm) cc_final: 0.6649 (mmpt) outliers start: 7 outliers final: 3 residues processed: 45 average time/residue: 1.9751 time to fit residues: 91.3322 Evaluate side-chains 44 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 47 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.084535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.070039 restraints weight = 11535.295| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.26 r_work: 0.3440 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4482 Z= 0.277 Angle : 0.625 5.806 6072 Z= 0.344 Chirality : 0.046 0.136 642 Planarity : 0.003 0.031 780 Dihedral : 5.100 16.154 576 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.41 % Allowed : 13.45 % Favored : 85.14 % 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: -3.59 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 60 HIS 0.005 0.001 HIS B 31 PHE 0.018 0.002 PHE D 22 TYR 0.018 0.002 TYR E 67 ARG 0.001 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.456 Fit side-chains REVERT: A 6 MET cc_start: 0.8526 (mtp) cc_final: 0.8256 (mtp) REVERT: B 36 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8416 (tt0) REVERT: C 47 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7537 (tm-30) REVERT: C 50 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8358 (mt-10) REVERT: D 6 MET cc_start: 0.7748 (ttp) cc_final: 0.7466 (ptm) REVERT: D 74 GLU cc_start: 0.8090 (pt0) cc_final: 0.7600 (pt0) REVERT: E 47 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7858 (tm-30) REVERT: F 12 ARG cc_start: 0.5074 (pmt170) cc_final: 0.4347 (pmt-80) REVERT: F 14 PRO cc_start: 0.5193 (Cg_exo) cc_final: 0.4934 (Cg_endo) REVERT: F 36 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: F 44 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: F 47 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: F 74 GLU cc_start: 0.8357 (pt0) cc_final: 0.7965 (pt0) REVERT: F 75 LYS cc_start: 0.7675 (mtpm) cc_final: 0.6652 (mmpt) REVERT: F 81 ARG cc_start: 0.8351 (mtt180) cc_final: 0.7270 (mmt180) outliers start: 7 outliers final: 3 residues processed: 45 average time/residue: 1.9442 time to fit residues: 89.9142 Evaluate side-chains 45 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 50.0000 chunk 6 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 40 optimal weight: 50.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.084362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.069826 restraints weight = 11324.877| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.25 r_work: 0.3424 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4482 Z= 0.345 Angle : 0.658 6.783 6072 Z= 0.364 Chirality : 0.047 0.138 642 Planarity : 0.003 0.032 780 Dihedral : 5.177 16.184 576 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.41 % Allowed : 13.45 % Favored : 85.14 % 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: -3.63 (0.28), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 60 HIS 0.005 0.001 HIS F 31 PHE 0.018 0.002 PHE D 22 TYR 0.018 0.002 TYR E 67 ARG 0.001 0.000 ARG D 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.563 Fit side-chains REVERT: B 36 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8418 (tt0) REVERT: C 47 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7546 (tm-30) REVERT: C 50 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8283 (mt-10) REVERT: D 6 MET cc_start: 0.7810 (ttp) cc_final: 0.7516 (ptm) REVERT: D 74 GLU cc_start: 0.8086 (pt0) cc_final: 0.7578 (pt0) REVERT: E 47 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7889 (tm-30) REVERT: E 50 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8472 (mt-10) REVERT: F 12 ARG cc_start: 0.5023 (pmt170) cc_final: 0.4321 (pmt-80) REVERT: F 14 PRO cc_start: 0.5215 (Cg_exo) cc_final: 0.4965 (Cg_endo) REVERT: F 36 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8409 (tt0) REVERT: F 44 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: F 47 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: F 74 GLU cc_start: 0.8378 (pt0) cc_final: 0.7975 (pt0) REVERT: F 75 LYS cc_start: 0.7761 (mtpm) cc_final: 0.6729 (mmpt) outliers start: 7 outliers final: 3 residues processed: 45 average time/residue: 1.9749 time to fit residues: 91.4246 Evaluate side-chains 44 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 20.0000 chunk 24 optimal weight: 50.0000 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.084427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.069890 restraints weight = 11431.237| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.25 r_work: 0.3427 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4482 Z= 0.331 Angle : 0.655 6.705 6072 Z= 0.361 Chirality : 0.047 0.138 642 Planarity : 0.003 0.031 780 Dihedral : 5.176 16.296 576 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.41 % Allowed : 13.25 % Favored : 85.34 % 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: -3.63 (0.28), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 60 HIS 0.005 0.001 HIS F 31 PHE 0.018 0.002 PHE D 22 TYR 0.018 0.002 TYR E 67 ARG 0.001 0.000 ARG D 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3242.23 seconds wall clock time: 58 minutes 12.53 seconds (3492.53 seconds total)