Starting phenix.real_space_refine on Fri Aug 22 12:56:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xo2_33334/08_2025/7xo2_33334.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo2_33334/08_2025/7xo2_33334.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 { model { file = "/net/cci-nas-00/data/ceres_data/7xo2_33334/08_2025/7xo2_33334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo2_33334/08_2025/7xo2_33334.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xo2_33334/08_2025/7xo2_33334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo2_33334/08_2025/7xo2_33334.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 3 Type Number sf(0) Gaussians C 1602 2.51 5 N 444 2.21 5 O 504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2550 Number of models: 1 Model: "" Number of chains: 1 Chain: "I" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Restraints were copied for chains: C, D, A, E, B Time building chain proxies: 0.61, per 1000 atoms: 0.24 Number of scatterers: 2550 At special positions: 0 Unit cell: (96.46, 94.34, 33.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 504 8.00 N 444 7.00 C 1602 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=0, symmetry=0 Time building additional restraints: 0.12 Conformation dependent library (CDL) restraints added in 69.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 56.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'I' and resid 37 through 45 removed outlier: 6.598A pdb=" N VAL D 37 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL E 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR D 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N SER E 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY D 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR E 44 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LYS D 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 48 through 57 removed outlier: 6.639A pdb=" N VAL I 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY D 51 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N HIS I 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA D 53 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N VAL I 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 10.566A pdb=" N VAL D 55 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N THR I 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 10.271A pdb=" N GLU D 57 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA I 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL D 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N HIS E 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY D 51 " --> pdb=" O HIS E 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 61 through 66 removed outlier: 6.349A pdb=" N GLU I 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR D 64 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL I 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL D 66 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASN I 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU D 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N THR E 64 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL E 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASN D 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'I' and resid 69 through 72 Processing sheet with id=AA5, first strand: chain 'I' and resid 75 through 79 Processing sheet with id=AA6, first strand: chain 'I' and resid 82 through 83 removed outlier: 6.488A pdb=" N VAL I 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL D 82 " --> pdb=" O GLU E 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'I' and resid 87 through 88 Processing sheet with id=AA8, first strand: chain 'I' and resid 92 through 96 Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 45 removed outlier: 6.631A pdb=" N VAL C 37 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL A 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR C 39 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N SER A 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY C 41 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N THR A 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS C 43 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 37 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL B 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N SER B 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY A 41 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR B 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LYS A 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 48 through 57 removed outlier: 6.946A pdb=" N VAL C 49 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N HIS A 50 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY C 51 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLY B 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N HIS A 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA B 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N VAL A 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 10.509A pdb=" N VAL B 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 10.201A pdb=" N GLU B 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ALA A 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 61 through 66 removed outlier: 6.250A pdb=" N GLU C 61 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR A 64 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL C 63 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL A 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN C 65 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLU A 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N THR B 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 69 through 72 Processing sheet with id=AB4, first strand: chain 'C' and resid 75 through 79 Processing sheet with id=AB5, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.573A pdb=" N VAL C 82 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 82 " --> pdb=" O GLU B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AB7, first strand: chain 'C' and resid 92 through 96 68 hydrogen bonds defined for protein. 204 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: 0.32 Time building geometry restraints manager: 0.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 438 1.29 - 1.36: 402 1.36 - 1.42: 102 1.42 - 1.48: 420 1.48 - 1.55: 1200 Bond restraints: 2562 Sorted by residual: bond pdb=" CA LYS A 60 " pdb=" C LYS A 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 3.00e-01 bond pdb=" CA LYS D 60 " pdb=" C LYS D 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 2.97e-01 bond pdb=" CA LYS C 60 " pdb=" C LYS C 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 2.72e-01 bond pdb=" CA LYS B 60 " pdb=" C LYS B 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 2.66e-01 bond pdb=" CA LYS E 60 " pdb=" C LYS E 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 2.53e-01 ... (remaining 2557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.44: 2874 0.44 - 0.89: 451 0.89 - 1.33: 104 1.33 - 1.77: 13 1.77 - 2.22: 20 Bond angle restraints: 3462 Sorted by residual: angle pdb=" C THR D 59 " pdb=" N LYS D 60 " pdb=" CA LYS D 60 " ideal model delta sigma weight residual 122.17 120.34 1.83 1.54e+00 4.22e-01 1.42e+00 angle pdb=" C THR C 59 " pdb=" N LYS C 60 " pdb=" CA LYS C 60 " ideal model delta sigma weight residual 122.17 120.35 1.82 1.54e+00 4.22e-01 1.40e+00 angle pdb=" C THR B 59 " pdb=" N LYS B 60 " pdb=" CA LYS B 60 " ideal model delta sigma weight residual 122.17 120.35 1.82 1.54e+00 4.22e-01 1.40e+00 angle pdb=" C THR E 59 " pdb=" N LYS E 60 " pdb=" CA LYS E 60 " ideal model delta sigma weight residual 122.17 120.35 1.82 1.54e+00 4.22e-01 1.39e+00 angle pdb=" C THR A 59 " pdb=" N LYS A 60 " pdb=" CA LYS A 60 " ideal model delta sigma weight residual 122.17 120.37 1.80 1.54e+00 4.22e-01 1.37e+00 ... (remaining 3457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.35: 1296 15.35 - 30.70: 96 30.70 - 46.05: 66 46.05 - 61.40: 24 61.40 - 76.75: 6 Dihedral angle restraints: 1488 sinusoidal: 492 harmonic: 996 Sorted by residual: dihedral pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " pdb=" CG GLU C 83 " pdb=" CD GLU C 83 " ideal model delta sinusoidal sigma weight residual -180.00 -127.38 -52.62 3 1.50e+01 4.44e-03 9.13e+00 dihedral pdb=" CA GLU D 83 " pdb=" CB GLU D 83 " pdb=" CG GLU D 83 " pdb=" CD GLU D 83 " ideal model delta sinusoidal sigma weight residual -180.00 -127.39 -52.61 3 1.50e+01 4.44e-03 9.13e+00 dihedral pdb=" CA GLU E 83 " pdb=" CB GLU E 83 " pdb=" CG GLU E 83 " pdb=" CD GLU E 83 " ideal model delta sinusoidal sigma weight residual -180.00 -127.41 -52.59 3 1.50e+01 4.44e-03 9.13e+00 ... (remaining 1485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 227 0.025 - 0.050: 107 0.050 - 0.075: 38 0.075 - 0.100: 17 0.100 - 0.125: 67 Chirality restraints: 456 Sorted by residual: chirality pdb=" CA ILE E 88 " pdb=" N ILE E 88 " pdb=" C ILE E 88 " pdb=" CB ILE E 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA ILE B 88 " pdb=" N ILE B 88 " pdb=" C ILE B 88 " pdb=" CB ILE B 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 453 not shown) Planarity restraints: 426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 59 " -0.002 2.00e-02 2.50e+03 4.26e-03 1.81e-01 pdb=" C THR E 59 " 0.007 2.00e-02 2.50e+03 pdb=" O THR E 59 " -0.003 2.00e-02 2.50e+03 pdb=" N LYS E 60 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 59 " 0.002 2.00e-02 2.50e+03 4.13e-03 1.70e-01 pdb=" C THR C 59 " -0.007 2.00e-02 2.50e+03 pdb=" O THR C 59 " 0.003 2.00e-02 2.50e+03 pdb=" N LYS C 60 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 59 " -0.002 2.00e-02 2.50e+03 4.00e-03 1.60e-01 pdb=" C THR D 59 " 0.007 2.00e-02 2.50e+03 pdb=" O THR D 59 " -0.003 2.00e-02 2.50e+03 pdb=" N LYS D 60 " -0.002 2.00e-02 2.50e+03 ... (remaining 423 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 1576 3.05 - 3.51: 2243 3.51 - 3.97: 3534 3.97 - 4.44: 3796 4.44 - 4.90: 7142 Nonbonded interactions: 18291 Sorted by model distance: nonbonded pdb=" NE2 GLN E 62 " pdb=" OG1 THR E 64 " model vdw 2.586 3.120 nonbonded pdb=" NE2 GLN A 62 " pdb=" OG1 THR A 64 " model vdw 2.586 3.120 nonbonded pdb=" NE2 GLN I 62 " pdb=" OG1 THR I 64 " model vdw 2.586 3.120 nonbonded pdb=" NE2 GLN B 62 " pdb=" OG1 THR B 64 " model vdw 2.586 3.120 nonbonded pdb=" NE2 GLN C 62 " pdb=" OG1 THR C 64 " model vdw 2.587 3.120 ... (remaining 18286 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: 0.01 Found NCS groups: ncs_group { reference = chain 'I' selection = chain 'C' selection = chain 'D' selection = chain 'A' selection = chain 'E' selection = chain 'B' } 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.540 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:5.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 : 0.001 0.014 2562 Z= 0.088 Angle : 0.376 2.215 3462 Z= 0.225 Chirality : 0.052 0.125 456 Planarity : 0.001 0.004 426 Dihedral : 18.118 76.747 864 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 18.60 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.67 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 39 PHE 0.002 0.000 PHE B 94 HIS 0.000 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00144 ( 2562) covalent geometry : angle 0.37587 ( 3462) hydrogen bonds : bond 0.19488 ( 68) hydrogen bonds : angle 8.33519 ( 204) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.062 Fit side-chains REVERT: E 58 LYS cc_start: 0.8958 (mmtp) cc_final: 0.6762 (pptt) REVERT: B 39 TYR cc_start: 0.8691 (t80) cc_final: 0.8257 (t80) REVERT: B 58 LYS cc_start: 0.8794 (mmtp) cc_final: 0.6507 (pptt) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.5406 time to fit residues: 17.0832 Evaluate side-chains 19 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.0370 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 overall best weight: 2.5864 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.098603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.087398 restraints weight = 4281.090| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.13 r_work: 0.3305 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2562 Z= 0.175 Angle : 0.451 2.676 3462 Z= 0.266 Chirality : 0.053 0.129 456 Planarity : 0.002 0.006 426 Dihedral : 4.173 13.491 372 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.26 % Allowed : 17.83 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.79 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 39 PHE 0.011 0.002 PHE I 94 HIS 0.003 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 2562) covalent geometry : angle 0.45081 ( 3462) hydrogen bonds : bond 0.03527 ( 68) hydrogen bonds : angle 5.16389 ( 204) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.102 Fit side-chains REVERT: I 60 LYS cc_start: 0.6198 (OUTLIER) cc_final: 0.3785 (tptp) REVERT: E 57 GLU cc_start: 0.8511 (pt0) cc_final: 0.8213 (pt0) REVERT: E 58 LYS cc_start: 0.9196 (mmtp) cc_final: 0.6694 (pptt) REVERT: E 60 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6329 (pmtt) REVERT: B 57 GLU cc_start: 0.8558 (pt0) cc_final: 0.8333 (pt0) REVERT: B 58 LYS cc_start: 0.9084 (mmtp) cc_final: 0.6568 (pptt) REVERT: B 60 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6298 (pmtt) outliers start: 11 outliers final: 3 residues processed: 35 average time/residue: 0.7325 time to fit residues: 26.1038 Evaluate side-chains 27 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 32 optimal weight: 0.0170 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 1.9822 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.099082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.088064 restraints weight = 4356.171| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.09 r_work: 0.3314 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2562 Z= 0.136 Angle : 0.409 2.527 3462 Z= 0.241 Chirality : 0.053 0.132 456 Planarity : 0.001 0.006 426 Dihedral : 4.182 14.124 372 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.65 % Allowed : 17.44 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.89 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 39 PHE 0.007 0.002 PHE C 94 HIS 0.003 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 2562) covalent geometry : angle 0.40944 ( 3462) hydrogen bonds : bond 0.02938 ( 68) hydrogen bonds : angle 4.78672 ( 204) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 19 time to evaluate : 0.102 Fit side-chains REVERT: I 43 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.7917 (ttpt) REVERT: I 60 LYS cc_start: 0.6118 (OUTLIER) cc_final: 0.3776 (tptp) REVERT: E 60 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.6306 (pmtt) REVERT: B 60 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6257 (pmtt) REVERT: B 87 SER cc_start: 0.9123 (p) cc_final: 0.8895 (t) outliers start: 12 outliers final: 3 residues processed: 30 average time/residue: 0.6957 time to fit residues: 21.2848 Evaluate side-chains 23 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 16 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.094325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.083515 restraints weight = 4395.005| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.10 r_work: 0.3240 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2562 Z= 0.220 Angle : 0.489 3.127 3462 Z= 0.285 Chirality : 0.054 0.137 456 Planarity : 0.002 0.007 426 Dihedral : 4.940 17.776 372 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 4.26 % Allowed : 18.99 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.43), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR I 39 PHE 0.009 0.002 PHE I 94 HIS 0.004 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 2562) covalent geometry : angle 0.48870 ( 3462) hydrogen bonds : bond 0.03273 ( 68) hydrogen bonds : angle 4.89881 ( 204) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.069 Fit side-chains REVERT: E 60 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.6365 (pmtt) REVERT: B 60 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.6228 (pmtt) REVERT: B 80 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9125 (mtpt) outliers start: 11 outliers final: 7 residues processed: 34 average time/residue: 0.8419 time to fit residues: 29.0690 Evaluate side-chains 35 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 80 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.0870 overall best weight: 3.4166 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.094786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.083999 restraints weight = 4312.690| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.07 r_work: 0.3250 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2562 Z= 0.212 Angle : 0.488 2.975 3462 Z= 0.285 Chirality : 0.054 0.136 456 Planarity : 0.002 0.007 426 Dihedral : 4.941 17.289 372 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.49 % Allowed : 20.93 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR I 39 PHE 0.009 0.002 PHE I 94 HIS 0.004 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 2562) covalent geometry : angle 0.48796 ( 3462) hydrogen bonds : bond 0.03071 ( 68) hydrogen bonds : angle 4.84961 ( 204) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.085 Fit side-chains REVERT: E 60 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.6421 (pmtt) REVERT: B 60 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.6263 (pmtt) outliers start: 9 outliers final: 7 residues processed: 33 average time/residue: 0.8175 time to fit residues: 27.4352 Evaluate side-chains 32 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.095049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.084242 restraints weight = 4422.437| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.10 r_work: 0.3250 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2562 Z= 0.199 Angle : 0.477 2.906 3462 Z= 0.279 Chirality : 0.054 0.135 456 Planarity : 0.002 0.007 426 Dihedral : 4.972 17.283 372 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 4.65 % Allowed : 20.16 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR I 39 PHE 0.009 0.002 PHE I 94 HIS 0.004 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 2562) covalent geometry : angle 0.47732 ( 3462) hydrogen bonds : bond 0.02975 ( 68) hydrogen bonds : angle 4.86593 ( 204) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 22 time to evaluate : 0.061 Fit side-chains REVERT: E 60 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.6409 (pmtt) REVERT: B 60 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6264 (pmtt) outliers start: 12 outliers final: 7 residues processed: 32 average time/residue: 0.9125 time to fit residues: 29.6211 Evaluate side-chains 30 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.092935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.082304 restraints weight = 4354.659| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.05 r_work: 0.3221 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 2562 Z= 0.263 Angle : 0.539 3.524 3462 Z= 0.315 Chirality : 0.056 0.137 456 Planarity : 0.002 0.007 426 Dihedral : 5.334 19.107 372 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.26 % Allowed : 20.54 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR I 39 PHE 0.010 0.002 PHE I 94 HIS 0.005 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00603 ( 2562) covalent geometry : angle 0.53930 ( 3462) hydrogen bonds : bond 0.03346 ( 68) hydrogen bonds : angle 4.99626 ( 204) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 23 time to evaluate : 0.087 Fit side-chains REVERT: A 46 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7597 (mt-10) REVERT: E 60 LYS cc_start: 0.7560 (OUTLIER) cc_final: 0.6440 (pmtt) REVERT: B 60 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.6242 (pmtt) outliers start: 11 outliers final: 7 residues processed: 32 average time/residue: 0.9383 time to fit residues: 30.4670 Evaluate side-chains 33 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 6 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.101528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.090703 restraints weight = 4374.800| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.21 r_work: 0.3363 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2562 Z= 0.091 Angle : 0.390 2.598 3462 Z= 0.230 Chirality : 0.053 0.134 456 Planarity : 0.001 0.006 426 Dihedral : 4.318 15.401 372 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.10 % Allowed : 23.26 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.000 TYR I 39 PHE 0.006 0.001 PHE C 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00185 ( 2562) covalent geometry : angle 0.38975 ( 3462) hydrogen bonds : bond 0.02051 ( 68) hydrogen bonds : angle 4.58178 ( 204) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.096 Fit side-chains REVERT: E 60 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6419 (pmtt) REVERT: B 60 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6219 (pmtt) REVERT: B 87 SER cc_start: 0.8860 (p) cc_final: 0.8601 (t) outliers start: 8 outliers final: 4 residues processed: 27 average time/residue: 0.7068 time to fit residues: 19.4684 Evaluate side-chains 25 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.097206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.086550 restraints weight = 4404.405| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.19 r_work: 0.3287 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2562 Z= 0.145 Angle : 0.419 2.596 3462 Z= 0.246 Chirality : 0.053 0.131 456 Planarity : 0.001 0.005 426 Dihedral : 4.522 15.740 372 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.33 % Allowed : 24.03 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR D 39 PHE 0.007 0.002 PHE C 94 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 2562) covalent geometry : angle 0.41909 ( 3462) hydrogen bonds : bond 0.02467 ( 68) hydrogen bonds : angle 4.64630 ( 204) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.093 Fit side-chains REVERT: E 60 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.6480 (pmtt) REVERT: B 60 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6226 (pmtt) REVERT: B 87 SER cc_start: 0.8953 (p) cc_final: 0.8663 (t) outliers start: 6 outliers final: 4 residues processed: 29 average time/residue: 0.7669 time to fit residues: 22.5969 Evaluate side-chains 29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.091623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.081076 restraints weight = 4499.702| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.07 r_work: 0.3195 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 2562 Z= 0.352 Angle : 0.614 4.020 3462 Z= 0.357 Chirality : 0.059 0.153 456 Planarity : 0.002 0.008 426 Dihedral : 5.675 21.838 372 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.71 % Allowed : 24.03 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR A 39 PHE 0.011 0.003 PHE I 94 HIS 0.005 0.003 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00816 ( 2562) covalent geometry : angle 0.61376 ( 3462) hydrogen bonds : bond 0.03717 ( 68) hydrogen bonds : angle 5.05964 ( 204) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.153 Fit side-chains REVERT: E 60 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.6529 (pmtt) REVERT: B 60 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.6333 (pmtt) outliers start: 7 outliers final: 5 residues processed: 30 average time/residue: 0.7905 time to fit residues: 24.1336 Evaluate side-chains 29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.100215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.089572 restraints weight = 4420.701| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.17 r_work: 0.3342 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2562 Z= 0.106 Angle : 0.407 2.908 3462 Z= 0.240 Chirality : 0.053 0.132 456 Planarity : 0.001 0.005 426 Dihedral : 4.474 15.964 372 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.33 % Allowed : 24.42 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.000 TYR C 39 PHE 0.007 0.001 PHE A 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 2562) covalent geometry : angle 0.40709 ( 3462) hydrogen bonds : bond 0.02103 ( 68) hydrogen bonds : angle 4.55593 ( 204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 929.88 seconds wall clock time: 16 minutes 33.92 seconds (993.92 seconds total)