Starting phenix.real_space_refine on Mon Nov 17 13:01:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lrq_0958/11_2025/6lrq_0958.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lrq_0958/11_2025/6lrq_0958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lrq_0958/11_2025/6lrq_0958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lrq_0958/11_2025/6lrq_0958.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lrq_0958/11_2025/6lrq_0958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lrq_0958/11_2025/6lrq_0958.map" } resolution = 3.49 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= 0.000 sd= 0.003 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 1644 2.51 5 N 456 2.21 5 O 528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2628 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 0.54, per 1000 atoms: 0.21 Number of scatterers: 2628 At special positions: 0 Unit cell: (107.124, 109.836, 33.9, 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 528 8.00 N 456 7.00 C 1644 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: 0.22 Conformation dependent library (CDL) restraints added in 107.7 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 636 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 13 sheets defined 0.0% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 55 removed outlier: 6.775A pdb=" N VAL A 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N HIS B 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY A 51 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N HIS C 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY B 51 " --> pdb=" O HIS C 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA5, first strand: chain 'A' and resid 76 through 83 removed outlier: 6.823A pdb=" N VAL B 77 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA A 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLN B 79 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS A 80 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 76 through 83 removed outlier: 6.823A pdb=" N VAL B 77 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA A 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLN B 79 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS A 80 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 9.812A pdb=" N THR C 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LYS B 80 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU C 83 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL B 82 " --> pdb=" O GLU C 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 88 through 96 removed outlier: 8.871A pdb=" N ALA A 89 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N THR B 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N ALA A 91 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N PHE B 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY A 93 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LYS B 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 95 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N ILE B 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N ALA C 91 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA B 90 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N GLY C 93 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N THR B 92 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL C 95 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N PHE B 94 " --> pdb=" O VAL C 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 48 through 55 removed outlier: 6.809A pdb=" N VAL D 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N HIS E 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY D 51 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL E 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N HIS F 50 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY E 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 61 through 62 Processing sheet with id=AB1, first strand: chain 'D' and resid 65 through 66 Processing sheet with id=AB2, first strand: chain 'D' and resid 70 through 71 Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 83 removed outlier: 8.917A pdb=" N ALA D 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N GLN E 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N ALA D 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 9.838A pdb=" N THR E 81 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS D 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLU E 83 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL D 82 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N ALA E 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 10.464A pdb=" N GLN F 79 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N ALA E 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR F 81 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS E 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N GLU F 83 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL E 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 88 through 96 removed outlier: 8.953A pdb=" N ILE D 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N ALA E 91 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA D 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLY E 93 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N THR D 92 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL E 95 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N PHE D 94 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N ALA E 89 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N THR F 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 9.105A pdb=" N ALA E 91 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N PHE F 94 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY E 93 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LYS F 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL E 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 34 hydrogen bonds defined for protein. 102 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: 0.31 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 462 1.29 - 1.35: 408 1.35 - 1.41: 102 1.41 - 1.48: 439 1.48 - 1.54: 1229 Bond restraints: 2640 Sorted by residual: bond pdb=" CB VAL B 77 " pdb=" CG1 VAL B 77 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.82e+00 bond pdb=" CB VAL A 77 " pdb=" CG1 VAL A 77 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.78e+00 bond pdb=" CB VAL F 77 " pdb=" CG1 VAL F 77 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.74e+00 bond pdb=" CB VAL E 77 " pdb=" CG1 VAL E 77 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.73e+00 bond pdb=" CB VAL C 77 " pdb=" CG1 VAL C 77 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.72e+00 ... (remaining 2635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 3162 1.28 - 2.56: 348 2.56 - 3.85: 54 3.85 - 5.13: 0 5.13 - 6.41: 6 Bond angle restraints: 3570 Sorted by residual: angle pdb=" N THR F 72 " pdb=" CA THR F 72 " pdb=" C THR F 72 " ideal model delta sigma weight residual 109.86 106.92 2.94 1.55e+00 4.16e-01 3.60e+00 angle pdb=" N THR D 72 " pdb=" CA THR D 72 " pdb=" C THR D 72 " ideal model delta sigma weight residual 109.86 106.93 2.93 1.55e+00 4.16e-01 3.57e+00 angle pdb=" C THR A 92 " pdb=" N GLY A 93 " pdb=" CA GLY A 93 " ideal model delta sigma weight residual 121.41 117.72 3.69 1.96e+00 2.60e-01 3.54e+00 angle pdb=" C THR F 92 " pdb=" N GLY F 93 " pdb=" CA GLY F 93 " ideal model delta sigma weight residual 121.41 117.73 3.68 1.96e+00 2.60e-01 3.53e+00 angle pdb=" C THR D 92 " pdb=" N GLY D 93 " pdb=" CA GLY D 93 " ideal model delta sigma weight residual 121.41 117.73 3.68 1.96e+00 2.60e-01 3.52e+00 ... (remaining 3565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.15: 1132 7.15 - 14.30: 224 14.30 - 21.44: 102 21.44 - 28.59: 47 28.59 - 35.74: 31 Dihedral angle restraints: 1536 sinusoidal: 522 harmonic: 1014 Sorted by residual: dihedral pdb=" CA LEU C 38 " pdb=" C LEU C 38 " pdb=" N TYR C 39 " pdb=" CA TYR C 39 " ideal model delta harmonic sigma weight residual 180.00 -164.84 -15.16 0 5.00e+00 4.00e-02 9.19e+00 dihedral pdb=" CA LEU E 38 " pdb=" C LEU E 38 " pdb=" N TYR E 39 " pdb=" CA TYR E 39 " ideal model delta harmonic sigma weight residual 180.00 -164.88 -15.12 0 5.00e+00 4.00e-02 9.15e+00 dihedral pdb=" CA LEU F 38 " pdb=" C LEU F 38 " pdb=" N TYR F 39 " pdb=" CA TYR F 39 " ideal model delta harmonic sigma weight residual -180.00 -164.88 -15.12 0 5.00e+00 4.00e-02 9.14e+00 ... (remaining 1533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 173 0.026 - 0.052: 170 0.052 - 0.079: 61 0.079 - 0.105: 42 0.105 - 0.131: 22 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA VAL E 55 " pdb=" N VAL E 55 " pdb=" C VAL E 55 " pdb=" CB VAL E 55 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA VAL B 55 " pdb=" N VAL B 55 " pdb=" C VAL B 55 " pdb=" CB VAL B 55 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA VAL D 55 " pdb=" N VAL D 55 " pdb=" C VAL D 55 " pdb=" CB VAL D 55 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 465 not shown) Planarity restraints: 444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 94 " 0.010 2.00e-02 2.50e+03 8.12e-03 1.15e+00 pdb=" CG PHE E 94 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE E 94 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE E 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE E 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 94 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 94 " -0.010 2.00e-02 2.50e+03 8.00e-03 1.12e+00 pdb=" CG PHE B 94 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE B 94 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 94 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 94 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 94 " -0.009 2.00e-02 2.50e+03 8.00e-03 1.12e+00 pdb=" CG PHE C 94 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE C 94 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 94 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 94 " -0.001 2.00e-02 2.50e+03 ... (remaining 441 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 345 2.74 - 3.28: 2948 3.28 - 3.82: 3970 3.82 - 4.36: 4253 4.36 - 4.90: 8364 Nonbonded interactions: 19880 Sorted by model distance: nonbonded pdb=" ND2 ASN A 65 " pdb=" O GLY A 68 " model vdw 2.205 3.120 nonbonded pdb=" ND2 ASN D 65 " pdb=" O GLY D 68 " model vdw 2.207 3.120 nonbonded pdb=" ND2 ASN C 65 " pdb=" O GLY C 68 " model vdw 2.207 3.120 nonbonded pdb=" ND2 ASN E 65 " pdb=" O GLY E 68 " model vdw 2.207 3.120 nonbonded pdb=" ND2 ASN B 65 " pdb=" O GLY B 68 " model vdw 2.207 3.120 ... (remaining 19875 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 '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: 1.510 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.130 Find NCS groups from input model: 0.030 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 : 0.009 0.044 2640 Z= 0.411 Angle : 0.850 6.409 3570 Z= 0.470 Chirality : 0.051 0.131 468 Planarity : 0.003 0.011 444 Dihedral : 11.881 35.739 900 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.75 % Favored : 85.25 % Rotamer: Outliers : 0.00 % Allowed : 17.78 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.51 (0.29), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 39 PHE 0.019 0.005 PHE E 94 HIS 0.004 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00857 ( 2640) covalent geometry : angle 0.84968 ( 3570) hydrogen bonds : bond 0.27601 ( 31) hydrogen bonds : angle 11.24739 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: B 61 GLU cc_start: 0.7600 (mp0) cc_final: 0.6557 (mp0) REVERT: D 39 TYR cc_start: 0.7053 (t80) cc_final: 0.6635 (p90) REVERT: E 61 GLU cc_start: 0.7959 (mp0) cc_final: 0.7446 (mp0) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0536 time to fit residues: 4.0259 Evaluate side-chains 50 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.108 ------------------------------------------------------------------------------- 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: 10.0000 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.0770 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.5016 r_free = 0.5016 target = 0.203826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.179901 restraints weight = 5218.205| |-----------------------------------------------------------------------------| r_work (start): 0.4760 rms_B_bonded: 4.69 r_work (final): 0.4760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2640 Z= 0.100 Angle : 0.529 4.617 3570 Z= 0.294 Chirality : 0.048 0.167 468 Planarity : 0.002 0.008 444 Dihedral : 4.599 11.562 378 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 7.78 % Allowed : 20.00 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR E 39 PHE 0.008 0.001 PHE B 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 2640) covalent geometry : angle 0.52890 ( 3570) hydrogen bonds : bond 0.03591 ( 31) hydrogen bonds : angle 6.68647 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.6818 (mp0) cc_final: 0.5800 (mp0) REVERT: B 61 GLU cc_start: 0.7534 (mp0) cc_final: 0.7206 (mp0) REVERT: D 61 GLU cc_start: 0.6914 (mp0) cc_final: 0.6449 (mp0) outliers start: 21 outliers final: 12 residues processed: 97 average time/residue: 0.0382 time to fit residues: 4.8373 Evaluate side-chains 74 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.4938 r_free = 0.4938 target = 0.185936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.164990 restraints weight = 5272.541| |-----------------------------------------------------------------------------| r_work (start): 0.4687 rms_B_bonded: 3.87 r_work: 0.4697 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2640 Z= 0.178 Angle : 0.616 7.788 3570 Z= 0.332 Chirality : 0.046 0.137 468 Planarity : 0.002 0.013 444 Dihedral : 5.079 16.005 378 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.39 % Favored : 86.61 % Rotamer: Outliers : 10.00 % Allowed : 22.22 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 39 PHE 0.011 0.003 PHE F 94 HIS 0.004 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 2640) covalent geometry : angle 0.61605 ( 3570) hydrogen bonds : bond 0.03495 ( 31) hydrogen bonds : angle 6.59842 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7239 (mp0) cc_final: 0.6353 (mp0) REVERT: B 61 GLU cc_start: 0.8099 (mp0) cc_final: 0.7466 (mp0) REVERT: C 57 GLU cc_start: 0.7420 (mp0) cc_final: 0.7146 (mt-10) REVERT: D 39 TYR cc_start: 0.6132 (t80) cc_final: 0.5882 (p90) REVERT: D 61 GLU cc_start: 0.7161 (mp0) cc_final: 0.6476 (mp0) REVERT: E 57 GLU cc_start: 0.7799 (mp0) cc_final: 0.7337 (mt-10) REVERT: E 61 GLU cc_start: 0.7262 (mp0) cc_final: 0.6501 (mp0) REVERT: F 61 GLU cc_start: 0.7639 (mp0) cc_final: 0.7058 (mp0) outliers start: 27 outliers final: 17 residues processed: 87 average time/residue: 0.0397 time to fit residues: 4.5005 Evaluate side-chains 79 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 21 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 = 0.5035 r_free = 0.5035 target = 0.215500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4994 r_free = 0.4994 target = 0.197854 restraints weight = 5661.780| |-----------------------------------------------------------------------------| r_work (start): 0.4838 rms_B_bonded: 2.64 r_work: 0.4847 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4756 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2640 Z= 0.182 Angle : 0.609 7.479 3570 Z= 0.330 Chirality : 0.046 0.132 468 Planarity : 0.002 0.014 444 Dihedral : 5.147 22.566 378 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 10.74 % Allowed : 19.63 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR A 39 PHE 0.009 0.003 PHE F 94 HIS 0.004 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 2640) covalent geometry : angle 0.60946 ( 3570) hydrogen bonds : bond 0.03266 ( 31) hydrogen bonds : angle 6.38823 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7269 (mp0) cc_final: 0.6482 (mp0) REVERT: B 61 GLU cc_start: 0.7940 (mp0) cc_final: 0.7356 (mp0) REVERT: D 61 GLU cc_start: 0.7189 (mp0) cc_final: 0.6525 (mp0) REVERT: E 39 TYR cc_start: 0.7358 (t80) cc_final: 0.6891 (t80) REVERT: E 49 VAL cc_start: 0.9088 (OUTLIER) cc_final: 0.8830 (p) REVERT: F 61 GLU cc_start: 0.7874 (mp0) cc_final: 0.7622 (mp0) outliers start: 29 outliers final: 26 residues processed: 82 average time/residue: 0.0356 time to fit residues: 3.7532 Evaluate side-chains 84 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 0.0030 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- 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 = 0.5054 r_free = 0.5054 target = 0.223068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.189643 restraints weight = 5537.955| |-----------------------------------------------------------------------------| r_work (start): 0.4799 rms_B_bonded: 3.73 r_work: 0.4816 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2640 Z= 0.115 Angle : 0.543 6.550 3570 Z= 0.295 Chirality : 0.045 0.126 468 Planarity : 0.002 0.013 444 Dihedral : 4.613 20.056 378 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 10.37 % Allowed : 24.07 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR A 39 PHE 0.006 0.002 PHE B 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 2640) covalent geometry : angle 0.54310 ( 3570) hydrogen bonds : bond 0.02701 ( 31) hydrogen bonds : angle 5.94097 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7249 (mp0) cc_final: 0.6475 (mp0) REVERT: B 61 GLU cc_start: 0.8093 (mp0) cc_final: 0.6986 (mp0) REVERT: C 57 GLU cc_start: 0.7420 (mp0) cc_final: 0.7187 (tt0) REVERT: D 61 GLU cc_start: 0.6988 (mp0) cc_final: 0.6061 (mp0) REVERT: E 57 GLU cc_start: 0.7932 (mp0) cc_final: 0.7511 (mt-10) REVERT: F 61 GLU cc_start: 0.7623 (mp0) cc_final: 0.7379 (mp0) outliers start: 28 outliers final: 20 residues processed: 88 average time/residue: 0.0415 time to fit residues: 4.6711 Evaluate side-chains 84 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 = 0.5012 r_free = 0.5012 target = 0.213471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.195620 restraints weight = 5715.067| |-----------------------------------------------------------------------------| r_work (start): 0.4851 rms_B_bonded: 2.64 r_work: 0.4916 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4841 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.4841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2640 Z= 0.229 Angle : 0.676 7.822 3570 Z= 0.363 Chirality : 0.047 0.128 468 Planarity : 0.003 0.015 444 Dihedral : 5.483 24.064 378 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.39 % Favored : 86.61 % Rotamer: Outliers : 11.48 % Allowed : 23.70 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR A 39 PHE 0.011 0.004 PHE D 94 HIS 0.004 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 2640) covalent geometry : angle 0.67630 ( 3570) hydrogen bonds : bond 0.03833 ( 31) hydrogen bonds : angle 6.39862 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 56 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: F 61 GLU cc_start: 0.8226 (mp0) cc_final: 0.7465 (mp0) outliers start: 31 outliers final: 28 residues processed: 81 average time/residue: 0.0402 time to fit residues: 4.2451 Evaluate side-chains 81 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.0170 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.4024 ------------------------------------------------------------------------------- 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 = 0.5026 r_free = 0.5026 target = 0.215595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.197709 restraints weight = 5721.185| |-----------------------------------------------------------------------------| r_work (start): 0.4856 rms_B_bonded: 2.70 r_work: 0.4919 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4856 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.4856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2640 Z= 0.180 Angle : 0.635 7.218 3570 Z= 0.339 Chirality : 0.046 0.126 468 Planarity : 0.002 0.013 444 Dihedral : 5.224 22.907 378 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 11.85 % Allowed : 24.44 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR A 39 PHE 0.009 0.003 PHE A 94 HIS 0.004 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 2640) covalent geometry : angle 0.63538 ( 3570) hydrogen bonds : bond 0.03229 ( 31) hydrogen bonds : angle 6.20259 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 0.062 Fit side-chains revert: symmetry clash REVERT: B 39 TYR cc_start: 0.6630 (t80) cc_final: 0.6378 (t80) REVERT: B 61 GLU cc_start: 0.8188 (mp0) cc_final: 0.7798 (mp0) REVERT: C 57 GLU cc_start: 0.6767 (mp0) cc_final: 0.6543 (mt-10) REVERT: D 61 GLU cc_start: 0.7407 (mp0) cc_final: 0.6641 (mp0) REVERT: F 61 GLU cc_start: 0.8134 (mp0) cc_final: 0.7497 (mp0) outliers start: 32 outliers final: 29 residues processed: 85 average time/residue: 0.0393 time to fit residues: 4.2745 Evaluate side-chains 87 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.5007 r_free = 0.5007 target = 0.213251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4964 r_free = 0.4964 target = 0.195160 restraints weight = 5835.702| |-----------------------------------------------------------------------------| r_work (start): 0.4777 rms_B_bonded: 2.70 r_work: 0.4713 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4612 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.4612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2640 Z= 0.240 Angle : 0.703 7.856 3570 Z= 0.375 Chirality : 0.047 0.132 468 Planarity : 0.003 0.014 444 Dihedral : 5.796 24.553 378 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer: Outliers : 11.48 % Allowed : 25.19 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR A 39 PHE 0.011 0.003 PHE D 94 HIS 0.004 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 2640) covalent geometry : angle 0.70274 ( 3570) hydrogen bonds : bond 0.03446 ( 31) hydrogen bonds : angle 6.62404 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 53 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: B 61 GLU cc_start: 0.8315 (mp0) cc_final: 0.7404 (mp0) REVERT: C 55 VAL cc_start: 0.7658 (t) cc_final: 0.7402 (t) REVERT: E 39 TYR cc_start: 0.7281 (t80) cc_final: 0.6916 (t80) REVERT: F 61 GLU cc_start: 0.7855 (mp0) cc_final: 0.6786 (mp0) outliers start: 31 outliers final: 26 residues processed: 78 average time/residue: 0.0400 time to fit residues: 4.0864 Evaluate side-chains 79 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 53 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.0370 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.9260 ------------------------------------------------------------------------------- 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 = 0.5118 r_free = 0.5118 target = 0.223645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5081 r_free = 0.5081 target = 0.206025 restraints weight = 5868.057| |-----------------------------------------------------------------------------| r_work (start): 0.4943 rms_B_bonded: 2.65 r_work: 0.4978 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4893 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.4893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2640 Z= 0.105 Angle : 0.574 6.540 3570 Z= 0.306 Chirality : 0.046 0.124 468 Planarity : 0.002 0.013 444 Dihedral : 4.577 18.880 378 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 8.15 % Allowed : 28.15 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR D 39 PHE 0.004 0.001 PHE B 94 HIS 0.001 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 2640) covalent geometry : angle 0.57361 ( 3570) hydrogen bonds : bond 0.02634 ( 31) hydrogen bonds : angle 5.84267 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7292 (mp0) cc_final: 0.6760 (mp0) REVERT: B 61 GLU cc_start: 0.8158 (mp0) cc_final: 0.7392 (mp0) REVERT: C 55 VAL cc_start: 0.7810 (t) cc_final: 0.7503 (t) REVERT: C 57 GLU cc_start: 0.7466 (mp0) cc_final: 0.7156 (mt-10) REVERT: D 61 GLU cc_start: 0.7096 (mp0) cc_final: 0.6787 (mp0) REVERT: E 57 GLU cc_start: 0.7700 (mp0) cc_final: 0.7484 (mt-10) REVERT: E 61 GLU cc_start: 0.7651 (mp0) cc_final: 0.7433 (mp0) REVERT: F 61 GLU cc_start: 0.7853 (mp0) cc_final: 0.7363 (mp0) outliers start: 22 outliers final: 16 residues processed: 84 average time/residue: 0.0406 time to fit residues: 4.3340 Evaluate side-chains 82 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.5048 r_free = 0.5048 target = 0.210349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.188170 restraints weight = 5452.510| |-----------------------------------------------------------------------------| r_work (start): 0.4847 rms_B_bonded: 3.67 r_work: 0.4873 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2640 Z= 0.138 Angle : 0.619 7.432 3570 Z= 0.324 Chirality : 0.046 0.123 468 Planarity : 0.002 0.024 444 Dihedral : 4.751 20.938 378 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % Rotamer: Outliers : 5.19 % Allowed : 32.96 % Favored : 61.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR B 39 PHE 0.006 0.002 PHE A 94 HIS 0.003 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 2640) covalent geometry : angle 0.61863 ( 3570) hydrogen bonds : bond 0.02949 ( 31) hydrogen bonds : angle 5.95217 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: B 61 GLU cc_start: 0.8155 (mp0) cc_final: 0.7339 (mp0) REVERT: C 55 VAL cc_start: 0.7544 (t) cc_final: 0.7229 (t) REVERT: D 61 GLU cc_start: 0.7077 (mp0) cc_final: 0.6856 (mp0) REVERT: E 39 TYR cc_start: 0.7234 (t80) cc_final: 0.6882 (t80) REVERT: E 57 GLU cc_start: 0.7539 (mp0) cc_final: 0.7336 (mt-10) REVERT: E 61 GLU cc_start: 0.7637 (mp0) cc_final: 0.7350 (mp0) REVERT: F 61 GLU cc_start: 0.7845 (mp0) cc_final: 0.7145 (mp0) outliers start: 14 outliers final: 14 residues processed: 73 average time/residue: 0.0384 time to fit residues: 3.6152 Evaluate side-chains 73 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.5119 r_free = 0.5119 target = 0.225061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5095 r_free = 0.5095 target = 0.207712 restraints weight = 5847.905| |-----------------------------------------------------------------------------| r_work (start): 0.4971 rms_B_bonded: 2.69 r_work: 0.5045 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4967 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.4967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2640 Z= 0.098 Angle : 0.583 9.233 3570 Z= 0.295 Chirality : 0.045 0.121 468 Planarity : 0.002 0.014 444 Dihedral : 4.325 17.678 378 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 5.19 % Allowed : 32.22 % Favored : 62.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR D 39 PHE 0.004 0.001 PHE E 94 HIS 0.002 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 2640) covalent geometry : angle 0.58318 ( 3570) hydrogen bonds : bond 0.02481 ( 31) hydrogen bonds : angle 5.66100 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 827.19 seconds wall clock time: 14 minutes 54.75 seconds (894.75 seconds total)