Starting phenix.real_space_refine on Wed Mar 5 16:12:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lrq_0958/03_2025/6lrq_0958.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lrq_0958/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6lrq_0958/03_2025/6lrq_0958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lrq_0958/03_2025/6lrq_0958.map" model { file = "/net/cci-nas-00/data/ceres_data/6lrq_0958/03_2025/6lrq_0958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lrq_0958/03_2025/6lrq_0958.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: C, B, E, D, F Time building chain proxies: 1.76, per 1000 atoms: 0.67 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: 0.65 Conformation dependent library (CDL) restraints added in 354.1 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: 0.39 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: 0.56 Time building geometry restraints manager: 0.77 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 1.440 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.190 Find NCS groups from input model: 0.060 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.470 ------------------------------------------------------------------------------- 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= 0.603 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.004 0.003 HIS E 50 PHE 0.019 0.005 PHE E 94 TYR 0.008 0.002 TYR D 39 *********************** 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 : 0.306 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: 0.6638 (p90) REVERT: E 61 GLU cc_start: 0.7959 (mp0) cc_final: 0.7447 (mp0) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1296 time to fit residues: 9.6511 Evaluate side-chains 48 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.5090 r_free = 0.5090 target = 0.223311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.206777 restraints weight = 5579.253| |-----------------------------------------------------------------------------| r_work (start): 0.4862 rms_B_bonded: 2.45 r_work: 0.4769 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.4675 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2640 Z= 0.145 Angle : 0.529 4.447 3570 Z= 0.293 Chirality : 0.048 0.176 468 Planarity : 0.002 0.009 444 Dihedral : 4.584 11.420 378 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 8.52 % Allowed : 18.89 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.008 0.001 PHE B 94 TYR 0.004 0.001 TYR E 39 *********************** 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 99 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7198 (mp0) cc_final: 0.5909 (mp0) REVERT: B 61 GLU cc_start: 0.8060 (mp0) cc_final: 0.7575 (mp0) REVERT: C 57 GLU cc_start: 0.7575 (mp0) cc_final: 0.7351 (mt-10) REVERT: D 61 GLU cc_start: 0.7356 (mp0) cc_final: 0.6798 (mp0) REVERT: E 57 GLU cc_start: 0.7757 (mp0) cc_final: 0.7283 (mt-10) REVERT: E 61 GLU cc_start: 0.7644 (mp0) cc_final: 0.7357 (mp0) outliers start: 23 outliers final: 13 residues processed: 97 average time/residue: 0.0894 time to fit residues: 11.0372 Evaluate side-chains 76 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 53 THR 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 20 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 22 optimal weight: 0.0470 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.212240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.194369 restraints weight = 5611.297| |-----------------------------------------------------------------------------| r_work (start): 0.4749 rms_B_bonded: 2.71 r_work: 0.4714 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4603 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.4603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2640 Z= 0.322 Angle : 0.647 8.241 3570 Z= 0.348 Chirality : 0.047 0.159 468 Planarity : 0.003 0.012 444 Dihedral : 5.388 17.446 378 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer: Outliers : 10.37 % Allowed : 20.74 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 50 PHE 0.013 0.003 PHE F 94 TYR 0.007 0.001 TYR B 39 *********************** 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 91 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7294 (mp0) cc_final: 0.6494 (mp0) REVERT: B 61 GLU cc_start: 0.7994 (mp0) cc_final: 0.7258 (mp0) REVERT: B 80 LYS cc_start: 0.8084 (ttpt) cc_final: 0.7882 (ttmt) REVERT: D 39 TYR cc_start: 0.6853 (t80) cc_final: 0.6278 (p90) REVERT: E 49 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8863 (p) REVERT: E 61 GLU cc_start: 0.6984 (mp0) cc_final: 0.5774 (mp0) REVERT: F 61 GLU cc_start: 0.7468 (mp0) cc_final: 0.6984 (mp0) outliers start: 28 outliers final: 20 residues processed: 84 average time/residue: 0.0964 time to fit residues: 10.3138 Evaluate side-chains 81 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 53 THR 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 54 THR 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 49 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.4983 r_free = 0.4983 target = 0.211073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.193186 restraints weight = 5779.844| |-----------------------------------------------------------------------------| r_work (start): 0.4831 rms_B_bonded: 2.74 r_work: 0.4893 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4819 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.4819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2640 Z= 0.407 Angle : 0.718 8.496 3570 Z= 0.388 Chirality : 0.048 0.132 468 Planarity : 0.003 0.014 444 Dihedral : 5.812 22.727 378 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.30 % Favored : 87.70 % Rotamer: Outliers : 12.96 % Allowed : 19.63 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 50 PHE 0.012 0.004 PHE F 94 TYR 0.011 0.002 TYR E 39 *********************** 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 95 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 60 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: B 61 GLU cc_start: 0.8302 (mp0) cc_final: 0.7538 (mp0) REVERT: D 61 GLU cc_start: 0.7571 (mp0) cc_final: 0.6772 (mp0) REVERT: F 61 GLU cc_start: 0.8260 (mp0) cc_final: 0.7970 (mp0) outliers start: 35 outliers final: 31 residues processed: 87 average time/residue: 0.0982 time to fit residues: 10.9537 Evaluate side-chains 86 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 55 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 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 49 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 72 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 54 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4998 r_free = 0.4998 target = 0.212123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4955 r_free = 0.4955 target = 0.194308 restraints weight = 5751.883| |-----------------------------------------------------------------------------| r_work (start): 0.4845 rms_B_bonded: 2.70 r_work: 0.4902 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4832 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2640 Z= 0.334 Angle : 0.663 7.588 3570 Z= 0.358 Chirality : 0.047 0.129 468 Planarity : 0.003 0.014 444 Dihedral : 5.547 21.865 378 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.66 % Favored : 86.34 % Rotamer: Outliers : 13.70 % Allowed : 21.85 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (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 HIS 0.004 0.002 HIS B 50 PHE 0.011 0.003 PHE A 94 TYR 0.008 0.002 TYR A 39 *********************** 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: 37 poor density : 57 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: B 61 GLU cc_start: 0.8318 (mp0) cc_final: 0.7685 (mp0) REVERT: D 61 GLU cc_start: 0.7599 (mp0) cc_final: 0.6900 (mp0) REVERT: E 49 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8669 (p) REVERT: F 61 GLU cc_start: 0.8304 (mp0) cc_final: 0.8053 (mp0) outliers start: 37 outliers final: 31 residues processed: 87 average time/residue: 0.0962 time to fit residues: 10.6186 Evaluate side-chains 86 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 54 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 54 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 GLN 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 48 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 72 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 54 THR 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 74 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 0.0030 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 0.0980 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.5112 r_free = 0.5112 target = 0.223784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.5072 r_free = 0.5072 target = 0.206662 restraints weight = 5791.117| |-----------------------------------------------------------------------------| r_work (start): 0.4954 rms_B_bonded: 2.65 r_work: 0.5027 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4959 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.4959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.4417 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= 0.133 Angle : 0.544 6.014 3570 Z= 0.296 Chirality : 0.046 0.122 468 Planarity : 0.002 0.021 444 Dihedral : 4.333 14.618 378 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 8.52 % Allowed : 26.30 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS F 50 PHE 0.002 0.001 PHE A 94 TYR 0.006 0.001 TYR A 39 *********************** 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 94 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7645 (mp0) cc_final: 0.6802 (mp0) REVERT: B 61 GLU cc_start: 0.8165 (mp0) cc_final: 0.7824 (mp0) REVERT: E 61 GLU cc_start: 0.7729 (mp0) cc_final: 0.7471 (mp0) REVERT: F 61 GLU cc_start: 0.8001 (mp0) cc_final: 0.7485 (mp0) outliers start: 23 outliers final: 12 residues processed: 89 average time/residue: 0.0939 time to fit residues: 10.6064 Evaluate side-chains 76 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 D residue 37 VAL Chi-restraints excluded: chain D residue 72 THR 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 70 VAL Chi-restraints excluded: chain F residue 37 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 0.0070 chunk 35 optimal weight: 0.0060 chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- 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 = 0.5078 r_free = 0.5078 target = 0.221634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5031 r_free = 0.5031 target = 0.204447 restraints weight = 6042.138| |-----------------------------------------------------------------------------| r_work (start): 0.4851 rms_B_bonded: 2.80 r_work: 0.4874 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4783 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2640 Z= 0.146 Angle : 0.571 7.640 3570 Z= 0.301 Chirality : 0.046 0.122 468 Planarity : 0.002 0.015 444 Dihedral : 4.390 18.921 378 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 7.41 % Allowed : 28.52 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.005 0.001 PHE A 94 TYR 0.007 0.001 TYR A 39 *********************** 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 88 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7267 (mp0) cc_final: 0.6666 (mp0) REVERT: B 61 GLU cc_start: 0.8305 (mp0) cc_final: 0.7577 (mp0) REVERT: E 57 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7144 (mp0) REVERT: F 61 GLU cc_start: 0.7942 (mp0) cc_final: 0.7587 (mp0) outliers start: 20 outliers final: 16 residues processed: 84 average time/residue: 0.1000 time to fit residues: 10.5876 Evaluate side-chains 78 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 48 VAL Chi-restraints excluded: chain B residue 54 THR 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 72 THR 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 E residue 79 GLN Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 0.2980 chunk 27 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 = 0.5022 r_free = 0.5022 target = 0.216701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.198989 restraints weight = 5806.372| |-----------------------------------------------------------------------------| r_work (start): 0.4868 rms_B_bonded: 2.75 r_work: 0.4932 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4860 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.4860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.4425 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= 0.251 Angle : 0.652 9.107 3570 Z= 0.340 Chirality : 0.046 0.138 468 Planarity : 0.002 0.013 444 Dihedral : 4.980 23.872 378 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 8.89 % Allowed : 27.04 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 50 PHE 0.008 0.003 PHE A 94 TYR 0.008 0.002 TYR A 39 *********************** 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 83 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7357 (mp0) cc_final: 0.7050 (mp0) REVERT: B 61 GLU cc_start: 0.8336 (mp0) cc_final: 0.7654 (mp0) REVERT: F 61 GLU cc_start: 0.8281 (mp0) cc_final: 0.7528 (mp0) outliers start: 24 outliers final: 21 residues processed: 80 average time/residue: 0.0986 time to fit residues: 10.0019 Evaluate side-chains 78 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 48 VAL 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 70 VAL Chi-restraints excluded: chain D residue 72 THR 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 E residue 79 GLN Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.214319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4964 r_free = 0.4964 target = 0.196253 restraints weight = 5843.405| |-----------------------------------------------------------------------------| r_work (start): 0.4852 rms_B_bonded: 2.75 r_work: 0.4915 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4839 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.4839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2640 Z= 0.325 Angle : 0.736 10.971 3570 Z= 0.381 Chirality : 0.046 0.145 468 Planarity : 0.003 0.014 444 Dihedral : 5.453 26.406 378 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % Rotamer: Outliers : 8.89 % Allowed : 27.04 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 50 PHE 0.010 0.003 PHE A 94 TYR 0.012 0.002 TYR B 39 *********************** 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 76 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: B 61 GLU cc_start: 0.8166 (mp0) cc_final: 0.7600 (mp0) REVERT: E 39 TYR cc_start: 0.6580 (t80) cc_final: 0.6373 (t80) REVERT: F 61 GLU cc_start: 0.8312 (mp0) cc_final: 0.7638 (mp0) outliers start: 24 outliers final: 23 residues processed: 72 average time/residue: 0.1016 time to fit residues: 9.2173 Evaluate side-chains 74 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 51 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 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 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 70 VAL Chi-restraints excluded: chain D residue 72 THR 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 E residue 79 GLN Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 11 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.0770 overall best weight: 1.8342 ------------------------------------------------------------------------------- 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 = 0.5037 r_free = 0.5037 target = 0.218376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.200706 restraints weight = 5864.333| |-----------------------------------------------------------------------------| r_work (start): 0.4884 rms_B_bonded: 2.75 r_work: 0.4947 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4876 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.4876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2640 Z= 0.220 Angle : 0.681 10.479 3570 Z= 0.349 Chirality : 0.046 0.133 468 Planarity : 0.002 0.014 444 Dihedral : 4.985 23.982 378 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 8.52 % Allowed : 27.04 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 50 PHE 0.007 0.002 PHE A 94 TYR 0.007 0.001 TYR A 39 ********************** 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 79 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 GLU cc_start: 0.8429 (mp0) cc_final: 0.7512 (mp0) REVERT: E 39 TYR cc_start: 0.6462 (t80) cc_final: 0.6261 (t80) REVERT: E 57 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7297 (mp0) REVERT: F 61 GLU cc_start: 0.8111 (mp0) cc_final: 0.7648 (mp0) outliers start: 23 outliers final: 21 residues processed: 75 average time/residue: 0.1038 time to fit residues: 9.9075 Evaluate side-chains 76 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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 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 70 VAL Chi-restraints excluded: chain D residue 72 THR 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 70 VAL Chi-restraints excluded: chain F residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.4988 r_free = 0.4988 target = 0.214294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.196159 restraints weight = 5851.838| |-----------------------------------------------------------------------------| r_work (start): 0.4835 rms_B_bonded: 2.76 r_work: 0.4901 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4822 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.4822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2640 Z= 0.321 Angle : 0.707 8.775 3570 Z= 0.374 Chirality : 0.047 0.153 468 Planarity : 0.003 0.015 444 Dihedral : 5.451 25.643 378 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % Rotamer: Outliers : 9.26 % Allowed : 25.56 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 50 PHE 0.009 0.003 PHE A 94 TYR 0.012 0.002 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1715.16 seconds wall clock time: 30 minutes 25.86 seconds (1825.86 seconds total)