Starting phenix.real_space_refine on Wed Sep 17 03:14:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rzf_54402/09_2025/9rzf_54402.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rzf_54402/09_2025/9rzf_54402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rzf_54402/09_2025/9rzf_54402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rzf_54402/09_2025/9rzf_54402.map" model { file = "/net/cci-nas-00/data/ceres_data/9rzf_54402/09_2025/9rzf_54402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rzf_54402/09_2025/9rzf_54402.cif" } resolution = 3.8 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= 0.001 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 1596 2.51 5 N 438 2.21 5 O 504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2538 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 423 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "B" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 423 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "C" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 423 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "D" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 423 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "E" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 423 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "F" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 423 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Time building chain proxies: 0.77, per 1000 atoms: 0.30 Number of scatterers: 2538 At special positions: 0 Unit cell: (86.376, 98.088, 33.672, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 504 8.00 N 438 7.00 C 1596 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: 0.20 Conformation dependent library (CDL) restraints added in 108.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.457A pdb=" N TYR A 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.810A pdb=" N LYS A 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 49 through 55 removed outlier: 6.984A pdb=" N HIS C 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLY A 51 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N HIS A 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N THR E 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL A 52 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL E 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR A 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 61 Processing sheet with id=AA5, first strand: chain 'C' and resid 69 through 78 removed outlier: 6.528A pdb=" N VAL A 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N GLY E 73 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR A 72 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N THR E 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N VAL E 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA A 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 81 through 83 removed outlier: 6.204A pdb=" N VAL A 82 " --> pdb=" O GLU C 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 88 through 96 removed outlier: 7.025A pdb=" N ALA C 90 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ALA A 91 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR C 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY A 93 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N ILE A 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA E 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N ALA A 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N GLY E 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N THR A 92 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N VAL E 95 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 94 " --> pdb=" O VAL E 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 38 through 39 removed outlier: 7.776A pdb=" N LEU B 38 " --> pdb=" O TYR D 39 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 44 through 46 removed outlier: 6.685A pdb=" N LYS B 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N GLU D 46 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS B 45 " --> pdb=" O GLU D 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 49 through 50 removed outlier: 6.601A pdb=" N VAL B 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.274A pdb=" N THR B 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 59 through 61 removed outlier: 6.411A pdb=" N LYS B 58 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLU D 61 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS B 60 " --> pdb=" O GLU D 61 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.417A pdb=" N ALA B 69 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL B 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 74 through 78 removed outlier: 6.843A pdb=" N VAL B 74 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N VAL F 77 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA B 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.750A pdb=" N THR B 81 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 88 through 96 removed outlier: 6.963A pdb=" N ILE B 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ALA D 91 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ALA B 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLY D 93 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N THR B 92 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N VAL D 95 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N PHE B 94 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA B 89 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR F 92 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE F 94 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 95 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS F 96 " --> pdb=" O VAL B 95 " (cutoff:3.500A) 42 hydrogen bonds defined for protein. 126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.32 Time building geometry restraints manager: 0.28 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: 432 1.29 - 1.36: 396 1.36 - 1.43: 102 1.43 - 1.50: 471 1.50 - 1.57: 1149 Bond restraints: 2550 Sorted by residual: bond pdb=" CB LYS A 43 " pdb=" CG LYS A 43 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.43e+00 bond pdb=" CA VAL C 66 " pdb=" CB VAL C 66 " ideal model delta sigma weight residual 1.542 1.554 -0.013 1.08e-02 8.57e+03 1.36e+00 bond pdb=" C GLU D 83 " pdb=" N GLY D 84 " ideal model delta sigma weight residual 1.331 1.316 0.015 1.46e-02 4.69e+03 9.92e-01 bond pdb=" CB VAL B 63 " pdb=" CG2 VAL B 63 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.26e-01 bond pdb=" C LYS A 43 " pdb=" O LYS A 43 " ideal model delta sigma weight residual 1.235 1.225 0.011 1.26e-02 6.30e+03 7.10e-01 ... (remaining 2545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 3210 1.55 - 3.09: 195 3.09 - 4.64: 36 4.64 - 6.18: 5 6.18 - 7.73: 4 Bond angle restraints: 3450 Sorted by residual: angle pdb=" N VAL C 66 " pdb=" CA VAL C 66 " pdb=" C VAL C 66 " ideal model delta sigma weight residual 112.43 107.00 5.43 9.20e-01 1.18e+00 3.48e+01 angle pdb=" C ASN E 65 " pdb=" N VAL E 66 " pdb=" CA VAL E 66 " ideal model delta sigma weight residual 122.77 118.74 4.03 1.05e+00 9.07e-01 1.47e+01 angle pdb=" C VAL C 66 " pdb=" CA VAL C 66 " pdb=" CB VAL C 66 " ideal model delta sigma weight residual 111.65 116.02 -4.37 1.22e+00 6.72e-01 1.28e+01 angle pdb=" CA VAL C 66 " pdb=" CB VAL C 66 " pdb=" CG1 VAL C 66 " ideal model delta sigma weight residual 110.40 116.28 -5.88 1.70e+00 3.46e-01 1.20e+01 angle pdb=" CB LYS A 43 " pdb=" CG LYS A 43 " pdb=" CD LYS A 43 " ideal model delta sigma weight residual 111.30 117.99 -6.69 2.30e+00 1.89e-01 8.47e+00 ... (remaining 3445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.05: 1283 14.05 - 28.09: 124 28.09 - 42.14: 51 42.14 - 56.19: 20 56.19 - 70.23: 10 Dihedral angle restraints: 1488 sinusoidal: 498 harmonic: 990 Sorted by residual: dihedral pdb=" CA THR B 44 " pdb=" C THR B 44 " pdb=" N LYS B 45 " pdb=" CA LYS B 45 " ideal model delta harmonic sigma weight residual 180.00 163.36 16.64 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA LYS A 45 " pdb=" C LYS A 45 " pdb=" N GLU A 46 " pdb=" CA GLU A 46 " ideal model delta harmonic sigma weight residual -180.00 -163.75 -16.25 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA VAL B 37 " pdb=" C VAL B 37 " pdb=" N LEU B 38 " pdb=" CA LEU B 38 " ideal model delta harmonic sigma weight residual -180.00 -164.22 -15.78 0 5.00e+00 4.00e-02 9.96e+00 ... (remaining 1485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 297 0.048 - 0.096: 113 0.096 - 0.144: 47 0.144 - 0.192: 3 0.192 - 0.240: 2 Chirality restraints: 462 Sorted by residual: chirality pdb=" CB VAL B 40 " pdb=" CA VAL B 40 " pdb=" CG1 VAL B 40 " pdb=" CG2 VAL B 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL D 52 " pdb=" CA VAL D 52 " pdb=" CG1 VAL D 52 " pdb=" CG2 VAL D 52 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB VAL E 66 " pdb=" CA VAL E 66 " pdb=" CG1 VAL E 66 " pdb=" CG2 VAL E 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 459 not shown) Planarity restraints: 420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 83 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" CD GLU D 83 " -0.040 2.00e-02 2.50e+03 pdb=" OE1 GLU D 83 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU D 83 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 66 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.76e+00 pdb=" C VAL C 66 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL C 66 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY C 67 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 43 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C LYS A 43 " 0.033 2.00e-02 2.50e+03 pdb=" O LYS A 43 " -0.013 2.00e-02 2.50e+03 pdb=" N THR A 44 " -0.011 2.00e-02 2.50e+03 ... (remaining 417 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 1442 3.03 - 3.50: 2384 3.50 - 3.97: 3730 3.97 - 4.43: 3945 4.43 - 4.90: 7200 Nonbonded interactions: 18701 Sorted by model distance: nonbonded pdb=" N VAL C 66 " pdb=" N GLY C 67 " model vdw 2.564 2.560 nonbonded pdb=" N ALA B 56 " pdb=" O ALA B 56 " model vdw 2.609 2.496 nonbonded pdb=" N ALA D 56 " pdb=" O ALA D 56 " model vdw 2.612 2.496 nonbonded pdb=" N ALA E 56 " pdb=" O ALA E 56 " model vdw 2.614 2.496 nonbonded pdb=" N ALA F 56 " pdb=" O ALA F 56 " model vdw 2.616 2.496 ... (remaining 18696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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 group one per residue 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: 4.270 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: 0.010 Process input model: 4.550 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 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 : 0.004 0.047 2550 Z= 0.192 Angle : 0.858 7.729 3450 Z= 0.484 Chirality : 0.057 0.240 462 Planarity : 0.004 0.023 420 Dihedral : 16.073 70.232 864 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.003 TYR E 39 PHE 0.019 0.004 PHE E 94 HIS 0.005 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 2550) covalent geometry : angle 0.85808 ( 3450) hydrogen bonds : bond 0.23096 ( 42) hydrogen bonds : angle 8.00288 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.102 Fit side-chains REVERT: A 58 LYS cc_start: 0.5473 (mtpt) cc_final: 0.5243 (mtpt) REVERT: C 60 LYS cc_start: 0.5191 (ttmt) cc_final: 0.4940 (mttt) REVERT: C 72 THR cc_start: 0.7790 (m) cc_final: 0.7302 (p) REVERT: C 83 GLU cc_start: 0.7382 (mp0) cc_final: 0.6328 (mp0) REVERT: D 83 GLU cc_start: 0.7178 (pm20) cc_final: 0.5410 (tp30) REVERT: D 96 LYS cc_start: 0.7167 (tttt) cc_final: 0.6613 (tttm) REVERT: E 43 LYS cc_start: 0.5837 (tmtt) cc_final: 0.4981 (mmtt) REVERT: E 79 GLN cc_start: 0.8408 (mp10) cc_final: 0.8162 (mp10) REVERT: E 83 GLU cc_start: 0.6883 (mp0) cc_final: 0.6384 (pm20) REVERT: F 43 LYS cc_start: 0.6286 (tmtt) cc_final: 0.5511 (mttm) REVERT: F 45 LYS cc_start: 0.7633 (mttt) cc_final: 0.6131 (mmmt) REVERT: F 60 LYS cc_start: 0.6608 (ttmt) cc_final: 0.4989 (tptt) REVERT: F 79 GLN cc_start: 0.8239 (mp10) cc_final: 0.7698 (mt0) REVERT: F 83 GLU cc_start: 0.6786 (mp0) cc_final: 0.5617 (pm20) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0856 time to fit residues: 8.9201 Evaluate side-chains 86 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.076 ------------------------------------------------------------------------------- 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: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.0370 chunk 13 optimal weight: 1.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** 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 = 0.4384 r_free = 0.4384 target = 0.175435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.169346 restraints weight = 3584.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.171387 restraints weight = 1751.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.172658 restraints weight = 985.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.173382 restraints weight = 603.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.173946 restraints weight = 409.345| |-----------------------------------------------------------------------------| r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2550 Z= 0.182 Angle : 0.629 4.389 3450 Z= 0.349 Chirality : 0.051 0.165 462 Planarity : 0.002 0.011 420 Dihedral : 5.584 15.682 366 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.03 % Allowed : 17.80 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR A 39 PHE 0.008 0.002 PHE B 94 HIS 0.005 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 2550) covalent geometry : angle 0.62881 ( 3450) hydrogen bonds : bond 0.03176 ( 42) hydrogen bonds : angle 5.70825 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.062 Fit side-chains REVERT: A 61 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 72 THR cc_start: 0.8134 (m) cc_final: 0.7739 (p) REVERT: B 96 LYS cc_start: 0.8077 (tttt) cc_final: 0.7692 (ttpt) REVERT: C 60 LYS cc_start: 0.5813 (ttmt) cc_final: 0.5609 (mttt) REVERT: C 83 GLU cc_start: 0.7171 (mp0) cc_final: 0.6483 (mp0) REVERT: D 83 GLU cc_start: 0.7392 (pm20) cc_final: 0.5327 (tp30) REVERT: D 96 LYS cc_start: 0.7328 (tttt) cc_final: 0.6932 (tttm) REVERT: E 43 LYS cc_start: 0.5889 (tmtt) cc_final: 0.5235 (mmtt) REVERT: E 79 GLN cc_start: 0.8410 (mp10) cc_final: 0.7707 (mt0) REVERT: F 43 LYS cc_start: 0.5939 (tmtt) cc_final: 0.5426 (tppt) REVERT: F 45 LYS cc_start: 0.7512 (mttt) cc_final: 0.6351 (mmmt) REVERT: F 60 LYS cc_start: 0.7026 (ttmt) cc_final: 0.5695 (tptt) REVERT: F 79 GLN cc_start: 0.8290 (mp10) cc_final: 0.7613 (mt0) outliers start: 8 outliers final: 7 residues processed: 93 average time/residue: 0.0719 time to fit residues: 7.5491 Evaluate side-chains 92 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 64 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4373 r_free = 0.4373 target = 0.173908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.167998 restraints weight = 3668.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.169998 restraints weight = 1779.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.171245 restraints weight = 978.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.171976 restraints weight = 585.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.172511 restraints weight = 394.013| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2550 Z= 0.179 Angle : 0.602 5.324 3450 Z= 0.339 Chirality : 0.051 0.164 462 Planarity : 0.003 0.022 420 Dihedral : 5.399 15.397 366 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.55 % Allowed : 23.48 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR A 39 PHE 0.008 0.002 PHE B 94 HIS 0.005 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 2550) covalent geometry : angle 0.60162 ( 3450) hydrogen bonds : bond 0.03209 ( 42) hydrogen bonds : angle 5.58823 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.094 Fit side-chains REVERT: A 61 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7737 (mt-10) REVERT: A 72 THR cc_start: 0.7958 (m) cc_final: 0.7499 (p) REVERT: A 83 GLU cc_start: 0.7433 (mp0) cc_final: 0.7213 (mp0) REVERT: B 75 THR cc_start: 0.6747 (t) cc_final: 0.6494 (p) REVERT: C 60 LYS cc_start: 0.5847 (ttmt) cc_final: 0.5626 (mttt) REVERT: C 83 GLU cc_start: 0.7151 (mp0) cc_final: 0.6714 (mp0) REVERT: D 83 GLU cc_start: 0.7469 (pm20) cc_final: 0.5165 (tp30) REVERT: D 96 LYS cc_start: 0.7398 (tttt) cc_final: 0.6979 (tttm) REVERT: E 43 LYS cc_start: 0.5949 (tmtt) cc_final: 0.5267 (mmtt) REVERT: E 79 GLN cc_start: 0.8433 (mp10) cc_final: 0.7781 (mt0) REVERT: E 82 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8583 (p) REVERT: E 96 LYS cc_start: 0.7647 (ptmt) cc_final: 0.7426 (ptmt) REVERT: F 43 LYS cc_start: 0.6176 (tmtt) cc_final: 0.5213 (tppt) REVERT: F 45 LYS cc_start: 0.7498 (mttt) cc_final: 0.6338 (mmmt) REVERT: F 60 LYS cc_start: 0.6741 (ttmt) cc_final: 0.5522 (tptt) REVERT: F 79 GLN cc_start: 0.8194 (mp10) cc_final: 0.7398 (mt0) REVERT: F 95 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8487 (p) outliers start: 12 outliers final: 7 residues processed: 95 average time/residue: 0.0737 time to fit residues: 7.9652 Evaluate side-chains 93 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.0060 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN D 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.177678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.171733 restraints weight = 3575.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.173795 restraints weight = 1687.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.175044 restraints weight = 930.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.175827 restraints weight = 551.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.176319 restraints weight = 349.543| |-----------------------------------------------------------------------------| r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2550 Z= 0.139 Angle : 0.542 4.766 3450 Z= 0.307 Chirality : 0.050 0.162 462 Planarity : 0.002 0.019 420 Dihedral : 5.004 13.984 366 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 7.58 % Allowed : 23.86 % Favored : 68.56 % 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 aren not related in a simple way. whole: -2.46 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR B 39 PHE 0.006 0.002 PHE B 94 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 2550) covalent geometry : angle 0.54192 ( 3450) hydrogen bonds : bond 0.02892 ( 42) hydrogen bonds : angle 5.25830 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.103 Fit side-chains REVERT: A 61 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7634 (mt-10) REVERT: A 72 THR cc_start: 0.8003 (m) cc_final: 0.7490 (p) REVERT: B 75 THR cc_start: 0.6588 (t) cc_final: 0.6277 (p) REVERT: C 60 LYS cc_start: 0.5910 (ttmt) cc_final: 0.5663 (mttt) REVERT: C 83 GLU cc_start: 0.7092 (mp0) cc_final: 0.6613 (mp0) REVERT: D 83 GLU cc_start: 0.7593 (pm20) cc_final: 0.5147 (tp30) REVERT: D 96 LYS cc_start: 0.7365 (tttt) cc_final: 0.6910 (tttm) REVERT: E 43 LYS cc_start: 0.6559 (tmtt) cc_final: 0.5794 (mmtt) REVERT: E 79 GLN cc_start: 0.8458 (mp10) cc_final: 0.7661 (mt0) REVERT: E 82 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8608 (p) REVERT: E 96 LYS cc_start: 0.7608 (ptmt) cc_final: 0.7375 (ptmt) REVERT: F 43 LYS cc_start: 0.6223 (tmtt) cc_final: 0.5211 (tppt) REVERT: F 45 LYS cc_start: 0.7443 (mttt) cc_final: 0.6306 (mmmt) REVERT: F 60 LYS cc_start: 0.6722 (ttmt) cc_final: 0.5499 (tptt) REVERT: F 79 GLN cc_start: 0.8043 (mp10) cc_final: 0.7311 (mt0) REVERT: F 95 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8496 (p) outliers start: 20 outliers final: 12 residues processed: 100 average time/residue: 0.0757 time to fit residues: 8.6526 Evaluate side-chains 98 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 = 0.4429 r_free = 0.4429 target = 0.177842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.171808 restraints weight = 3653.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.173950 restraints weight = 1671.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.175256 restraints weight = 902.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.176047 restraints weight = 530.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.176540 restraints weight = 329.916| |-----------------------------------------------------------------------------| r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2550 Z= 0.121 Angle : 0.520 4.279 3450 Z= 0.294 Chirality : 0.049 0.159 462 Planarity : 0.002 0.016 420 Dihedral : 4.699 13.503 366 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 6.44 % Allowed : 26.89 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR E 39 PHE 0.007 0.002 PHE E 94 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 2550) covalent geometry : angle 0.52026 ( 3450) hydrogen bonds : bond 0.02739 ( 42) hydrogen bonds : angle 5.17309 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.117 Fit side-chains REVERT: A 59 THR cc_start: 0.7964 (m) cc_final: 0.7591 (t) REVERT: A 61 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7642 (mt-10) REVERT: A 72 THR cc_start: 0.7952 (m) cc_final: 0.7440 (p) REVERT: C 60 LYS cc_start: 0.5969 (ttmt) cc_final: 0.5700 (mttt) REVERT: C 83 GLU cc_start: 0.7046 (mp0) cc_final: 0.6533 (mp0) REVERT: D 83 GLU cc_start: 0.7422 (pm20) cc_final: 0.5001 (tp30) REVERT: D 96 LYS cc_start: 0.7353 (tttt) cc_final: 0.6895 (tttm) REVERT: E 43 LYS cc_start: 0.6490 (tmtt) cc_final: 0.5692 (mmtt) REVERT: E 79 GLN cc_start: 0.8391 (mp10) cc_final: 0.7939 (mt0) REVERT: F 43 LYS cc_start: 0.6066 (tmtt) cc_final: 0.5423 (tppt) REVERT: F 45 LYS cc_start: 0.7231 (mttt) cc_final: 0.6253 (mmmt) REVERT: F 60 LYS cc_start: 0.6637 (ttmt) cc_final: 0.5514 (tptt) REVERT: F 79 GLN cc_start: 0.8034 (mp10) cc_final: 0.7384 (mt0) REVERT: F 95 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8506 (p) outliers start: 17 outliers final: 14 residues processed: 98 average time/residue: 0.0706 time to fit residues: 7.9204 Evaluate side-chains 101 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.0170 chunk 27 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.184080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.178279 restraints weight = 3566.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.180327 restraints weight = 1687.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.181579 restraints weight = 907.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.182362 restraints weight = 538.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.182796 restraints weight = 345.348| |-----------------------------------------------------------------------------| r_work (final): 0.4475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2550 Z= 0.111 Angle : 0.522 7.781 3450 Z= 0.288 Chirality : 0.049 0.156 462 Planarity : 0.002 0.013 420 Dihedral : 4.531 14.740 366 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 6.82 % Allowed : 29.17 % Favored : 64.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.37 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR E 39 PHE 0.007 0.001 PHE A 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 2550) covalent geometry : angle 0.52215 ( 3450) hydrogen bonds : bond 0.02653 ( 42) hydrogen bonds : angle 5.06954 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.102 Fit side-chains REVERT: A 59 THR cc_start: 0.7967 (m) cc_final: 0.7586 (t) REVERT: A 61 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7465 (mt-10) REVERT: A 79 GLN cc_start: 0.7590 (mt0) cc_final: 0.7252 (mt0) REVERT: B 40 VAL cc_start: 0.7955 (p) cc_final: 0.7592 (t) REVERT: C 60 LYS cc_start: 0.5976 (ttmt) cc_final: 0.5705 (mttt) REVERT: C 83 GLU cc_start: 0.6946 (mp0) cc_final: 0.6495 (mp0) REVERT: D 83 GLU cc_start: 0.7270 (pm20) cc_final: 0.4834 (tp30) REVERT: D 96 LYS cc_start: 0.7332 (tttt) cc_final: 0.6891 (tttm) REVERT: E 43 LYS cc_start: 0.6527 (tmtt) cc_final: 0.5803 (mmtt) REVERT: E 79 GLN cc_start: 0.8383 (mp10) cc_final: 0.7978 (mt0) REVERT: F 43 LYS cc_start: 0.6101 (tmtt) cc_final: 0.5429 (tppt) REVERT: F 45 LYS cc_start: 0.7086 (mttt) cc_final: 0.6253 (mmmt) REVERT: F 57 GLU cc_start: 0.4756 (pt0) cc_final: 0.4306 (tp30) REVERT: F 60 LYS cc_start: 0.6663 (ttmt) cc_final: 0.5606 (tptt) REVERT: F 79 GLN cc_start: 0.8079 (mp10) cc_final: 0.7273 (mt0) REVERT: F 95 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8504 (p) outliers start: 18 outliers final: 16 residues processed: 98 average time/residue: 0.0823 time to fit residues: 9.2222 Evaluate side-chains 99 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4305 r_free = 0.4305 target = 0.167767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.161816 restraints weight = 3760.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.163902 restraints weight = 1696.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.165118 restraints weight = 906.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.165923 restraints weight = 542.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.166421 restraints weight = 352.862| |-----------------------------------------------------------------------------| r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 2550 Z= 0.274 Angle : 0.721 7.600 3450 Z= 0.397 Chirality : 0.053 0.158 462 Planarity : 0.003 0.013 420 Dihedral : 5.636 17.394 366 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 7.95 % Allowed : 29.55 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR A 39 PHE 0.008 0.002 PHE B 94 HIS 0.006 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00626 ( 2550) covalent geometry : angle 0.72102 ( 3450) hydrogen bonds : bond 0.02916 ( 42) hydrogen bonds : angle 5.69265 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.106 Fit side-chains REVERT: A 59 THR cc_start: 0.7728 (m) cc_final: 0.7501 (t) REVERT: A 72 THR cc_start: 0.7896 (m) cc_final: 0.7484 (p) REVERT: A 82 VAL cc_start: 0.8863 (OUTLIER) cc_final: 0.8352 (p) REVERT: C 83 GLU cc_start: 0.7053 (mp0) cc_final: 0.6693 (mp0) REVERT: D 83 GLU cc_start: 0.7760 (pm20) cc_final: 0.5468 (tp30) REVERT: D 96 LYS cc_start: 0.7488 (tttt) cc_final: 0.7066 (tttm) REVERT: E 43 LYS cc_start: 0.6565 (tmtt) cc_final: 0.5805 (mmtt) REVERT: E 79 GLN cc_start: 0.8641 (mp10) cc_final: 0.8252 (mt0) REVERT: F 43 LYS cc_start: 0.6278 (tmtt) cc_final: 0.5133 (tppt) REVERT: F 45 LYS cc_start: 0.7225 (mttt) cc_final: 0.6180 (mmmt) REVERT: F 60 LYS cc_start: 0.6493 (ttmt) cc_final: 0.5328 (tptt) REVERT: F 79 GLN cc_start: 0.8304 (mp10) cc_final: 0.7299 (mt0) REVERT: F 95 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8630 (p) outliers start: 21 outliers final: 17 residues processed: 106 average time/residue: 0.0720 time to fit residues: 8.7893 Evaluate side-chains 105 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.171456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.165486 restraints weight = 3793.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.167582 restraints weight = 1699.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.168806 restraints weight = 906.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.169633 restraints weight = 559.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.170135 restraints weight = 359.916| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2550 Z= 0.192 Angle : 0.645 8.500 3450 Z= 0.354 Chirality : 0.051 0.163 462 Planarity : 0.003 0.012 420 Dihedral : 5.276 15.290 366 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 7.20 % Allowed : 30.68 % Favored : 62.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR A 39 PHE 0.008 0.002 PHE B 94 HIS 0.005 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 2550) covalent geometry : angle 0.64500 ( 3450) hydrogen bonds : bond 0.02753 ( 42) hydrogen bonds : angle 5.49434 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.122 Fit side-chains REVERT: A 59 THR cc_start: 0.7742 (m) cc_final: 0.7475 (t) REVERT: A 72 THR cc_start: 0.7929 (m) cc_final: 0.7585 (p) REVERT: A 79 GLN cc_start: 0.7782 (mt0) cc_final: 0.7516 (mt0) REVERT: A 82 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8149 (p) REVERT: B 75 THR cc_start: 0.6986 (t) cc_final: 0.6692 (p) REVERT: B 79 GLN cc_start: 0.7182 (mt0) cc_final: 0.6979 (mt0) REVERT: C 83 GLU cc_start: 0.6943 (mp0) cc_final: 0.6526 (mp0) REVERT: D 83 GLU cc_start: 0.7531 (pm20) cc_final: 0.5371 (tp30) REVERT: D 96 LYS cc_start: 0.7473 (tttt) cc_final: 0.6921 (tttm) REVERT: E 43 LYS cc_start: 0.6453 (tmtt) cc_final: 0.5757 (mttp) REVERT: E 79 GLN cc_start: 0.8618 (mp10) cc_final: 0.8163 (mt0) REVERT: F 43 LYS cc_start: 0.6365 (tmtt) cc_final: 0.5188 (tppt) REVERT: F 45 LYS cc_start: 0.7028 (mttt) cc_final: 0.6074 (mmmt) REVERT: F 60 LYS cc_start: 0.6466 (ttmt) cc_final: 0.5283 (tptt) REVERT: F 79 GLN cc_start: 0.8118 (mp10) cc_final: 0.7086 (mt0) REVERT: F 95 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8623 (p) outliers start: 19 outliers final: 17 residues processed: 104 average time/residue: 0.0838 time to fit residues: 9.9615 Evaluate side-chains 106 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 0.0070 chunk 1 optimal weight: 0.0170 chunk 32 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.2994 ------------------------------------------------------------------------------- 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 = 0.4529 r_free = 0.4529 target = 0.184234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.178066 restraints weight = 3602.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.180204 restraints weight = 1704.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.181511 restraints weight = 922.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.182330 restraints weight = 549.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.182853 restraints weight = 354.853| |-----------------------------------------------------------------------------| r_work (final): 0.4510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2550 Z= 0.106 Angle : 0.544 8.850 3450 Z= 0.297 Chirality : 0.049 0.159 462 Planarity : 0.002 0.011 420 Dihedral : 4.544 16.919 366 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 6.44 % Allowed : 31.82 % Favored : 61.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.49 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR E 39 PHE 0.006 0.001 PHE A 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 2550) covalent geometry : angle 0.54389 ( 3450) hydrogen bonds : bond 0.02493 ( 42) hydrogen bonds : angle 4.95448 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.105 Fit side-chains REVERT: A 59 THR cc_start: 0.7984 (m) cc_final: 0.7637 (t) REVERT: A 72 THR cc_start: 0.8010 (m) cc_final: 0.7754 (p) REVERT: A 79 GLN cc_start: 0.7519 (mt0) cc_final: 0.7148 (mt0) REVERT: A 82 VAL cc_start: 0.9008 (OUTLIER) cc_final: 0.8205 (t) REVERT: B 74 VAL cc_start: 0.6629 (OUTLIER) cc_final: 0.6240 (m) REVERT: B 75 THR cc_start: 0.7152 (t) cc_final: 0.6856 (p) REVERT: B 79 GLN cc_start: 0.7155 (mt0) cc_final: 0.6917 (mt0) REVERT: C 79 GLN cc_start: 0.7887 (mt0) cc_final: 0.7411 (mt0) REVERT: C 83 GLU cc_start: 0.6810 (mp0) cc_final: 0.6503 (mp0) REVERT: D 83 GLU cc_start: 0.7040 (pm20) cc_final: 0.4680 (tp30) REVERT: D 96 LYS cc_start: 0.7345 (tttt) cc_final: 0.6836 (tttm) REVERT: E 43 LYS cc_start: 0.6048 (tmtt) cc_final: 0.5581 (mttp) REVERT: E 79 GLN cc_start: 0.8455 (mp10) cc_final: 0.8073 (mt0) REVERT: F 43 LYS cc_start: 0.6372 (tmtt) cc_final: 0.5279 (tppt) REVERT: F 45 LYS cc_start: 0.7141 (mttt) cc_final: 0.6278 (mmmt) REVERT: F 60 LYS cc_start: 0.6784 (ttmt) cc_final: 0.5898 (tptt) REVERT: F 79 GLN cc_start: 0.7966 (mp10) cc_final: 0.7088 (mt0) REVERT: F 95 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8505 (p) outliers start: 17 outliers final: 12 residues processed: 104 average time/residue: 0.0808 time to fit residues: 9.6362 Evaluate side-chains 103 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 28 optimal weight: 0.0670 chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 = 0.4510 r_free = 0.4510 target = 0.183555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.177557 restraints weight = 3658.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.179692 restraints weight = 1695.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.180959 restraints weight = 923.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.181702 restraints weight = 553.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.182235 restraints weight = 365.180| |-----------------------------------------------------------------------------| r_work (final): 0.4489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2550 Z= 0.124 Angle : 0.560 8.525 3450 Z= 0.310 Chirality : 0.049 0.160 462 Planarity : 0.002 0.025 420 Dihedral : 4.589 15.649 366 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 6.06 % Allowed : 32.95 % Favored : 60.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR E 39 PHE 0.007 0.001 PHE B 94 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 2550) covalent geometry : angle 0.56030 ( 3450) hydrogen bonds : bond 0.02518 ( 42) hydrogen bonds : angle 4.99958 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.101 Fit side-chains REVERT: A 59 THR cc_start: 0.7975 (m) cc_final: 0.7642 (t) REVERT: A 72 THR cc_start: 0.8022 (m) cc_final: 0.7774 (p) REVERT: A 79 GLN cc_start: 0.7712 (mt0) cc_final: 0.7355 (mt0) REVERT: A 82 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8189 (t) REVERT: B 79 GLN cc_start: 0.7199 (mt0) cc_final: 0.6967 (mt0) REVERT: C 79 GLN cc_start: 0.7952 (mt0) cc_final: 0.7523 (mt0) REVERT: C 83 GLU cc_start: 0.6880 (mp0) cc_final: 0.6541 (mp0) REVERT: D 83 GLU cc_start: 0.7250 (pm20) cc_final: 0.4834 (tp30) REVERT: D 96 LYS cc_start: 0.7365 (tttt) cc_final: 0.6845 (tttm) REVERT: E 43 LYS cc_start: 0.6381 (tmtt) cc_final: 0.5797 (mttp) REVERT: E 79 GLN cc_start: 0.8490 (mp10) cc_final: 0.8095 (mt0) REVERT: F 43 LYS cc_start: 0.6375 (tmtt) cc_final: 0.5254 (tppt) REVERT: F 45 LYS cc_start: 0.7131 (mttt) cc_final: 0.6269 (mmmt) REVERT: F 60 LYS cc_start: 0.6798 (ttmt) cc_final: 0.5877 (tptt) REVERT: F 79 GLN cc_start: 0.7992 (mp10) cc_final: 0.7113 (mt0) REVERT: F 95 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8519 (p) outliers start: 16 outliers final: 14 residues processed: 99 average time/residue: 0.0741 time to fit residues: 8.3990 Evaluate side-chains 102 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.179975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.174178 restraints weight = 3664.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.176151 restraints weight = 1721.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.177355 restraints weight = 959.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.178142 restraints weight = 579.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.178622 restraints weight = 373.889| |-----------------------------------------------------------------------------| r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2550 Z= 0.166 Angle : 0.607 8.255 3450 Z= 0.335 Chirality : 0.050 0.160 462 Planarity : 0.003 0.025 420 Dihedral : 4.948 15.876 366 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 6.06 % Allowed : 32.58 % Favored : 61.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR E 39 PHE 0.008 0.002 PHE B 94 HIS 0.004 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 2550) covalent geometry : angle 0.60673 ( 3450) hydrogen bonds : bond 0.02609 ( 42) hydrogen bonds : angle 5.18727 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 762.48 seconds wall clock time: 13 minutes 53.87 seconds (833.87 seconds total)