Starting phenix.real_space_refine on Wed Jun 11 10:19:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9be8_44473/06_2025/9be8_44473.cif Found real_map, /net/cci-nas-00/data/ceres_data/9be8_44473/06_2025/9be8_44473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9be8_44473/06_2025/9be8_44473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9be8_44473/06_2025/9be8_44473.map" model { file = "/net/cci-nas-00/data/ceres_data/9be8_44473/06_2025/9be8_44473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9be8_44473/06_2025/9be8_44473.cif" } resolution = 4.14 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 82 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 24 5.16 5 C 4038 2.51 5 N 1134 2.21 5 O 1212 1.98 5 H 6342 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12750 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2100 Classifications: {'peptide': 134} Link IDs: {'TRANS': 133} Chain breaks: 1 Chain: "I" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2100 Classifications: {'peptide': 134} Link IDs: {'TRANS': 133} Chain breaks: 1 Chain: "L" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2100 Classifications: {'peptide': 134} Link IDs: {'TRANS': 133} Chain breaks: 1 Chain: "O" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2100 Classifications: {'peptide': 134} Link IDs: {'TRANS': 133} Chain breaks: 1 Chain: "B" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2100 Classifications: {'peptide': 134} Link IDs: {'TRANS': 133} Chain breaks: 1 Chain: "F" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2100 Classifications: {'peptide': 134} Link IDs: {'TRANS': 133} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "I" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "O" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 7.09, per 1000 atoms: 0.56 Number of scatterers: 12750 At special positions: 0 Unit cell: (100.386, 102.102, 51.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 O 1212 8.00 N 1134 7.00 C 4038 6.00 H 6342 1.00 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: 3.09 Conformation dependent library (CDL) restraints added in 991.5 milliseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1476 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 45.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 71 removed outlier: 3.500A pdb=" N VAL A 11 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 43 " --> pdb=" O ILE L 143 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER L 139 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA L 140 " --> pdb=" O MET L 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL L 105 " --> pdb=" O LEU L 124 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU L 122 " --> pdb=" O VAL L 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 38 removed outlier: 7.418A pdb=" N PHE A 32 " --> pdb=" O THR A 25 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR A 25 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS A 34 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN A 20 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 54 " --> pdb=" O MET A 24 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER A 53 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 124 removed outlier: 3.580A pdb=" N GLU A 122 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 105 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA A 140 " --> pdb=" O MET A 110 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER A 139 " --> pdb=" O GLN B 47 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 43 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 68 through 71 removed outlier: 3.501A pdb=" N VAL I 11 " --> pdb=" O GLN I 64 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL I 43 " --> pdb=" O ILE O 143 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER O 139 " --> pdb=" O GLN I 47 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA O 140 " --> pdb=" O MET O 110 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL O 105 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU O 122 " --> pdb=" O VAL O 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 32 through 38 removed outlier: 7.418A pdb=" N PHE I 32 " --> pdb=" O THR I 25 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR I 25 " --> pdb=" O PHE I 32 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS I 34 " --> pdb=" O GLY I 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN I 20 " --> pdb=" O ARG I 58 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA I 54 " --> pdb=" O MET I 24 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER I 53 " --> pdb=" O GLN I 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 122 through 124 removed outlier: 3.579A pdb=" N GLU I 122 " --> pdb=" O VAL I 107 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL I 105 " --> pdb=" O LEU I 124 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA I 140 " --> pdb=" O MET I 110 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER I 139 " --> pdb=" O GLN L 47 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL L 43 " --> pdb=" O ILE I 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 32 through 38 removed outlier: 7.418A pdb=" N PHE L 32 " --> pdb=" O THR L 25 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR L 25 " --> pdb=" O PHE L 32 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS L 34 " --> pdb=" O GLY L 23 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN L 20 " --> pdb=" O ARG L 58 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA L 54 " --> pdb=" O MET L 24 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER L 53 " --> pdb=" O GLN L 133 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 68 through 71 removed outlier: 3.995A pdb=" N VAL O 43 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER F 139 " --> pdb=" O GLN O 47 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA F 140 " --> pdb=" O MET F 110 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL F 105 " --> pdb=" O LEU F 124 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU F 122 " --> pdb=" O VAL F 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 32 through 38 removed outlier: 7.419A pdb=" N PHE O 32 " --> pdb=" O THR O 25 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR O 25 " --> pdb=" O PHE O 32 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS O 34 " --> pdb=" O GLY O 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN O 20 " --> pdb=" O ARG O 58 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA O 54 " --> pdb=" O MET O 24 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER O 53 " --> pdb=" O GLN O 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 32 through 38 removed outlier: 7.418A pdb=" N PHE B 32 " --> pdb=" O THR B 25 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR B 25 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS B 34 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 20 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA B 54 " --> pdb=" O MET B 24 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER B 53 " --> pdb=" O GLN B 133 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 122 through 124 removed outlier: 3.579A pdb=" N GLU B 122 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 105 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA B 140 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER B 139 " --> pdb=" O GLN F 47 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL F 43 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL F 11 " --> pdb=" O GLN F 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 32 through 38 removed outlier: 7.419A pdb=" N PHE F 32 " --> pdb=" O THR F 25 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR F 25 " --> pdb=" O PHE F 32 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS F 34 " --> pdb=" O GLY F 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN F 20 " --> pdb=" O ARG F 58 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA F 54 " --> pdb=" O MET F 24 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER F 53 " --> pdb=" O GLN F 133 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 783 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: 4.45 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6342 1.03 - 1.23: 7 1.23 - 1.42: 2747 1.42 - 1.61: 3708 1.61 - 1.81: 48 Bond restraints: 12852 Sorted by residual: bond pdb=" CA TRP F 201 " pdb=" C TRP F 201 " ideal model delta sigma weight residual 1.525 1.507 0.018 2.10e-02 2.27e+03 7.48e-01 bond pdb=" CA GLY O 109 " pdb=" C GLY O 109 " ideal model delta sigma weight residual 1.516 1.521 -0.005 8.10e-03 1.52e+04 4.08e-01 bond pdb=" CA GLY I 109 " pdb=" C GLY I 109 " ideal model delta sigma weight residual 1.516 1.521 -0.005 8.10e-03 1.52e+04 3.85e-01 bond pdb=" C TRP I 201 " pdb=" OXT TRP I 201 " ideal model delta sigma weight residual 1.231 1.219 0.012 2.00e-02 2.50e+03 3.81e-01 bond pdb=" C TRP F 201 " pdb=" OXT TRP F 201 " ideal model delta sigma weight residual 1.231 1.219 0.012 2.00e-02 2.50e+03 3.72e-01 ... (remaining 12847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.63: 20502 0.63 - 1.25: 2418 1.25 - 1.88: 165 1.88 - 2.51: 9 2.51 - 3.14: 6 Bond angle restraints: 23100 Sorted by residual: angle pdb=" N HIS B 119 " pdb=" CA HIS B 119 " pdb=" C HIS B 119 " ideal model delta sigma weight residual 108.56 111.70 -3.14 1.74e+00 3.30e-01 3.25e+00 angle pdb=" N HIS A 119 " pdb=" CA HIS A 119 " pdb=" C HIS A 119 " ideal model delta sigma weight residual 108.56 111.67 -3.11 1.74e+00 3.30e-01 3.19e+00 angle pdb=" N HIS F 119 " pdb=" CA HIS F 119 " pdb=" C HIS F 119 " ideal model delta sigma weight residual 108.56 111.66 -3.10 1.74e+00 3.30e-01 3.17e+00 angle pdb=" N HIS O 119 " pdb=" CA HIS O 119 " pdb=" C HIS O 119 " ideal model delta sigma weight residual 108.56 111.65 -3.09 1.74e+00 3.30e-01 3.15e+00 angle pdb=" N HIS L 119 " pdb=" CA HIS L 119 " pdb=" C HIS L 119 " ideal model delta sigma weight residual 108.56 111.61 -3.05 1.74e+00 3.30e-01 3.07e+00 ... (remaining 23095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 5485 17.30 - 34.59: 354 34.59 - 51.88: 60 51.88 - 69.18: 48 69.18 - 86.47: 23 Dihedral angle restraints: 5970 sinusoidal: 3198 harmonic: 2772 Sorted by residual: dihedral pdb=" CB GLU F 73 " pdb=" CG GLU F 73 " pdb=" CD GLU F 73 " pdb=" OE1 GLU F 73 " ideal model delta sinusoidal sigma weight residual 0.00 -86.47 86.47 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CB GLU A 73 " pdb=" CG GLU A 73 " pdb=" CD GLU A 73 " pdb=" OE1 GLU A 73 " ideal model delta sinusoidal sigma weight residual 0.00 -86.42 86.42 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CB GLU I 73 " pdb=" CG GLU I 73 " pdb=" CD GLU I 73 " pdb=" OE1 GLU I 73 " ideal model delta sinusoidal sigma weight residual 0.00 -86.42 86.42 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 5967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 588 0.027 - 0.055: 249 0.055 - 0.082: 9 0.082 - 0.109: 51 0.109 - 0.136: 69 Chirality restraints: 966 Sorted by residual: chirality pdb=" CA ILE A 131 " pdb=" N ILE A 131 " pdb=" C ILE A 131 " pdb=" CB ILE A 131 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ILE F 131 " pdb=" N ILE F 131 " pdb=" C ILE F 131 " pdb=" CB ILE F 131 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE I 131 " pdb=" N ILE I 131 " pdb=" C ILE I 131 " pdb=" CB ILE I 131 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 963 not shown) Planarity restraints: 1902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 32 " 0.003 2.00e-02 2.50e+03 2.70e-03 2.18e-01 pdb=" CG PHE L 32 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 PHE L 32 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE L 32 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE L 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE L 32 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE L 32 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE L 32 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE L 32 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE L 32 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE L 32 " 0.000 2.00e-02 2.50e+03 pdb=" HZ PHE L 32 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 32 " 0.002 2.00e-02 2.50e+03 2.61e-03 2.04e-01 pdb=" CG PHE O 32 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 PHE O 32 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE O 32 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE O 32 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE O 32 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE O 32 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE O 32 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE O 32 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE O 32 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE O 32 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE O 32 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 32 " 0.003 2.00e-02 2.50e+03 2.56e-03 1.96e-01 pdb=" CG PHE B 32 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE B 32 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 32 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 32 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 32 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE B 32 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE B 32 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE B 32 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE B 32 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE B 32 " 0.000 2.00e-02 2.50e+03 ... (remaining 1899 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 827 2.22 - 2.82: 27931 2.82 - 3.41: 30827 3.41 - 4.01: 44083 4.01 - 4.60: 66901 Nonbonded interactions: 170569 Sorted by model distance: nonbonded pdb=" H ARG I 26 " pdb=" O HIS I 51 " model vdw 1.630 2.450 nonbonded pdb=" H ARG L 26 " pdb=" O HIS L 51 " model vdw 1.630 2.450 nonbonded pdb=" H ARG A 26 " pdb=" O HIS A 51 " model vdw 1.631 2.450 nonbonded pdb=" H ARG B 26 " pdb=" O HIS B 51 " model vdw 1.631 2.450 nonbonded pdb=" H ARG F 26 " pdb=" O HIS F 51 " model vdw 1.631 2.450 ... (remaining 170564 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' } 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.230 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 30.650 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6510 Z= 0.089 Angle : 0.350 3.136 8712 Z= 0.210 Chirality : 0.046 0.136 966 Planarity : 0.001 0.004 1110 Dihedral : 15.124 86.475 2358 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.87 (0.29), residues: 780 helix: None (None), residues: 0 sheet: 1.77 (0.27), residues: 336 loop : -0.41 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 201 HIS 0.003 0.001 HIS A 51 PHE 0.008 0.001 PHE L 32 TYR 0.002 0.000 TYR L 153 ARG 0.002 0.000 ARG F 144 Details of bonding type rmsd hydrogen bonds : bond 0.27884 ( 279) hydrogen bonds : angle 8.66852 ( 783) covalent geometry : bond 0.00165 ( 6510) covalent geometry : angle 0.34982 ( 8712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8549 (mp0) cc_final: 0.8163 (mp0) REVERT: I 64 GLN cc_start: 0.8557 (mt0) cc_final: 0.8188 (mm-40) REVERT: I 119 HIS cc_start: 0.7058 (t70) cc_final: 0.6815 (t70) REVERT: I 122 GLU cc_start: 0.8384 (mp0) cc_final: 0.7890 (mp0) REVERT: L 36 GLU cc_start: 0.8010 (mp0) cc_final: 0.7587 (mp0) REVERT: L 64 GLN cc_start: 0.8553 (mt0) cc_final: 0.8088 (mm-40) REVERT: L 119 HIS cc_start: 0.7142 (t70) cc_final: 0.6918 (t70) REVERT: L 122 GLU cc_start: 0.8396 (mp0) cc_final: 0.7943 (mp0) REVERT: L 137 HIS cc_start: 0.7368 (m-70) cc_final: 0.7148 (m90) REVERT: O 122 GLU cc_start: 0.8432 (mp0) cc_final: 0.8011 (mp0) REVERT: B 64 GLN cc_start: 0.8540 (mt0) cc_final: 0.8151 (mm-40) REVERT: B 119 HIS cc_start: 0.7055 (t70) cc_final: 0.6837 (t70) REVERT: B 122 GLU cc_start: 0.8309 (mp0) cc_final: 0.7809 (mp0) REVERT: F 36 GLU cc_start: 0.7924 (mp0) cc_final: 0.7538 (mp0) REVERT: F 64 GLN cc_start: 0.8575 (mt0) cc_final: 0.8081 (mm-40) REVERT: F 122 GLU cc_start: 0.8376 (mp0) cc_final: 0.7887 (mp0) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2864 time to fit residues: 124.8889 Evaluate side-chains 256 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN O 33 HIS B 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.139183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107729 restraints weight = 34825.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.113947 restraints weight = 19505.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118465 restraints weight = 13223.092| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6510 Z= 0.212 Angle : 0.518 4.546 8712 Z= 0.308 Chirality : 0.048 0.161 966 Planarity : 0.003 0.017 1110 Dihedral : 6.938 75.917 846 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % 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: 1.05 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 1.75 (0.28), residues: 342 loop : -0.18 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 201 HIS 0.007 0.002 HIS A 120 PHE 0.014 0.002 PHE L 10 TYR 0.009 0.003 TYR I 153 ARG 0.004 0.001 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.05860 ( 279) hydrogen bonds : angle 6.11916 ( 783) covalent geometry : bond 0.00463 ( 6510) covalent geometry : angle 0.51764 ( 8712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 122 GLU cc_start: 0.8355 (mp0) cc_final: 0.7887 (mp0) REVERT: L 36 GLU cc_start: 0.7826 (mp0) cc_final: 0.7369 (mp0) REVERT: L 110 MET cc_start: 0.7762 (mmt) cc_final: 0.6991 (mmt) REVERT: L 122 GLU cc_start: 0.8370 (mp0) cc_final: 0.7877 (mp0) REVERT: L 137 HIS cc_start: 0.7539 (m-70) cc_final: 0.7295 (m90) REVERT: O 64 GLN cc_start: 0.8835 (mt0) cc_final: 0.8555 (mm-40) REVERT: O 122 GLU cc_start: 0.8401 (mp0) cc_final: 0.7999 (mp0) REVERT: B 42 GLU cc_start: 0.7040 (mp0) cc_final: 0.6697 (mp0) REVERT: B 122 GLU cc_start: 0.8275 (mp0) cc_final: 0.7825 (mp0) REVERT: B 136 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7257 (tp30) REVERT: F 36 GLU cc_start: 0.7660 (mp0) cc_final: 0.7314 (mp0) REVERT: F 110 MET cc_start: 0.7742 (mmt) cc_final: 0.7040 (mmt) REVERT: F 122 GLU cc_start: 0.8341 (mp0) cc_final: 0.7868 (mp0) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.3537 time to fit residues: 151.2577 Evaluate side-chains 255 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.136799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105769 restraints weight = 35039.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.112038 restraints weight = 19658.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.116637 restraints weight = 13319.108| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6510 Z= 0.198 Angle : 0.483 4.426 8712 Z= 0.285 Chirality : 0.047 0.178 966 Planarity : 0.002 0.009 1110 Dihedral : 6.793 72.645 846 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: 0.94 (0.30), residues: 780 helix: None (None), residues: 0 sheet: 1.60 (0.28), residues: 342 loop : -0.18 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 201 HIS 0.004 0.001 HIS A 137 PHE 0.018 0.002 PHE I 95 TYR 0.011 0.003 TYR L 67 ARG 0.002 0.000 ARG O 117 Details of bonding type rmsd hydrogen bonds : bond 0.04764 ( 279) hydrogen bonds : angle 5.57008 ( 783) covalent geometry : bond 0.00431 ( 6510) covalent geometry : angle 0.48263 ( 8712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7459 (mp0) cc_final: 0.6540 (mp0) REVERT: I 64 GLN cc_start: 0.8942 (mt0) cc_final: 0.8742 (mm-40) REVERT: I 122 GLU cc_start: 0.8347 (mp0) cc_final: 0.7876 (mp0) REVERT: L 36 GLU cc_start: 0.7794 (mp0) cc_final: 0.7388 (mp0) REVERT: L 122 GLU cc_start: 0.8373 (mp0) cc_final: 0.7860 (mp0) REVERT: L 137 HIS cc_start: 0.7635 (m-70) cc_final: 0.7418 (m90) REVERT: O 39 ASP cc_start: 0.7367 (t0) cc_final: 0.7139 (t70) REVERT: O 42 GLU cc_start: 0.7339 (mp0) cc_final: 0.6538 (mp0) REVERT: O 122 GLU cc_start: 0.8339 (mp0) cc_final: 0.7904 (mp0) REVERT: B 122 GLU cc_start: 0.8303 (mp0) cc_final: 0.7811 (mp0) REVERT: B 136 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7336 (tp30) REVERT: F 36 GLU cc_start: 0.7730 (mp0) cc_final: 0.7341 (mp0) REVERT: F 122 GLU cc_start: 0.8334 (mp0) cc_final: 0.7821 (mp0) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.3232 time to fit residues: 136.1395 Evaluate side-chains 247 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS A 51 HIS O 8 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102759 restraints weight = 34237.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.108804 restraints weight = 19330.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.113089 restraints weight = 13210.498| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6510 Z= 0.202 Angle : 0.465 4.183 8712 Z= 0.277 Chirality : 0.047 0.182 966 Planarity : 0.003 0.021 1110 Dihedral : 6.734 70.930 846 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.15 % Allowed : 2.65 % Favored : 97.20 % 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: 0.83 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 1.39 (0.29), residues: 348 loop : -0.14 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP I 201 HIS 0.003 0.001 HIS L 137 PHE 0.010 0.002 PHE L 95 TYR 0.015 0.003 TYR F 153 ARG 0.003 0.000 ARG L 144 Details of bonding type rmsd hydrogen bonds : bond 0.04321 ( 279) hydrogen bonds : angle 5.29279 ( 783) covalent geometry : bond 0.00441 ( 6510) covalent geometry : angle 0.46492 ( 8712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7441 (mp0) cc_final: 0.6570 (mp0) REVERT: I 122 GLU cc_start: 0.8267 (mp0) cc_final: 0.7995 (mp0) REVERT: I 136 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7196 (mm-30) REVERT: L 36 GLU cc_start: 0.7827 (mp0) cc_final: 0.7390 (mp0) REVERT: L 122 GLU cc_start: 0.8259 (mp0) cc_final: 0.7950 (mp0) REVERT: O 42 GLU cc_start: 0.7421 (mp0) cc_final: 0.6624 (mp0) REVERT: O 122 GLU cc_start: 0.8196 (mp0) cc_final: 0.7944 (mp0) REVERT: B 71 ASP cc_start: 0.7849 (p0) cc_final: 0.7626 (p0) REVERT: B 122 GLU cc_start: 0.8183 (mp0) cc_final: 0.7868 (mp0) REVERT: B 136 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7319 (mm-30) REVERT: F 36 GLU cc_start: 0.7757 (mp0) cc_final: 0.7348 (mp0) REVERT: F 71 ASP cc_start: 0.7945 (p0) cc_final: 0.7732 (p0) REVERT: F 122 GLU cc_start: 0.8160 (mp0) cc_final: 0.7861 (mp0) outliers start: 1 outliers final: 1 residues processed: 281 average time/residue: 0.2920 time to fit residues: 123.4167 Evaluate side-chains 243 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS B 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.133861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.101813 restraints weight = 34729.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.107818 restraints weight = 19777.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.112013 restraints weight = 13627.257| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6510 Z= 0.237 Angle : 0.491 4.180 8712 Z= 0.289 Chirality : 0.047 0.189 966 Planarity : 0.003 0.017 1110 Dihedral : 6.719 69.240 846 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: 0.58 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 1.14 (0.29), residues: 348 loop : -0.23 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 201 HIS 0.005 0.001 HIS B 119 PHE 0.020 0.002 PHE O 9 TYR 0.016 0.004 TYR F 153 ARG 0.002 0.000 ARG L 144 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 279) hydrogen bonds : angle 5.21317 ( 783) covalent geometry : bond 0.00522 ( 6510) covalent geometry : angle 0.49098 ( 8712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7426 (mp0) cc_final: 0.6662 (mp0) REVERT: A 67 TYR cc_start: 0.8970 (m-80) cc_final: 0.8680 (m-80) REVERT: I 42 GLU cc_start: 0.7394 (mp0) cc_final: 0.7145 (mp0) REVERT: I 122 GLU cc_start: 0.8220 (mp0) cc_final: 0.7829 (mp0) REVERT: I 136 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7310 (mm-30) REVERT: L 36 GLU cc_start: 0.7856 (mp0) cc_final: 0.7407 (mp0) REVERT: L 42 GLU cc_start: 0.7309 (mp0) cc_final: 0.6902 (mp0) REVERT: L 122 GLU cc_start: 0.8146 (mp0) cc_final: 0.7661 (mp0) REVERT: O 42 GLU cc_start: 0.7533 (mp0) cc_final: 0.6663 (mp0) REVERT: O 122 GLU cc_start: 0.8211 (mp0) cc_final: 0.7901 (mp0) REVERT: B 71 ASP cc_start: 0.7861 (p0) cc_final: 0.7652 (p0) REVERT: B 118 PHE cc_start: 0.7260 (m-80) cc_final: 0.6993 (m-80) REVERT: B 122 GLU cc_start: 0.8140 (mp0) cc_final: 0.7753 (mp0) REVERT: B 136 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7249 (mm-30) REVERT: B 153 TYR cc_start: 0.8702 (m-80) cc_final: 0.8371 (m-80) REVERT: F 36 GLU cc_start: 0.7739 (mp0) cc_final: 0.7303 (mp0) REVERT: F 122 GLU cc_start: 0.8005 (mp0) cc_final: 0.7580 (mp0) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.2603 time to fit residues: 107.4803 Evaluate side-chains 236 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS B 8 ASN F 33 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.135218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.103059 restraints weight = 34773.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.109125 restraints weight = 19426.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113425 restraints weight = 13307.510| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6510 Z= 0.124 Angle : 0.433 3.861 8712 Z= 0.258 Chirality : 0.049 0.202 966 Planarity : 0.002 0.013 1110 Dihedral : 6.435 68.047 846 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.15 % Allowed : 1.62 % Favored : 98.23 % 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: 0.73 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 1.19 (0.29), residues: 348 loop : -0.07 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP L 201 HIS 0.016 0.002 HIS A 120 PHE 0.016 0.001 PHE O 95 TYR 0.013 0.003 TYR A 153 ARG 0.002 0.000 ARG L 144 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 279) hydrogen bonds : angle 5.00268 ( 783) covalent geometry : bond 0.00270 ( 6510) covalent geometry : angle 0.43278 ( 8712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7239 (mp0) cc_final: 0.6485 (mp0) REVERT: A 118 PHE cc_start: 0.7521 (p90) cc_final: 0.7290 (p90) REVERT: I 136 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7387 (tp30) REVERT: L 42 GLU cc_start: 0.7245 (mp0) cc_final: 0.6602 (mp0) REVERT: L 110 MET cc_start: 0.8113 (mmt) cc_final: 0.7537 (mmt) REVERT: L 122 GLU cc_start: 0.7990 (mp0) cc_final: 0.7771 (mp0) REVERT: O 42 GLU cc_start: 0.7471 (mp0) cc_final: 0.6592 (mp0) REVERT: O 122 GLU cc_start: 0.8189 (mp0) cc_final: 0.7897 (mp0) REVERT: B 71 ASP cc_start: 0.7827 (p0) cc_final: 0.7612 (p0) REVERT: B 136 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7362 (tp30) REVERT: B 153 TYR cc_start: 0.8729 (m-80) cc_final: 0.8431 (m-80) REVERT: F 110 MET cc_start: 0.8058 (mmt) cc_final: 0.7554 (mmt) REVERT: F 122 GLU cc_start: 0.7881 (mp0) cc_final: 0.7499 (mp0) outliers start: 1 outliers final: 1 residues processed: 277 average time/residue: 0.2516 time to fit residues: 102.5041 Evaluate side-chains 241 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS L 33 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.131960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.100303 restraints weight = 34163.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106043 restraints weight = 19210.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110156 restraints weight = 13331.779| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6510 Z= 0.243 Angle : 0.496 4.688 8712 Z= 0.290 Chirality : 0.048 0.192 966 Planarity : 0.003 0.019 1110 Dihedral : 6.525 68.251 846 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: 0.57 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 1.05 (0.30), residues: 348 loop : -0.14 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 201 HIS 0.013 0.001 HIS A 120 PHE 0.013 0.002 PHE I 9 TYR 0.015 0.003 TYR O 153 ARG 0.002 0.000 ARG L 144 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 279) hydrogen bonds : angle 5.01377 ( 783) covalent geometry : bond 0.00543 ( 6510) covalent geometry : angle 0.49567 ( 8712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7439 (mp0) cc_final: 0.6604 (mp0) REVERT: I 136 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7418 (mm-30) REVERT: L 42 GLU cc_start: 0.7370 (mp0) cc_final: 0.6730 (mp0) REVERT: L 122 GLU cc_start: 0.7887 (mp0) cc_final: 0.7497 (mp0) REVERT: O 42 GLU cc_start: 0.7516 (mp0) cc_final: 0.6632 (mp0) REVERT: O 122 GLU cc_start: 0.8142 (mp0) cc_final: 0.7806 (mp0) REVERT: B 36 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8036 (mm-30) REVERT: B 136 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7259 (mm-30) REVERT: F 42 GLU cc_start: 0.7309 (mp0) cc_final: 0.6875 (mp0) REVERT: F 122 GLU cc_start: 0.7897 (mp0) cc_final: 0.7455 (mp0) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.2610 time to fit residues: 106.8484 Evaluate side-chains 234 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS B 8 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.134974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.102512 restraints weight = 34421.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.108465 restraints weight = 19195.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.112824 restraints weight = 13199.417| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6510 Z= 0.115 Angle : 0.433 4.074 8712 Z= 0.256 Chirality : 0.049 0.197 966 Planarity : 0.002 0.012 1110 Dihedral : 6.355 67.672 846 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 0.15 % Allowed : 0.88 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.68 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 1.01 (0.30), residues: 348 loop : 0.03 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 201 HIS 0.009 0.001 HIS B 120 PHE 0.011 0.001 PHE F 9 TYR 0.013 0.003 TYR I 153 ARG 0.002 0.000 ARG L 144 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 279) hydrogen bonds : angle 4.86586 ( 783) covalent geometry : bond 0.00260 ( 6510) covalent geometry : angle 0.43322 ( 8712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7370 (mp0) cc_final: 0.6579 (mp0) REVERT: A 67 TYR cc_start: 0.9140 (m-80) cc_final: 0.8794 (m-10) REVERT: I 67 TYR cc_start: 0.8962 (m-80) cc_final: 0.8654 (m-80) REVERT: I 136 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7453 (tp30) REVERT: L 42 GLU cc_start: 0.7273 (mp0) cc_final: 0.6899 (mp0) REVERT: L 122 GLU cc_start: 0.7907 (mp0) cc_final: 0.7517 (mp0) REVERT: O 42 GLU cc_start: 0.7406 (mp0) cc_final: 0.6528 (mp0) REVERT: O 67 TYR cc_start: 0.9181 (m-80) cc_final: 0.8574 (m-10) REVERT: O 96 PHE cc_start: 0.9143 (p90) cc_final: 0.8940 (p90) REVERT: O 122 GLU cc_start: 0.8080 (mp0) cc_final: 0.7779 (mp0) REVERT: O 136 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7185 (mm-30) REVERT: B 8 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7371 (t160) REVERT: B 118 PHE cc_start: 0.7406 (m-80) cc_final: 0.7139 (m-80) REVERT: B 136 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7403 (tp30) REVERT: F 8 ASN cc_start: 0.8149 (t0) cc_final: 0.7321 (t0) REVERT: F 42 GLU cc_start: 0.7270 (mp0) cc_final: 0.6905 (mp0) REVERT: F 110 MET cc_start: 0.8193 (mmm) cc_final: 0.7993 (mmm) REVERT: F 122 GLU cc_start: 0.7871 (mp0) cc_final: 0.7508 (mp0) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.2520 time to fit residues: 102.6989 Evaluate side-chains 245 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS O 33 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.132152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.099552 restraints weight = 34562.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.105285 restraints weight = 19837.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.109189 restraints weight = 13871.855| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6510 Z= 0.231 Angle : 0.479 4.707 8712 Z= 0.281 Chirality : 0.048 0.199 966 Planarity : 0.002 0.017 1110 Dihedral : 6.413 68.079 846 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 0.63 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 0.92 (0.30), residues: 348 loop : 0.07 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 201 HIS 0.006 0.001 HIS I 120 PHE 0.019 0.002 PHE O 118 TYR 0.024 0.003 TYR L 153 ARG 0.001 0.000 ARG B 144 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 279) hydrogen bonds : angle 4.95222 ( 783) covalent geometry : bond 0.00528 ( 6510) covalent geometry : angle 0.47873 ( 8712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7449 (mp0) cc_final: 0.6618 (mp0) REVERT: I 67 TYR cc_start: 0.9107 (m-80) cc_final: 0.8490 (m-80) REVERT: I 136 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7442 (tp30) REVERT: L 42 GLU cc_start: 0.7398 (mp0) cc_final: 0.6919 (mp0) REVERT: L 122 GLU cc_start: 0.7866 (mp0) cc_final: 0.7505 (mp0) REVERT: O 67 TYR cc_start: 0.9131 (m-80) cc_final: 0.8612 (m-10) REVERT: O 122 GLU cc_start: 0.7923 (mp0) cc_final: 0.7556 (mp0) REVERT: B 136 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7246 (mm-30) REVERT: F 42 GLU cc_start: 0.7308 (mp0) cc_final: 0.6904 (mp0) REVERT: F 110 MET cc_start: 0.8363 (mmm) cc_final: 0.8162 (mmm) REVERT: F 122 GLU cc_start: 0.7834 (mp0) cc_final: 0.7476 (mp0) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.2557 time to fit residues: 100.7697 Evaluate side-chains 228 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.133513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.101528 restraints weight = 35027.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.107261 restraints weight = 20122.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.111352 restraints weight = 14082.339| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6510 Z= 0.131 Angle : 0.444 5.547 8712 Z= 0.259 Chirality : 0.048 0.201 966 Planarity : 0.002 0.012 1110 Dihedral : 6.248 67.797 846 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.71 % 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: 0.69 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 0.87 (0.29), residues: 348 loop : 0.20 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 201 HIS 0.006 0.001 HIS I 120 PHE 0.010 0.001 PHE B 9 TYR 0.016 0.002 TYR O 153 ARG 0.002 0.000 ARG L 144 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 279) hydrogen bonds : angle 4.87096 ( 783) covalent geometry : bond 0.00301 ( 6510) covalent geometry : angle 0.44416 ( 8712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7333 (mp0) cc_final: 0.6581 (mp0) REVERT: I 42 GLU cc_start: 0.7477 (mp0) cc_final: 0.6772 (mp0) REVERT: I 67 TYR cc_start: 0.9129 (m-80) cc_final: 0.8518 (m-80) REVERT: I 110 MET cc_start: 0.8213 (mmm) cc_final: 0.7939 (mmm) REVERT: I 125 ASP cc_start: 0.8624 (m-30) cc_final: 0.8150 (m-30) REVERT: I 136 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7400 (tp30) REVERT: L 42 GLU cc_start: 0.7260 (mp0) cc_final: 0.6665 (mp0) REVERT: L 118 PHE cc_start: 0.7579 (m-80) cc_final: 0.7343 (m-80) REVERT: L 122 GLU cc_start: 0.7848 (mp0) cc_final: 0.7500 (mp0) REVERT: O 42 GLU cc_start: 0.7283 (mp0) cc_final: 0.6584 (mp0) REVERT: O 67 TYR cc_start: 0.9125 (m-80) cc_final: 0.8633 (m-10) REVERT: O 122 GLU cc_start: 0.7892 (mp0) cc_final: 0.7678 (mp0) REVERT: O 136 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7313 (tp30) REVERT: B 8 ASN cc_start: 0.8005 (OUTLIER) cc_final: 0.7546 (t160) REVERT: B 118 PHE cc_start: 0.7487 (m-80) cc_final: 0.7251 (m-80) REVERT: B 136 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7330 (tp30) REVERT: F 42 GLU cc_start: 0.7258 (mp0) cc_final: 0.6898 (mp0) REVERT: F 122 GLU cc_start: 0.7819 (mp0) cc_final: 0.7448 (mp0) outliers start: 1 outliers final: 0 residues processed: 260 average time/residue: 0.2656 time to fit residues: 104.5378 Evaluate side-chains 231 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 0.0970 chunk 61 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.134021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102176 restraints weight = 35094.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.107692 restraints weight = 20388.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.111841 restraints weight = 14376.219| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.6061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6510 Z= 0.136 Angle : 0.447 6.149 8712 Z= 0.261 Chirality : 0.048 0.200 966 Planarity : 0.002 0.013 1110 Dihedral : 6.144 67.843 846 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 0.73 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 0.94 (0.30), residues: 348 loop : 0.19 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 201 HIS 0.015 0.001 HIS O 120 PHE 0.011 0.001 PHE O 118 TYR 0.013 0.003 TYR B 67 ARG 0.001 0.000 ARG B 144 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 279) hydrogen bonds : angle 4.80615 ( 783) covalent geometry : bond 0.00306 ( 6510) covalent geometry : angle 0.44729 ( 8712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5028.05 seconds wall clock time: 88 minutes 39.98 seconds (5319.98 seconds total)