Starting phenix.real_space_refine on Thu May 15 04:44:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9be8_44473/05_2025/9be8_44473.cif Found real_map, /net/cci-nas-00/data/ceres_data/9be8_44473/05_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_44473/05_2025/9be8_44473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9be8_44473/05_2025/9be8_44473.map" model { file = "/net/cci-nas-00/data/ceres_data/9be8_44473/05_2025/9be8_44473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9be8_44473/05_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-5687/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: 5.97, per 1000 atoms: 0.47 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: 3.08 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.35 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: 4.59 Time building geometry restraints manager: 3.69 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.210 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.020 Find NCS groups from input model: 0.190 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.010 ------------------------------------------------------------------------------- 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 : 1.058 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: 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: 0.2838 time to fit residues: 123.2443 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 : 1.053 ------------------------------------------------------------------------------- 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 = 0.107730 restraints weight = 34825.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.113952 restraints weight = 19504.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118449 restraints weight = 13219.740| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- 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 : 1.164 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: 0.8356 (mp0) cc_final: 0.7888 (mp0) REVERT: L 36 GLU cc_start: 0.7826 (mp0) cc_final: 0.7369 (mp0) REVERT: L 110 MET cc_start: 0.7763 (mmt) cc_final: 0.6993 (mmt) REVERT: L 122 GLU cc_start: 0.8370 (mp0) cc_final: 0.7877 (mp0) REVERT: L 137 HIS cc_start: 0.7538 (m-70) cc_final: 0.7294 (m90) REVERT: O 64 GLN cc_start: 0.8835 (mt0) cc_final: 0.8555 (mm-40) REVERT: O 122 GLU cc_start: 0.8403 (mp0) cc_final: 0.8000 (mp0) REVERT: B 42 GLU cc_start: 0.7040 (mp0) cc_final: 0.6697 (mp0) REVERT: B 122 GLU cc_start: 0.8276 (mp0) cc_final: 0.7826 (mp0) REVERT: B 136 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7259 (tp30) REVERT: F 36 GLU cc_start: 0.7661 (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: 0.7867 (mp0) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.2664 time to fit residues: 113.8701 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 : 0.970 ------------------------------------------------------------------------------- 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: 0.9980 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: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.137670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106958 restraints weight = 35020.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113275 restraints weight = 19512.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117944 restraints weight = 13158.576| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6510 Z= 0.183 Angle : 0.471 4.182 8712 Z= 0.280 Chirality : 0.047 0.175 966 Planarity : 0.002 0.008 1110 Dihedral : 6.776 73.187 846 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: 1.00 (0.30), residues: 780 helix: None (None), residues: 0 sheet: 1.65 (0.28), residues: 342 loop : -0.15 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 201 HIS 0.003 0.001 HIS A 137 PHE 0.017 0.002 PHE I 95 TYR 0.012 0.003 TYR B 153 ARG 0.002 0.000 ARG O 117 Details of bonding type rmsd hydrogen bonds : bond 0.04777 ( 279) hydrogen bonds : angle 5.59858 ( 783) covalent geometry : bond 0.00397 ( 6510) covalent geometry : angle 0.47130 ( 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 300 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.060 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: 0.7447 (mp0) cc_final: 0.6570 (mp0) REVERT: I 122 GLU cc_start: 0.8340 (mp0) cc_final: 0.7859 (mp0) REVERT: L 36 GLU cc_start: 0.7788 (mp0) cc_final: 0.7395 (mp0) REVERT: L 64 GLN cc_start: 0.8955 (mt0) cc_final: 0.8742 (mm110) REVERT: L 118 PHE cc_start: 0.7131 (m-80) cc_final: 0.6847 (m-80) REVERT: L 122 GLU cc_start: 0.8374 (mp0) cc_final: 0.7849 (mp0) REVERT: L 137 HIS cc_start: 0.7647 (m-70) cc_final: 0.7420 (m90) REVERT: O 39 ASP cc_start: 0.7377 (t0) cc_final: 0.7163 (t70) REVERT: O 42 GLU cc_start: 0.7330 (mp0) cc_final: 0.6513 (mp0) REVERT: O 118 PHE cc_start: 0.7218 (m-80) cc_final: 0.6901 (m-80) REVERT: O 122 GLU cc_start: 0.8327 (mp0) cc_final: 0.7893 (mp0) REVERT: B 122 GLU cc_start: 0.8294 (mp0) cc_final: 0.7771 (mp0) REVERT: B 136 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7293 (tp30) REVERT: F 36 GLU cc_start: 0.7700 (mp0) cc_final: 0.7333 (mp0) REVERT: F 118 PHE cc_start: 0.7146 (m-80) cc_final: 0.6892 (m-80) REVERT: F 122 GLU cc_start: 0.8349 (mp0) cc_final: 0.7831 (mp0) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.3248 time to fit residues: 138.3355 Evaluate side-chains 252 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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: 0.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.137604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105972 restraints weight = 34149.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.112187 restraints weight = 19227.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116717 restraints weight = 13109.932| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6510 Z= 0.148 Angle : 0.436 3.859 8712 Z= 0.262 Chirality : 0.047 0.181 966 Planarity : 0.002 0.017 1110 Dihedral : 6.658 71.452 846 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: 1.09 (0.30), residues: 780 helix: None (None), residues: 0 sheet: 1.63 (0.28), residues: 342 loop : 0.01 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP I 201 HIS 0.003 0.001 HIS A 51 PHE 0.018 0.002 PHE B 95 TYR 0.013 0.003 TYR F 153 ARG 0.003 0.000 ARG L 144 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 279) hydrogen bonds : angle 5.27526 ( 783) covalent geometry : bond 0.00323 ( 6510) covalent geometry : angle 0.43622 ( 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 284 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.113 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: A 42 GLU cc_start: 0.7412 (mp0) cc_final: 0.6610 (mp0) REVERT: I 122 GLU cc_start: 0.8333 (mp0) cc_final: 0.8072 (mp0) REVERT: I 136 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7199 (mm-30) REVERT: L 36 GLU cc_start: 0.7795 (mp0) cc_final: 0.7385 (mp0) REVERT: L 64 GLN cc_start: 0.8882 (mt0) cc_final: 0.8628 (mm-40) REVERT: L 118 PHE cc_start: 0.7276 (m-80) cc_final: 0.6647 (m-80) REVERT: L 122 GLU cc_start: 0.8293 (mp0) cc_final: 0.7979 (mp0) REVERT: O 42 GLU cc_start: 0.7383 (mp0) cc_final: 0.6673 (mp0) REVERT: O 67 TYR cc_start: 0.8556 (m-80) cc_final: 0.8317 (m-80) REVERT: O 122 GLU cc_start: 0.8238 (mp0) cc_final: 0.7982 (mp0) REVERT: B 42 GLU cc_start: 0.7292 (mp0) cc_final: 0.7089 (mp0) REVERT: B 122 GLU cc_start: 0.8234 (mp0) cc_final: 0.7713 (mp0) REVERT: B 136 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7310 (tp30) REVERT: F 36 GLU cc_start: 0.7693 (mp0) cc_final: 0.7312 (mp0) REVERT: F 118 PHE cc_start: 0.7160 (m-80) cc_final: 0.6902 (m-80) REVERT: F 122 GLU cc_start: 0.8237 (mp0) cc_final: 0.7981 (mp0) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.2550 time to fit residues: 106.5407 Evaluate side-chains 241 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 8 optimal weight: 0.0060 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.137656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.105600 restraints weight = 34441.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.111841 restraints weight = 19328.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116171 restraints weight = 13205.502| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6510 Z= 0.134 Angle : 0.440 3.779 8712 Z= 0.261 Chirality : 0.048 0.186 966 Planarity : 0.002 0.013 1110 Dihedral : 6.530 70.461 846 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.01 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 1.46 (0.29), residues: 348 loop : 0.04 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 201 HIS 0.014 0.001 HIS F 120 PHE 0.016 0.002 PHE A 95 TYR 0.016 0.003 TYR I 153 ARG 0.002 0.000 ARG L 144 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 279) hydrogen bonds : angle 5.10200 ( 783) covalent geometry : bond 0.00292 ( 6510) covalent geometry : angle 0.44017 ( 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 280 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 1.126 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: A 42 GLU cc_start: 0.7327 (mp0) cc_final: 0.6498 (mp0) REVERT: A 67 TYR cc_start: 0.8708 (m-80) cc_final: 0.8338 (m-80) REVERT: I 136 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7208 (mm-30) REVERT: I 153 TYR cc_start: 0.8673 (m-80) cc_final: 0.8279 (m-80) REVERT: L 36 GLU cc_start: 0.7791 (mp0) cc_final: 0.7381 (mp0) REVERT: L 67 TYR cc_start: 0.9183 (m-80) cc_final: 0.8778 (m-80) REVERT: L 122 GLU cc_start: 0.8225 (mp0) cc_final: 0.7950 (mp0) REVERT: O 42 GLU cc_start: 0.7413 (mp0) cc_final: 0.6656 (mp0) REVERT: O 122 GLU cc_start: 0.8250 (mp0) cc_final: 0.8020 (mp0) REVERT: B 118 PHE cc_start: 0.7083 (m-80) cc_final: 0.6805 (m-80) REVERT: B 136 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7338 (tp30) REVERT: F 36 GLU cc_start: 0.7658 (mp0) cc_final: 0.7277 (mp0) REVERT: F 122 GLU cc_start: 0.8003 (mp0) cc_final: 0.7803 (mp0) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.2481 time to fit residues: 103.4446 Evaluate side-chains 242 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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: 5.9990 chunk 54 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.135874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.104167 restraints weight = 34687.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.110312 restraints weight = 19342.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114688 restraints weight = 13222.173| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6510 Z= 0.125 Angle : 0.429 4.753 8712 Z= 0.254 Chirality : 0.048 0.184 966 Planarity : 0.002 0.012 1110 Dihedral : 6.385 70.062 846 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % 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: 1.05 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 1.45 (0.29), residues: 348 loop : 0.10 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 201 HIS 0.015 0.002 HIS B 120 PHE 0.011 0.002 PHE O 95 TYR 0.011 0.003 TYR B 67 ARG 0.002 0.000 ARG F 144 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 279) hydrogen bonds : angle 4.97246 ( 783) covalent geometry : bond 0.00272 ( 6510) covalent geometry : angle 0.42868 ( 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 282 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.978 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: A 42 GLU cc_start: 0.7269 (mp0) cc_final: 0.6475 (mp0) REVERT: I 8 ASN cc_start: 0.8010 (t0) cc_final: 0.7379 (t0) REVERT: I 136 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7238 (mm-30) REVERT: I 153 TYR cc_start: 0.8824 (m-80) cc_final: 0.8362 (m-80) REVERT: L 36 GLU cc_start: 0.7758 (mp0) cc_final: 0.7349 (mp0) REVERT: L 42 GLU cc_start: 0.7236 (mp0) cc_final: 0.6687 (mp0) REVERT: O 42 GLU cc_start: 0.7406 (mp0) cc_final: 0.6609 (mp0) REVERT: O 67 TYR cc_start: 0.8991 (m-80) cc_final: 0.8780 (m-80) REVERT: O 118 PHE cc_start: 0.7258 (m-80) cc_final: 0.6942 (m-80) REVERT: O 122 GLU cc_start: 0.8133 (mp0) cc_final: 0.7926 (mp0) REVERT: B 36 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8042 (mm-30) REVERT: B 118 PHE cc_start: 0.7062 (m-80) cc_final: 0.6808 (m-80) REVERT: B 136 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7360 (tp30) REVERT: F 36 GLU cc_start: 0.7673 (mp0) cc_final: 0.7285 (mp0) REVERT: F 122 GLU cc_start: 0.7938 (mp0) cc_final: 0.7543 (mp0) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.2553 time to fit residues: 106.9169 Evaluate side-chains 246 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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: 3.9990 chunk 17 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 ASN B 51 HIS F 33 HIS ** F 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.129316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.096818 restraints weight = 35049.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.102442 restraints weight = 20371.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.106460 restraints weight = 14212.815| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 6510 Z= 0.349 Angle : 0.580 4.944 8712 Z= 0.339 Chirality : 0.048 0.206 966 Planarity : 0.003 0.025 1110 Dihedral : 6.827 69.149 846 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.15 % Allowed : 1.92 % Favored : 97.94 % 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: 1.08 (0.29), residues: 348 loop : -0.17 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 201 HIS 0.013 0.002 HIS L 120 PHE 0.020 0.003 PHE O 9 TYR 0.018 0.004 TYR L 153 ARG 0.002 0.000 ARG B 144 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 279) hydrogen bonds : angle 5.26972 ( 783) covalent geometry : bond 0.00775 ( 6510) covalent geometry : angle 0.58031 ( 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 261 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 1.033 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: 0.7501 (mp0) cc_final: 0.7056 (mp0) REVERT: L 36 GLU cc_start: 0.7908 (mp0) cc_final: 0.7401 (mp0) REVERT: L 42 GLU cc_start: 0.7437 (mp0) cc_final: 0.6878 (mp0) REVERT: L 153 TYR cc_start: 0.8959 (m-80) cc_final: 0.8647 (m-80) REVERT: O 122 GLU cc_start: 0.8103 (mp0) cc_final: 0.7797 (mp0) REVERT: B 36 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8119 (mm-30) REVERT: B 118 PHE cc_start: 0.7255 (m-80) cc_final: 0.6745 (m-80) REVERT: F 36 GLU cc_start: 0.7820 (mp0) cc_final: 0.7326 (mp0) REVERT: F 42 GLU cc_start: 0.7428 (mp0) cc_final: 0.6747 (mp0) REVERT: F 122 GLU cc_start: 0.7817 (mp0) cc_final: 0.7504 (mp0) outliers start: 1 outliers final: 1 residues processed: 261 average time/residue: 0.2396 time to fit residues: 93.2335 Evaluate side-chains 227 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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: 3.9990 chunk 68 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 8 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.133287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.101525 restraints weight = 34742.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.107555 restraints weight = 19301.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111765 restraints weight = 13150.371| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6510 Z= 0.131 Angle : 0.451 4.027 8712 Z= 0.267 Chirality : 0.049 0.198 966 Planarity : 0.002 0.014 1110 Dihedral : 6.573 68.687 846 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 0.15 % Allowed : 1.18 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.60 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 0.98 (0.29), residues: 348 loop : -0.04 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP L 201 HIS 0.007 0.001 HIS B 120 PHE 0.013 0.002 PHE A 48 TYR 0.022 0.003 TYR B 67 ARG 0.002 0.000 ARG L 144 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 279) hydrogen bonds : angle 5.00997 ( 783) covalent geometry : bond 0.00292 ( 6510) covalent geometry : angle 0.45133 ( 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 270 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 1.103 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: 0.7357 (mp0) cc_final: 0.6398 (mp0) REVERT: I 136 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7389 (tp30) REVERT: I 153 TYR cc_start: 0.8865 (m-80) cc_final: 0.8437 (m-80) REVERT: L 8 ASN cc_start: 0.8412 (t0) cc_final: 0.7768 (t0) REVERT: L 42 GLU cc_start: 0.7416 (mp0) cc_final: 0.7039 (mp0) REVERT: O 42 GLU cc_start: 0.7329 (mp0) cc_final: 0.7045 (mp0) REVERT: O 122 GLU cc_start: 0.8045 (mp0) cc_final: 0.7764 (mp0) REVERT: O 136 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7355 (mm-30) REVERT: B 118 PHE cc_start: 0.7218 (m-80) cc_final: 0.6753 (m-80) REVERT: B 136 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7418 (tp30) REVERT: B 153 TYR cc_start: 0.8761 (m-80) cc_final: 0.8383 (m-80) REVERT: F 42 GLU cc_start: 0.7363 (mp0) cc_final: 0.6778 (mp0) outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.2585 time to fit residues: 105.5302 Evaluate side-chains 245 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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: 1.9990 chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.132787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.101158 restraints weight = 34432.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106941 restraints weight = 19307.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.111093 restraints weight = 13276.455| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6510 Z= 0.190 Angle : 0.461 3.944 8712 Z= 0.273 Chirality : 0.048 0.203 966 Planarity : 0.002 0.014 1110 Dihedral : 6.502 69.335 846 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 0.15 % Allowed : 0.74 % 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: 0.54 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 0.87 (0.30), residues: 348 loop : -0.00 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 201 HIS 0.007 0.001 HIS O 120 PHE 0.018 0.002 PHE O 118 TYR 0.022 0.004 TYR B 67 ARG 0.001 0.000 ARG B 144 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 279) hydrogen bonds : angle 4.99571 ( 783) covalent geometry : bond 0.00437 ( 6510) covalent geometry : angle 0.46103 ( 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 268 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 0.994 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: A 42 GLU cc_start: 0.7470 (mp0) cc_final: 0.6524 (mp0) REVERT: A 153 TYR cc_start: 0.8241 (m-80) cc_final: 0.8011 (m-80) REVERT: I 136 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7346 (tp30) REVERT: I 153 TYR cc_start: 0.8878 (m-80) cc_final: 0.8514 (m-80) REVERT: L 8 ASN cc_start: 0.8452 (t0) cc_final: 0.7778 (t0) REVERT: L 42 GLU cc_start: 0.7464 (mp0) cc_final: 0.7032 (mp0) REVERT: O 42 GLU cc_start: 0.7277 (mp0) cc_final: 0.6980 (mp0) REVERT: O 122 GLU cc_start: 0.8028 (mp0) cc_final: 0.7770 (mp0) REVERT: B 38 LEU cc_start: 0.8672 (mt) cc_final: 0.8464 (mt) REVERT: B 118 PHE cc_start: 0.7132 (m-80) cc_final: 0.6754 (m-80) REVERT: B 136 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7350 (tp30) REVERT: F 42 GLU cc_start: 0.7409 (mp0) cc_final: 0.6745 (mp0) outliers start: 1 outliers final: 0 residues processed: 267 average time/residue: 0.2321 time to fit residues: 92.7992 Evaluate side-chains 239 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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: 3.9990 chunk 61 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.133555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.101690 restraints weight = 34263.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107472 restraints weight = 19050.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.111743 restraints weight = 13092.335| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6510 Z= 0.109 Angle : 0.455 7.092 8712 Z= 0.264 Chirality : 0.050 0.206 966 Planarity : 0.002 0.014 1110 Dihedral : 6.342 68.495 846 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.62 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 0.83 (0.30), residues: 348 loop : 0.15 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP L 201 HIS 0.005 0.001 HIS B 120 PHE 0.017 0.002 PHE O 118 TYR 0.020 0.003 TYR B 67 ARG 0.002 0.000 ARG B 144 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 279) hydrogen bonds : angle 4.95138 ( 783) covalent geometry : bond 0.00252 ( 6510) covalent geometry : angle 0.45507 ( 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 264 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.094 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: 0.7388 (mp0) cc_final: 0.6520 (mp0) REVERT: I 136 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7386 (tp30) REVERT: L 8 ASN cc_start: 0.8371 (t0) cc_final: 0.7721 (t0) REVERT: L 42 GLU cc_start: 0.7292 (mp0) cc_final: 0.6893 (mp0) REVERT: L 118 PHE cc_start: 0.7622 (m-80) cc_final: 0.7390 (m-80) REVERT: O 42 GLU cc_start: 0.7270 (mp0) cc_final: 0.6980 (mp0) REVERT: O 122 GLU cc_start: 0.7962 (mp0) cc_final: 0.7724 (mp0) REVERT: O 136 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7412 (tp30) REVERT: B 38 LEU cc_start: 0.8706 (mt) cc_final: 0.8483 (mt) REVERT: B 42 GLU cc_start: 0.7383 (mp0) cc_final: 0.6608 (mp0) REVERT: B 118 PHE cc_start: 0.7206 (m-80) cc_final: 0.6800 (m-80) REVERT: B 136 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7311 (tp30) REVERT: F 8 ASN cc_start: 0.8168 (t0) cc_final: 0.7156 (t0) REVERT: F 42 GLU cc_start: 0.7123 (mp0) cc_final: 0.6453 (mp0) REVERT: F 118 PHE cc_start: 0.7564 (m-80) cc_final: 0.7344 (m-80) REVERT: F 122 GLU cc_start: 0.7840 (mp0) cc_final: 0.7530 (mp0) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2497 time to fit residues: 98.4262 Evaluate side-chains 231 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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: 3.9990 chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS I 33 HIS O 33 HIS B 33 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.097792 restraints weight = 34738.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103214 restraints weight = 20078.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.107127 restraints weight = 14092.681| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 6510 Z= 0.286 Angle : 0.525 4.568 8712 Z= 0.309 Chirality : 0.048 0.198 966 Planarity : 0.003 0.022 1110 Dihedral : 6.545 69.692 846 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.41 (0.30), residues: 780 helix: None (None), residues: 0 sheet: 0.75 (0.30), residues: 348 loop : -0.07 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 201 HIS 0.004 0.001 HIS A 120 PHE 0.021 0.003 PHE L 9 TYR 0.018 0.004 TYR L 153 ARG 0.001 0.000 ARG I 144 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 279) hydrogen bonds : angle 5.08190 ( 783) covalent geometry : bond 0.00648 ( 6510) covalent geometry : angle 0.52498 ( 8712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4501.84 seconds wall clock time: 78 minutes 50.70 seconds (4730.70 seconds total)