Starting phenix.real_space_refine on Sat Aug 23 14:32:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9be8_44473/08_2025/9be8_44473.cif Found real_map, /net/cci-nas-00/data/ceres_data/9be8_44473/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9be8_44473/08_2025/9be8_44473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9be8_44473/08_2025/9be8_44473.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9be8_44473/08_2025/9be8_44473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9be8_44473/08_2025/9be8_44473.map" } resolution = 4.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.03, per 1000 atoms: 0.16 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: 0.98 Conformation dependent library (CDL) restraints added in 471.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.41 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: 2.94 Time building geometry restraints manager: 1.43 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'B' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.080 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.100 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.560 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.002 0.000 ARG F 144 TYR 0.002 0.000 TYR L 153 PHE 0.008 0.001 PHE L 32 TRP 0.006 0.001 TRP O 201 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00165 ( 6510) covalent geometry : angle 0.34982 ( 8712) hydrogen bonds : bond 0.27884 ( 279) hydrogen bonds : angle 8.66852 ( 783) *********************** 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 : 0.350 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: A 122 GLU cc_start: 0.8549 (mp0) cc_final: 0.8163 (mp0) REVERT: I 64 GLN cc_start: 0.8557 (mt0) cc_final: 0.8189 (mm-40) REVERT: I 119 HIS cc_start: 0.7058 (t70) cc_final: 0.6813 (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: 0.7588 (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: 0.6917 (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: 0.8149 (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: 0.7537 (mp0) REVERT: F 64 GLN cc_start: 0.8575 (mt0) cc_final: 0.8082 (mm-40) REVERT: F 122 GLU cc_start: 0.8376 (mp0) cc_final: 0.7888 (mp0) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.1282 time to fit residues: 56.9418 Evaluate side-chains 257 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS L 47 GLN O 33 HIS B 51 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.140689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.109466 restraints weight = 34535.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.115791 restraints weight = 19042.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.120278 restraints weight = 12773.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.123575 restraints weight = 9537.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.125834 restraints weight = 7548.339| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6510 Z= 0.184 Angle : 0.506 4.686 8712 Z= 0.304 Chirality : 0.048 0.165 966 Planarity : 0.003 0.016 1110 Dihedral : 6.931 76.189 846 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.69 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 1.76 (0.28), residues: 342 loop : -0.14 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 117 TYR 0.009 0.002 TYR I 153 PHE 0.015 0.002 PHE L 10 TRP 0.005 0.001 TRP F 201 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 6510) covalent geometry : angle 0.50612 ( 8712) hydrogen bonds : bond 0.05446 ( 279) hydrogen bonds : angle 6.12932 ( 783) *********************** 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 293 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.342 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 67 TYR cc_start: 0.8198 (m-80) cc_final: 0.7676 (m-10) REVERT: A 122 GLU cc_start: 0.8441 (mp0) cc_final: 0.8096 (mp0) REVERT: I 122 GLU cc_start: 0.8347 (mp0) cc_final: 0.7871 (mp0) REVERT: L 36 GLU cc_start: 0.7817 (mp0) cc_final: 0.7378 (mp0) REVERT: L 67 TYR cc_start: 0.8366 (m-80) cc_final: 0.8151 (m-10) REVERT: L 122 GLU cc_start: 0.8384 (mp0) cc_final: 0.7923 (mp0) REVERT: L 137 HIS cc_start: 0.7461 (m-70) cc_final: 0.7219 (m90) REVERT: O 64 GLN cc_start: 0.8857 (mt0) cc_final: 0.8567 (mm-40) REVERT: O 67 TYR cc_start: 0.8220 (m-80) cc_final: 0.7623 (m-10) REVERT: O 95 PHE cc_start: 0.8944 (p90) cc_final: 0.8716 (p90) REVERT: O 122 GLU cc_start: 0.8420 (mp0) cc_final: 0.7953 (mp0) REVERT: B 122 GLU cc_start: 0.8329 (mp0) cc_final: 0.7820 (mp0) REVERT: B 136 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7258 (tp30) REVERT: F 36 GLU cc_start: 0.7685 (mp0) cc_final: 0.7335 (mp0) REVERT: F 67 TYR cc_start: 0.8235 (m-80) cc_final: 0.7900 (m-10) REVERT: F 122 GLU cc_start: 0.8338 (mp0) cc_final: 0.7856 (mp0) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.1034 time to fit residues: 45.8100 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 : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS B 8 ASN B 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.134536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.103169 restraints weight = 34980.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.109287 restraints weight = 19753.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113644 restraints weight = 13404.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116809 restraints weight = 10116.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.119038 restraints weight = 8128.756| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 6510 Z= 0.256 Angle : 0.525 5.037 8712 Z= 0.310 Chirality : 0.047 0.176 966 Planarity : 0.003 0.051 1110 Dihedral : 6.890 72.363 846 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.15 % Allowed : 3.10 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.30), residues: 780 helix: None (None), residues: 0 sheet: 1.54 (0.28), residues: 342 loop : -0.26 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 117 TYR 0.017 0.004 TYR I 153 PHE 0.017 0.002 PHE O 10 TRP 0.005 0.001 TRP L 201 HIS 0.005 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 6510) covalent geometry : angle 0.52496 ( 8712) hydrogen bonds : bond 0.05085 ( 279) hydrogen bonds : angle 5.70210 ( 783) *********************** 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 293 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 0.268 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: A 42 GLU cc_start: 0.7524 (mp0) cc_final: 0.6610 (mp0) REVERT: A 122 GLU cc_start: 0.8340 (mp0) cc_final: 0.8114 (mp0) REVERT: I 122 GLU cc_start: 0.8337 (mp0) cc_final: 0.8089 (mp0) REVERT: L 36 GLU cc_start: 0.7860 (mp0) cc_final: 0.7411 (mp0) REVERT: L 122 GLU cc_start: 0.8333 (mp0) cc_final: 0.8083 (mp0) REVERT: O 39 ASP cc_start: 0.7355 (t0) cc_final: 0.7114 (t70) REVERT: O 42 GLU cc_start: 0.7437 (mp0) cc_final: 0.6539 (mp0) REVERT: O 122 GLU cc_start: 0.8323 (mp0) cc_final: 0.8076 (mp0) REVERT: B 122 GLU cc_start: 0.8257 (mp0) cc_final: 0.8002 (mp0) REVERT: B 136 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7261 (mm-30) REVERT: F 36 GLU cc_start: 0.7793 (mp0) cc_final: 0.7379 (mp0) REVERT: F 122 GLU cc_start: 0.8301 (mp0) cc_final: 0.7777 (mp0) outliers start: 1 outliers final: 1 residues processed: 293 average time/residue: 0.1374 time to fit residues: 57.0862 Evaluate side-chains 238 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 B 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.136350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104902 restraints weight = 34552.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.111076 restraints weight = 19245.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.115384 restraints weight = 13066.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.118243 restraints weight = 9858.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120615 restraints weight = 8013.520| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4261 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= 0.119 Angle : 0.435 3.642 8712 Z= 0.261 Chirality : 0.049 0.183 966 Planarity : 0.002 0.023 1110 Dihedral : 6.701 71.576 846 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.30), residues: 780 helix: None (None), residues: 0 sheet: 1.47 (0.28), residues: 342 loop : -0.03 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 144 TYR 0.011 0.003 TYR A 153 PHE 0.014 0.001 PHE A 95 TRP 0.001 0.000 TRP A 201 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6510) covalent geometry : angle 0.43494 ( 8712) hydrogen bonds : bond 0.03940 ( 279) hydrogen bonds : angle 5.31786 ( 783) *********************** 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 287 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.327 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: 0.7466 (mp0) cc_final: 0.6591 (mp0) REVERT: A 67 TYR cc_start: 0.8682 (m-80) cc_final: 0.8313 (m-80) REVERT: A 122 GLU cc_start: 0.8277 (mp0) cc_final: 0.8076 (mp0) REVERT: I 122 GLU cc_start: 0.8285 (mp0) cc_final: 0.8073 (mp0) REVERT: I 136 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7156 (mm-30) REVERT: L 36 GLU cc_start: 0.7788 (mp0) cc_final: 0.7388 (mp0) REVERT: O 39 ASP cc_start: 0.7420 (t0) cc_final: 0.7213 (t70) REVERT: O 42 GLU cc_start: 0.7413 (mp0) cc_final: 0.6394 (mp0) REVERT: O 67 TYR cc_start: 0.8723 (m-80) cc_final: 0.8414 (m-80) REVERT: B 122 GLU cc_start: 0.8192 (mp0) cc_final: 0.7980 (mp0) REVERT: B 136 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7353 (tp30) REVERT: F 36 GLU cc_start: 0.7791 (mp0) cc_final: 0.7367 (mp0) REVERT: F 122 GLU cc_start: 0.8169 (mp0) cc_final: 0.7895 (mp0) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.1161 time to fit residues: 50.4805 Evaluate side-chains 244 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 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 = 0.3622 r_free = 0.3622 target = 0.132327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.100618 restraints weight = 34848.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.106396 restraints weight = 20030.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110592 restraints weight = 13875.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.113532 restraints weight = 10598.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115613 restraints weight = 8649.733| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6510 Z= 0.242 Angle : 0.495 4.340 8712 Z= 0.294 Chirality : 0.047 0.179 966 Planarity : 0.003 0.018 1110 Dihedral : 6.634 69.455 846 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.30), residues: 780 helix: None (None), residues: 0 sheet: 1.20 (0.29), residues: 348 loop : -0.11 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 144 TYR 0.025 0.004 TYR B 67 PHE 0.017 0.002 PHE B 95 TRP 0.002 0.000 TRP F 201 HIS 0.014 0.002 HIS I 120 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 6510) covalent geometry : angle 0.49493 ( 8712) hydrogen bonds : bond 0.04230 ( 279) hydrogen bonds : angle 5.21996 ( 783) *********************** 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 273 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 0.330 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: 0.7450 (mp0) cc_final: 0.6547 (mp0) REVERT: A 122 GLU cc_start: 0.8147 (mp0) cc_final: 0.7943 (mp0) REVERT: I 122 GLU cc_start: 0.8184 (mp0) cc_final: 0.7959 (mp0) REVERT: L 36 GLU cc_start: 0.7849 (mp0) cc_final: 0.7392 (mp0) REVERT: O 42 GLU cc_start: 0.7489 (mp0) cc_final: 0.6601 (mp0) REVERT: B 122 GLU cc_start: 0.8066 (mp0) cc_final: 0.7842 (mp0) REVERT: B 136 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7214 (mm-30) REVERT: F 36 GLU cc_start: 0.7786 (mp0) cc_final: 0.7322 (mp0) REVERT: F 122 GLU cc_start: 0.8027 (mp0) cc_final: 0.7572 (mp0) outliers start: 1 outliers final: 1 residues processed: 272 average time/residue: 0.1068 time to fit residues: 44.5353 Evaluate side-chains 229 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 44 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.134803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103243 restraints weight = 34245.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.109249 restraints weight = 19095.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113525 restraints weight = 13020.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116456 restraints weight = 9888.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118681 restraints weight = 8049.038| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6510 Z= 0.134 Angle : 0.439 3.868 8712 Z= 0.261 Chirality : 0.048 0.192 966 Planarity : 0.002 0.016 1110 Dihedral : 6.477 68.843 846 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 1.17 (0.29), residues: 348 loop : -0.06 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 144 TYR 0.020 0.003 TYR B 67 PHE 0.016 0.001 PHE O 9 TRP 0.001 0.000 TRP L 201 HIS 0.011 0.002 HIS L 120 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6510) covalent geometry : angle 0.43873 ( 8712) hydrogen bonds : bond 0.03669 ( 279) hydrogen bonds : angle 5.04754 ( 783) *********************** 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 271 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.228 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: A 42 GLU cc_start: 0.7357 (mp0) cc_final: 0.6579 (mp0) REVERT: I 8 ASN cc_start: 0.7492 (t0) cc_final: 0.7166 (t0) REVERT: I 136 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7331 (tp30) REVERT: L 36 GLU cc_start: 0.7822 (mp0) cc_final: 0.7406 (mp0) REVERT: L 42 GLU cc_start: 0.7188 (mp0) cc_final: 0.6811 (mp0) REVERT: O 42 GLU cc_start: 0.7438 (mp0) cc_final: 0.6544 (mp0) REVERT: B 136 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7309 (tp30) REVERT: F 36 GLU cc_start: 0.7721 (mp0) cc_final: 0.7320 (mp0) REVERT: F 122 GLU cc_start: 0.7915 (mp0) cc_final: 0.7528 (mp0) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1100 time to fit residues: 45.2852 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 : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 HIS F 33 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.131999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.099670 restraints weight = 34307.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105545 restraints weight = 19238.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.109747 restraints weight = 13230.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.112713 restraints weight = 10126.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114684 restraints weight = 8286.658| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6510 Z= 0.217 Angle : 0.464 5.152 8712 Z= 0.274 Chirality : 0.047 0.189 966 Planarity : 0.002 0.016 1110 Dihedral : 6.525 69.108 846 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 1.04 (0.30), residues: 348 loop : -0.11 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 144 TYR 0.029 0.004 TYR B 67 PHE 0.013 0.002 PHE O 9 TRP 0.002 0.000 TRP F 201 HIS 0.007 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 6510) covalent geometry : angle 0.46401 ( 8712) hydrogen bonds : bond 0.03950 ( 279) hydrogen bonds : angle 5.03901 ( 783) *********************** 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 267 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.340 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: A 42 GLU cc_start: 0.7508 (mp0) cc_final: 0.6670 (mp0) REVERT: A 57 ILE cc_start: 0.9640 (mm) cc_final: 0.9424 (mt) REVERT: A 118 PHE cc_start: 0.7501 (p90) cc_final: 0.7208 (p90) REVERT: A 153 TYR cc_start: 0.8654 (m-80) cc_final: 0.8058 (m-80) REVERT: I 136 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7320 (mm-30) REVERT: L 36 GLU cc_start: 0.7834 (mp0) cc_final: 0.7381 (mp0) REVERT: L 42 GLU cc_start: 0.7324 (mp0) cc_final: 0.6669 (mp0) REVERT: O 42 GLU cc_start: 0.7455 (mp0) cc_final: 0.6570 (mp0) REVERT: B 136 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7256 (mm-30) REVERT: B 153 TYR cc_start: 0.8622 (m-80) cc_final: 0.8177 (m-10) REVERT: F 122 GLU cc_start: 0.7842 (mp0) cc_final: 0.7500 (mp0) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1117 time to fit residues: 45.0230 Evaluate side-chains 237 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.133032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.100878 restraints weight = 33914.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.106609 restraints weight = 19023.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110875 restraints weight = 13184.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113667 restraints weight = 10120.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115771 restraints weight = 8355.028| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6510 Z= 0.139 Angle : 0.431 3.544 8712 Z= 0.256 Chirality : 0.048 0.198 966 Planarity : 0.002 0.013 1110 Dihedral : 6.439 69.051 846 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 0.15 % Allowed : 0.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 0.96 (0.30), residues: 348 loop : 0.01 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 144 TYR 0.020 0.003 TYR B 67 PHE 0.012 0.001 PHE I 9 TRP 0.001 0.000 TRP A 201 HIS 0.005 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6510) covalent geometry : angle 0.43111 ( 8712) hydrogen bonds : bond 0.03527 ( 279) hydrogen bonds : angle 4.97364 ( 783) *********************** 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 266 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 0.368 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: A 42 GLU cc_start: 0.7389 (mp0) cc_final: 0.6535 (mp0) REVERT: I 118 PHE cc_start: 0.7321 (m-80) cc_final: 0.7112 (m-80) REVERT: I 136 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7393 (tp30) REVERT: L 42 GLU cc_start: 0.7418 (mp0) cc_final: 0.6991 (mp0) REVERT: O 42 GLU cc_start: 0.7436 (mp0) cc_final: 0.6496 (mp0) REVERT: O 136 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7181 (mm-30) REVERT: B 118 PHE cc_start: 0.7392 (m-80) cc_final: 0.7127 (m-80) REVERT: B 136 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7284 (tp30) REVERT: B 153 TYR cc_start: 0.8633 (m-80) cc_final: 0.8397 (m-80) REVERT: F 42 GLU cc_start: 0.7318 (mp0) cc_final: 0.6925 (mp0) REVERT: F 122 GLU cc_start: 0.7844 (mp0) cc_final: 0.7467 (mp0) outliers start: 1 outliers final: 1 residues processed: 265 average time/residue: 0.1122 time to fit residues: 44.7968 Evaluate side-chains 237 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.132886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.100273 restraints weight = 34294.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.106156 restraints weight = 19357.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.110289 restraints weight = 13392.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113243 restraints weight = 10300.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.115156 restraints weight = 8489.235| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6510 Z= 0.149 Angle : 0.437 6.126 8712 Z= 0.257 Chirality : 0.048 0.197 966 Planarity : 0.002 0.013 1110 Dihedral : 6.332 68.922 846 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.24 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 0.87 (0.30), residues: 348 loop : 0.05 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.011 0.002 TYR B 67 PHE 0.012 0.001 PHE I 9 TRP 0.001 0.000 TRP F 201 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6510) covalent geometry : angle 0.43723 ( 8712) hydrogen bonds : bond 0.03482 ( 279) hydrogen bonds : angle 4.93499 ( 783) *********************** 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 259 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.284 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: A 42 GLU cc_start: 0.7429 (mp0) cc_final: 0.6607 (mp0) REVERT: A 153 TYR cc_start: 0.8667 (m-80) cc_final: 0.8253 (m-10) REVERT: I 110 MET cc_start: 0.8234 (mmm) cc_final: 0.7986 (mmm) REVERT: I 136 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7359 (tp30) REVERT: L 42 GLU cc_start: 0.7418 (mp0) cc_final: 0.6770 (mp0) REVERT: O 42 GLU cc_start: 0.7166 (mp0) cc_final: 0.6263 (mp0) REVERT: O 136 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7221 (mm-30) REVERT: B 110 MET cc_start: 0.8217 (mmm) cc_final: 0.7951 (mmm) REVERT: B 136 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7283 (tp30) REVERT: B 153 TYR cc_start: 0.8603 (m-80) cc_final: 0.8394 (m-80) REVERT: F 42 GLU cc_start: 0.7230 (mp0) cc_final: 0.6867 (mp0) REVERT: F 122 GLU cc_start: 0.7814 (mp0) cc_final: 0.7465 (mp0) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.0953 time to fit residues: 38.0283 Evaluate side-chains 229 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.133913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.101609 restraints weight = 34165.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.107454 restraints weight = 19102.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111772 restraints weight = 13215.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114809 restraints weight = 10096.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116844 restraints weight = 8246.310| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6510 Z= 0.105 Angle : 0.426 5.627 8712 Z= 0.249 Chirality : 0.048 0.195 966 Planarity : 0.002 0.015 1110 Dihedral : 6.158 68.434 846 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 0.91 (0.30), residues: 348 loop : 0.12 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.010 0.002 TYR B 67 PHE 0.010 0.001 PHE I 9 TRP 0.001 0.000 TRP L 201 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 6510) covalent geometry : angle 0.42577 ( 8712) hydrogen bonds : bond 0.03237 ( 279) hydrogen bonds : angle 4.83863 ( 783) ********************** 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 260 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 0.376 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: A 42 GLU cc_start: 0.7387 (mp0) cc_final: 0.6625 (mp0) REVERT: A 153 TYR cc_start: 0.8397 (m-80) cc_final: 0.8098 (m-10) REVERT: I 136 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7406 (tp30) REVERT: I 153 TYR cc_start: 0.8928 (m-80) cc_final: 0.8494 (m-80) REVERT: L 42 GLU cc_start: 0.7306 (mp0) cc_final: 0.6654 (mp0) REVERT: O 136 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7176 (mm-30) REVERT: B 8 ASN cc_start: 0.7381 (OUTLIER) cc_final: 0.6846 (t160) REVERT: B 42 GLU cc_start: 0.7441 (mp0) cc_final: 0.6877 (mp0) REVERT: B 110 MET cc_start: 0.8207 (mmm) cc_final: 0.7984 (mmm) REVERT: B 136 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7288 (tp30) REVERT: F 42 GLU cc_start: 0.7221 (mp0) cc_final: 0.6904 (mp0) REVERT: F 122 GLU cc_start: 0.7790 (mp0) cc_final: 0.7480 (mp0) outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.1155 time to fit residues: 46.0983 Evaluate side-chains 235 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 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 B 33 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.131555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.098823 restraints weight = 34484.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.104454 restraints weight = 19886.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.108574 restraints weight = 13988.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.111317 restraints weight = 10881.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113458 restraints weight = 9063.779| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5992 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= 0.202 Angle : 0.476 9.158 8712 Z= 0.275 Chirality : 0.047 0.195 966 Planarity : 0.002 0.019 1110 Dihedral : 6.195 68.302 846 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.31), residues: 780 helix: None (None), residues: 0 sheet: 0.78 (0.30), residues: 348 loop : 0.08 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 117 TYR 0.013 0.003 TYR A 153 PHE 0.013 0.002 PHE I 9 TRP 0.001 0.000 TRP F 201 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 6510) covalent geometry : angle 0.47592 ( 8712) hydrogen bonds : bond 0.03697 ( 279) hydrogen bonds : angle 4.89979 ( 783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2341.69 seconds wall clock time: 40 minutes 42.09 seconds (2442.09 seconds total)