Starting phenix.real_space_refine on Wed Sep 17 03:21:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ckl_45651/09_2025/9ckl_45651.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ckl_45651/09_2025/9ckl_45651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ckl_45651/09_2025/9ckl_45651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ckl_45651/09_2025/9ckl_45651.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ckl_45651/09_2025/9ckl_45651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ckl_45651/09_2025/9ckl_45651.map" } resolution = 2.68 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1888 2.51 5 N 512 2.21 5 O 600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3000 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 375 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain breaks: 1 Chain: "B" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 375 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain breaks: 1 Chain: "C" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 375 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain breaks: 1 Chain: "D" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 375 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 375 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain breaks: 1 Chain: "F" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 375 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain breaks: 1 Chain: "G" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 375 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain breaks: 1 Chain: "H" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 375 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain breaks: 1 Time building chain proxies: 0.93, per 1000 atoms: 0.31 Number of scatterers: 3000 At special positions: 0 Unit cell: (93.24, 64.68, 35.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 600 8.00 N 512 7.00 C 1888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.21 Conformation dependent library (CDL) restraints added in 179.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 736 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 43 removed outlier: 6.334A pdb=" N LEU A 38 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N GLY C 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 40 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N LYS C 43 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER A 42 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU C 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N GLY E 41 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL C 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N LYS E 43 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER C 42 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU E 38 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N GLY G 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL E 40 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N LYS G 43 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER E 42 " --> pdb=" O LYS G 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 56 removed outlier: 6.415A pdb=" N HIS A 50 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR C 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL A 52 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL C 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR A 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N HIS C 50 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY E 51 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N HIS E 50 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N THR G 53 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL E 52 " --> pdb=" O THR G 53 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL G 55 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR E 54 " --> pdb=" O VAL G 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 64 through 65 removed outlier: 6.077A pdb=" N THR A 64 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR C 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR E 64 " --> pdb=" O ASN G 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 70 through 72 removed outlier: 6.272A pdb=" N VAL A 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL C 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL E 70 " --> pdb=" O VAL G 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 75 through 79 removed outlier: 6.002A pdb=" N THR E 75 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ALA G 78 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL E 77 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA8, first strand: chain 'A' and resid 88 through 89 Processing sheet with id=AA9, first strand: chain 'B' and resid 37 through 43 removed outlier: 6.362A pdb=" N LEU B 38 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N GLY D 41 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 40 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LYS D 43 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER B 42 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU D 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N GLY F 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL D 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LYS F 43 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER D 42 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU F 38 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N GLY H 41 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL F 40 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N LYS H 43 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER F 42 " --> pdb=" O LYS H 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 46 through 47 Processing sheet with id=AB2, first strand: chain 'B' and resid 50 through 56 removed outlier: 6.423A pdb=" N HIS B 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR D 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL B 52 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL D 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N THR B 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N HIS D 50 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY F 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N HIS F 50 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N THR H 53 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL F 52 " --> pdb=" O THR H 53 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL H 55 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR F 54 " --> pdb=" O VAL H 55 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 64 through 65 removed outlier: 6.095A pdb=" N THR B 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR D 64 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N THR F 64 " --> pdb=" O ASN H 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 70 through 72 removed outlier: 6.282A pdb=" N VAL B 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL D 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL F 70 " --> pdb=" O VAL H 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 75 through 79 removed outlier: 6.111A pdb=" N THR D 75 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA F 78 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL D 77 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR F 75 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ALA H 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL F 77 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=AB7, first strand: chain 'B' and resid 88 through 89 32 hydrogen bonds defined for protein. 96 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.40 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 512 1.29 - 1.35: 464 1.35 - 1.42: 136 1.42 - 1.48: 524 1.48 - 1.55: 1372 Bond restraints: 3008 Sorted by residual: bond pdb=" CG LEU E 38 " pdb=" CD1 LEU E 38 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.40e+00 bond pdb=" CG LEU F 38 " pdb=" CD1 LEU F 38 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.15e+00 bond pdb=" CG LEU C 38 " pdb=" CD1 LEU C 38 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.04e+00 bond pdb=" CG LEU D 38 " pdb=" CD1 LEU D 38 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.92e+00 bond pdb=" CG LEU G 38 " pdb=" CD1 LEU G 38 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.32e+00 ... (remaining 3003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 3616 1.01 - 2.02: 409 2.02 - 3.03: 41 3.03 - 4.05: 6 4.05 - 5.06: 8 Bond angle restraints: 4080 Sorted by residual: angle pdb=" CA GLY B 93 " pdb=" C GLY B 93 " pdb=" N PHE B 94 " ideal model delta sigma weight residual 115.58 117.48 -1.90 1.07e+00 8.73e-01 3.15e+00 angle pdb=" CA GLY A 93 " pdb=" C GLY A 93 " pdb=" N PHE A 94 " ideal model delta sigma weight residual 115.58 117.47 -1.89 1.07e+00 8.73e-01 3.12e+00 angle pdb=" CD1 LEU F 38 " pdb=" CG LEU F 38 " pdb=" CD2 LEU F 38 " ideal model delta sigma weight residual 110.80 107.13 3.67 2.20e+00 2.07e-01 2.78e+00 angle pdb=" CD1 LEU E 38 " pdb=" CG LEU E 38 " pdb=" CD2 LEU E 38 " ideal model delta sigma weight residual 110.80 107.16 3.64 2.20e+00 2.07e-01 2.73e+00 angle pdb=" N SER D 87 " pdb=" CA SER D 87 " pdb=" C SER D 87 " ideal model delta sigma weight residual 108.46 110.84 -2.38 1.51e+00 4.39e-01 2.49e+00 ... (remaining 4075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.84: 1398 6.84 - 13.67: 200 13.67 - 20.50: 50 20.50 - 27.34: 16 27.34 - 34.17: 24 Dihedral angle restraints: 1688 sinusoidal: 512 harmonic: 1176 Sorted by residual: dihedral pdb=" CA VAL F 66 " pdb=" C VAL F 66 " pdb=" N GLY F 67 " pdb=" CA GLY F 67 " ideal model delta harmonic sigma weight residual 180.00 -152.89 -27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA VAL E 66 " pdb=" C VAL E 66 " pdb=" N GLY E 67 " pdb=" CA GLY E 67 " ideal model delta harmonic sigma weight residual -180.00 -153.08 -26.92 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA VAL G 66 " pdb=" C VAL G 66 " pdb=" N GLY G 67 " pdb=" CA GLY G 67 " ideal model delta harmonic sigma weight residual -180.00 -154.64 -25.36 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 1685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 256 0.036 - 0.073: 169 0.073 - 0.109: 99 0.109 - 0.145: 33 0.145 - 0.182: 3 Chirality restraints: 560 Sorted by residual: chirality pdb=" CA TYR D 39 " pdb=" N TYR D 39 " pdb=" C TYR D 39 " pdb=" CB TYR D 39 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.26e-01 chirality pdb=" CA TYR C 39 " pdb=" N TYR C 39 " pdb=" C TYR C 39 " pdb=" CB TYR C 39 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA TYR E 39 " pdb=" N TYR E 39 " pdb=" C TYR E 39 " pdb=" CB TYR E 39 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.71e-01 ... (remaining 557 not shown) Planarity restraints: 496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 39 " 0.014 2.00e-02 2.50e+03 2.12e-02 9.00e+00 pdb=" CG TYR D 39 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR D 39 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR D 39 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR D 39 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR D 39 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D 39 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 39 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 39 " -0.013 2.00e-02 2.50e+03 2.10e-02 8.81e+00 pdb=" CG TYR C 39 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR C 39 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR C 39 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR C 39 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR C 39 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 39 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 39 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 39 " -0.011 2.00e-02 2.50e+03 1.97e-02 7.76e+00 pdb=" CG TYR E 39 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR E 39 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR E 39 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR E 39 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR E 39 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR E 39 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 39 " 0.002 2.00e-02 2.50e+03 ... (remaining 493 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 521 2.79 - 3.32: 2519 3.32 - 3.84: 4697 3.84 - 4.37: 5165 4.37 - 4.90: 10155 Nonbonded interactions: 23057 Sorted by model distance: nonbonded pdb=" O THR F 81 " pdb=" OG1 THR H 81 " model vdw 2.262 3.040 nonbonded pdb=" O THR E 81 " pdb=" OG1 THR G 81 " model vdw 2.271 3.040 nonbonded pdb=" O THR A 81 " pdb=" OG1 THR C 81 " model vdw 2.410 3.040 nonbonded pdb=" O THR B 81 " pdb=" OG1 THR D 81 " model vdw 2.412 3.040 nonbonded pdb=" ND2 ASN A 65 " pdb=" O ALA A 91 " model vdw 2.429 3.120 ... (remaining 23052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.240 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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 : 0.005 0.061 3008 Z= 0.244 Angle : 0.678 5.057 4080 Z= 0.391 Chirality : 0.059 0.182 560 Planarity : 0.003 0.021 496 Dihedral : 8.937 34.169 952 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.35), residues: 416 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.047 0.012 TYR D 39 PHE 0.017 0.006 PHE F 94 HIS 0.011 0.005 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 3008) covalent geometry : angle 0.67850 ( 4080) hydrogen bonds : bond 0.16595 ( 32) hydrogen bonds : angle 6.65879 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2348 time to fit residues: 16.7346 Evaluate side-chains 48 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.0060 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN H 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.179282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.158086 restraints weight = 3275.849| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.23 r_work: 0.4121 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.4002 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3008 Z= 0.197 Angle : 0.569 4.977 4080 Z= 0.327 Chirality : 0.054 0.124 560 Planarity : 0.002 0.006 496 Dihedral : 6.293 24.368 440 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.62 % Allowed : 5.26 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.67 (0.36), residues: 416 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.004 TYR G 39 PHE 0.009 0.003 PHE G 94 HIS 0.008 0.004 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 3008) covalent geometry : angle 0.56864 ( 4080) hydrogen bonds : bond 0.02672 ( 32) hydrogen bonds : angle 4.48319 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: B 79 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: F 43 LYS cc_start: 0.8052 (mttt) cc_final: 0.7604 (mptp) outliers start: 11 outliers final: 7 residues processed: 64 average time/residue: 0.3242 time to fit residues: 21.7829 Evaluate side-chains 59 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 74 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 0.0870 chunk 12 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN H 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.173185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.153167 restraints weight = 3340.763| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 2.17 r_work: 0.4081 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3970 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.048 3008 Z= 0.409 Angle : 0.815 6.043 4080 Z= 0.466 Chirality : 0.062 0.137 560 Planarity : 0.004 0.010 496 Dihedral : 7.932 34.735 440 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 6.25 % Allowed : 11.18 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.85 % 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: -3.39 (0.34), residues: 416 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.26), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.004 TYR G 39 PHE 0.015 0.005 PHE G 94 HIS 0.008 0.004 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00867 ( 3008) covalent geometry : angle 0.81513 ( 4080) hydrogen bonds : bond 0.04200 ( 32) hydrogen bonds : angle 4.76019 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: B 79 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7905 (tt0) outliers start: 19 outliers final: 14 residues processed: 51 average time/residue: 0.3478 time to fit residues: 18.5305 Evaluate side-chains 56 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 2 optimal weight: 0.0470 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 65 ASN ** C 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN H 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.186530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.165205 restraints weight = 3124.628| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 2.19 r_work: 0.4190 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4065 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3008 Z= 0.123 Angle : 0.474 4.082 4080 Z= 0.267 Chirality : 0.052 0.119 560 Planarity : 0.002 0.007 496 Dihedral : 5.463 20.165 440 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.59 % Allowed : 18.75 % Favored : 75.66 % 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: -3.00 (0.36), residues: 416 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 39 PHE 0.005 0.002 PHE G 94 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 3008) covalent geometry : angle 0.47353 ( 4080) hydrogen bonds : bond 0.01641 ( 32) hydrogen bonds : angle 3.90374 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.082 Fit side-chains REVERT: A 79 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: B 79 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: E 38 LEU cc_start: 0.8151 (tt) cc_final: 0.7913 (tm) REVERT: E 43 LYS cc_start: 0.8118 (mttt) cc_final: 0.7651 (mptp) REVERT: F 38 LEU cc_start: 0.8163 (tt) cc_final: 0.7945 (tm) REVERT: F 43 LYS cc_start: 0.8131 (mttt) cc_final: 0.7610 (mptp) REVERT: G 38 LEU cc_start: 0.8504 (tt) cc_final: 0.8303 (tm) outliers start: 17 outliers final: 8 residues processed: 60 average time/residue: 0.2624 time to fit residues: 16.5929 Evaluate side-chains 57 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 48 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.0070 chunk 21 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 0.0980 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN H 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.185747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.164116 restraints weight = 3102.826| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 2.20 r_work: 0.4177 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.4055 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3008 Z= 0.140 Angle : 0.505 6.958 4080 Z= 0.279 Chirality : 0.052 0.119 560 Planarity : 0.002 0.006 496 Dihedral : 5.449 20.648 440 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 5.92 % Allowed : 20.39 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.93 (0.37), residues: 416 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR C 39 PHE 0.006 0.002 PHE E 94 HIS 0.003 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3008) covalent geometry : angle 0.50539 ( 4080) hydrogen bonds : bond 0.01716 ( 32) hydrogen bonds : angle 3.99058 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.115 Fit side-chains REVERT: E 43 LYS cc_start: 0.8135 (mttt) cc_final: 0.7640 (mptp) REVERT: F 43 LYS cc_start: 0.8151 (mttt) cc_final: 0.7626 (mptp) outliers start: 18 outliers final: 10 residues processed: 54 average time/residue: 0.2935 time to fit residues: 16.6755 Evaluate side-chains 54 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain H residue 48 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN H 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.177495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.156619 restraints weight = 3263.592| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 2.19 r_work: 0.4121 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4007 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 3008 Z= 0.322 Angle : 0.718 7.318 4080 Z= 0.406 Chirality : 0.058 0.134 560 Planarity : 0.003 0.009 496 Dihedral : 7.140 31.885 440 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 6.91 % Allowed : 21.71 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.93 % 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: -3.39 (0.35), residues: 416 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.003 TYR B 39 PHE 0.013 0.004 PHE E 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00686 ( 3008) covalent geometry : angle 0.71785 ( 4080) hydrogen bonds : bond 0.03461 ( 32) hydrogen bonds : angle 4.60749 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 55 average time/residue: 0.2879 time to fit residues: 16.7018 Evaluate side-chains 58 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN G 79 GLN H 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.178151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.157712 restraints weight = 3253.797| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.19 r_work: 0.4131 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4016 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3008 Z= 0.262 Angle : 0.652 6.800 4080 Z= 0.366 Chirality : 0.056 0.132 560 Planarity : 0.003 0.008 496 Dihedral : 6.821 29.427 440 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 7.24 % Allowed : 20.39 % Favored : 72.37 % 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: -3.45 (0.35), residues: 416 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.003 TYR B 39 PHE 0.011 0.003 PHE F 94 HIS 0.004 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 3008) covalent geometry : angle 0.65189 ( 4080) hydrogen bonds : bond 0.03044 ( 32) hydrogen bonds : angle 4.46604 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 43 LYS cc_start: 0.8049 (mttt) cc_final: 0.7587 (mptp) REVERT: F 43 LYS cc_start: 0.8080 (mttt) cc_final: 0.7597 (mptp) outliers start: 22 outliers final: 13 residues processed: 58 average time/residue: 0.3775 time to fit residues: 22.7553 Evaluate side-chains 62 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 22 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 65 ASN ** C 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN H 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.182026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.161446 restraints weight = 3175.384| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 2.18 r_work: 0.4161 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4047 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3008 Z= 0.156 Angle : 0.534 6.218 4080 Z= 0.297 Chirality : 0.053 0.132 560 Planarity : 0.002 0.011 496 Dihedral : 5.801 22.562 440 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.28 % Allowed : 23.03 % Favored : 72.70 % 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: -3.23 (0.36), residues: 416 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR C 39 PHE 0.007 0.002 PHE F 94 HIS 0.003 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3008) covalent geometry : angle 0.53375 ( 4080) hydrogen bonds : bond 0.02013 ( 32) hydrogen bonds : angle 4.07901 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 43 LYS cc_start: 0.8102 (mttt) cc_final: 0.7623 (mptp) REVERT: F 43 LYS cc_start: 0.8109 (mttt) cc_final: 0.7626 (mptp) outliers start: 13 outliers final: 11 residues processed: 55 average time/residue: 0.3475 time to fit residues: 19.9399 Evaluate side-chains 58 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** C 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN H 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.180853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.160104 restraints weight = 3188.716| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 2.19 r_work: 0.4148 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4034 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3008 Z= 0.182 Angle : 0.562 6.301 4080 Z= 0.314 Chirality : 0.053 0.129 560 Planarity : 0.002 0.007 496 Dihedral : 5.978 24.216 440 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.93 % Allowed : 22.70 % Favored : 72.37 % 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: -3.23 (0.36), residues: 416 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 39 PHE 0.008 0.002 PHE F 94 HIS 0.003 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 3008) covalent geometry : angle 0.56216 ( 4080) hydrogen bonds : bond 0.02250 ( 32) hydrogen bonds : angle 4.18777 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 43 LYS cc_start: 0.8100 (mttt) cc_final: 0.7602 (mptp) REVERT: F 43 LYS cc_start: 0.8098 (mttt) cc_final: 0.7597 (mptp) outliers start: 15 outliers final: 11 residues processed: 54 average time/residue: 0.3426 time to fit residues: 19.3718 Evaluate side-chains 58 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 65 ASN B 79 GLN ** C 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN H 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.177734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.157519 restraints weight = 3221.294| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 2.16 r_work: 0.4122 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4006 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3008 Z= 0.276 Angle : 0.670 6.634 4080 Z= 0.378 Chirality : 0.056 0.134 560 Planarity : 0.003 0.010 496 Dihedral : 6.910 30.596 440 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.61 % Allowed : 23.36 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -3.47 (0.35), residues: 416 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.003 TYR B 39 PHE 0.013 0.003 PHE F 94 HIS 0.004 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00591 ( 3008) covalent geometry : angle 0.67000 ( 4080) hydrogen bonds : bond 0.03137 ( 32) hydrogen bonds : angle 4.58583 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.8100 (mttt) cc_final: 0.7594 (mptp) outliers start: 14 outliers final: 12 residues processed: 52 average time/residue: 0.3430 time to fit residues: 18.7360 Evaluate side-chains 57 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 0.0570 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN H 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.181688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.161105 restraints weight = 3155.415| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 2.18 r_work: 0.4157 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4043 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3008 Z= 0.170 Angle : 0.548 6.228 4080 Z= 0.304 Chirality : 0.053 0.131 560 Planarity : 0.002 0.006 496 Dihedral : 5.938 23.735 440 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.93 % Allowed : 23.03 % Favored : 72.04 % 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: -3.26 (0.36), residues: 416 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR C 39 PHE 0.006 0.002 PHE G 94 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3008) covalent geometry : angle 0.54775 ( 4080) hydrogen bonds : bond 0.02142 ( 32) hydrogen bonds : angle 4.20425 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1228.21 seconds wall clock time: 21 minutes 46.38 seconds (1306.38 seconds total)