Starting phenix.real_space_refine on Mon Nov 18 11:57:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjh_18447/11_2024/8qjh_18447_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjh_18447/11_2024/8qjh_18447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjh_18447/11_2024/8qjh_18447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjh_18447/11_2024/8qjh_18447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjh_18447/11_2024/8qjh_18447_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjh_18447/11_2024/8qjh_18447_neut.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 11052 2.51 5 N 2628 2.21 5 O 2748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16584 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1382 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 165} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 5.60, per 1000 atoms: 0.34 Number of scatterers: 16584 At special positions: 0 Unit cell: (99.45, 91.65, 142.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 2748 8.00 N 2628 7.00 C 11052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 168 " distance=2.03 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: 4.06 Conformation dependent library (CDL) restraints added in 2.2 seconds 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4008 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 74.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 23 through 42 removed outlier: 4.142A pdb=" N GLU A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 99 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 130 through 157 removed outlier: 4.205A pdb=" N THR A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 217 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 23 through 42 removed outlier: 4.142A pdb=" N GLU B 41 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.517A pdb=" N VAL B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 99 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 130 through 157 removed outlier: 4.204A pdb=" N THR B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 217 Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 23 through 42 removed outlier: 4.142A pdb=" N GLU C 41 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL C 63 " --> pdb=" O GLY C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 99 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 130 through 157 removed outlier: 4.205A pdb=" N THR C 134 " --> pdb=" O THR C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 217 Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 23 through 42 removed outlier: 4.142A pdb=" N GLU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER D 42 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 69 removed outlier: 3.517A pdb=" N VAL D 63 " --> pdb=" O GLY D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 99 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 130 through 157 removed outlier: 4.206A pdb=" N THR D 134 " --> pdb=" O THR D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 217 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 23 through 42 removed outlier: 4.143A pdb=" N GLU E 41 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER E 42 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL E 63 " --> pdb=" O GLY E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 99 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 130 through 157 removed outlier: 4.205A pdb=" N THR E 134 " --> pdb=" O THR E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 217 Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 23 through 42 removed outlier: 4.143A pdb=" N GLU F 41 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER F 42 " --> pdb=" O VAL F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL F 63 " --> pdb=" O GLY F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 99 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 130 through 157 removed outlier: 4.206A pdb=" N THR F 134 " --> pdb=" O THR F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 217 Processing helix chain 'G' and resid 18 through 23 Processing helix chain 'G' and resid 23 through 42 removed outlier: 4.142A pdb=" N GLU G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER G 42 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL G 63 " --> pdb=" O GLY G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 99 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 130 through 157 removed outlier: 4.206A pdb=" N THR G 134 " --> pdb=" O THR G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 217 Processing helix chain 'H' and resid 18 through 23 Processing helix chain 'H' and resid 23 through 42 removed outlier: 4.143A pdb=" N GLU H 41 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 99 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 130 through 157 removed outlier: 4.206A pdb=" N THR H 134 " --> pdb=" O THR H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 217 Processing helix chain 'I' and resid 18 through 23 Processing helix chain 'I' and resid 23 through 42 removed outlier: 4.142A pdb=" N GLU I 41 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER I 42 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL I 63 " --> pdb=" O GLY I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 99 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 130 through 157 removed outlier: 4.205A pdb=" N THR I 134 " --> pdb=" O THR I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 217 Processing helix chain 'J' and resid 18 through 23 Processing helix chain 'J' and resid 23 through 42 removed outlier: 4.143A pdb=" N GLU J 41 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL J 63 " --> pdb=" O GLY J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 99 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 130 through 157 removed outlier: 4.206A pdb=" N THR J 134 " --> pdb=" O THR J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 217 Processing helix chain 'K' and resid 18 through 23 Processing helix chain 'K' and resid 23 through 42 removed outlier: 4.143A pdb=" N GLU K 41 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER K 42 " --> pdb=" O VAL K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL K 63 " --> pdb=" O GLY K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 99 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 130 through 157 removed outlier: 4.206A pdb=" N THR K 134 " --> pdb=" O THR K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 217 Processing helix chain 'L' and resid 18 through 23 Processing helix chain 'L' and resid 23 through 42 removed outlier: 4.143A pdb=" N GLU L 41 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER L 42 " --> pdb=" O VAL L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL L 63 " --> pdb=" O GLY L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 99 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 130 through 157 removed outlier: 4.205A pdb=" N THR L 134 " --> pdb=" O THR L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.923A pdb=" N ILE A 52 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 removed outlier: 3.923A pdb=" N ILE B 52 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.923A pdb=" N ILE C 52 " --> pdb=" O PHE C 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 removed outlier: 3.924A pdb=" N ILE D 52 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 removed outlier: 3.924A pdb=" N ILE E 52 " --> pdb=" O PHE E 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.923A pdb=" N ILE F 52 " --> pdb=" O PHE F 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.924A pdb=" N ILE G 52 " --> pdb=" O PHE G 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 removed outlier: 3.923A pdb=" N ILE H 52 " --> pdb=" O PHE H 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53 removed outlier: 3.923A pdb=" N ILE I 52 " --> pdb=" O PHE I 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53 removed outlier: 3.923A pdb=" N ILE J 52 " --> pdb=" O PHE J 180 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 removed outlier: 3.923A pdb=" N ILE K 52 " --> pdb=" O PHE K 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.924A pdb=" N ILE L 52 " --> pdb=" O PHE L 180 " (cutoff:3.500A) 1224 hydrogen bonds defined for protein. 3636 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: 5.22 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4908 1.35 - 1.46: 4449 1.46 - 1.58: 7479 1.58 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 17052 Sorted by residual: bond pdb=" C THR J 86 " pdb=" N PRO J 87 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.28e-02 6.10e+03 3.92e-01 bond pdb=" C THR K 86 " pdb=" N PRO K 87 " ideal model delta sigma weight residual 1.335 1.342 -0.008 1.28e-02 6.10e+03 3.61e-01 bond pdb=" C THR F 86 " pdb=" N PRO F 87 " ideal model delta sigma weight residual 1.335 1.342 -0.008 1.28e-02 6.10e+03 3.60e-01 bond pdb=" C THR I 86 " pdb=" N PRO I 87 " ideal model delta sigma weight residual 1.335 1.342 -0.008 1.28e-02 6.10e+03 3.44e-01 bond pdb=" C ARG I 183 " pdb=" O ARG I 183 " ideal model delta sigma weight residual 1.235 1.232 0.003 4.70e-03 4.53e+04 3.33e-01 ... (remaining 17047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 22857 1.06 - 2.12: 298 2.12 - 3.19: 89 3.19 - 4.25: 59 4.25 - 5.31: 13 Bond angle restraints: 23316 Sorted by residual: angle pdb=" CA CYS H 173 " pdb=" CB CYS H 173 " pdb=" SG CYS H 173 " ideal model delta sigma weight residual 114.40 110.74 3.66 2.30e+00 1.89e-01 2.53e+00 angle pdb=" CA CYS L 60 " pdb=" CB CYS L 60 " pdb=" SG CYS L 60 " ideal model delta sigma weight residual 114.40 110.74 3.66 2.30e+00 1.89e-01 2.53e+00 angle pdb=" CA CYS J 60 " pdb=" CB CYS J 60 " pdb=" SG CYS J 60 " ideal model delta sigma weight residual 114.40 110.75 3.65 2.30e+00 1.89e-01 2.52e+00 angle pdb=" CA CYS J 173 " pdb=" CB CYS J 173 " pdb=" SG CYS J 173 " ideal model delta sigma weight residual 114.40 110.76 3.64 2.30e+00 1.89e-01 2.51e+00 angle pdb=" CA CYS B 173 " pdb=" CB CYS B 173 " pdb=" SG CYS B 173 " ideal model delta sigma weight residual 114.40 110.76 3.64 2.30e+00 1.89e-01 2.51e+00 ... (remaining 23311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.53: 8479 8.53 - 17.07: 801 17.07 - 25.60: 279 25.60 - 34.14: 194 34.14 - 42.67: 60 Dihedral angle restraints: 9813 sinusoidal: 3657 harmonic: 6156 Sorted by residual: dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 173 " pdb=" CB CYS A 173 " ideal model delta sinusoidal sigma weight residual -86.00 -119.90 33.90 1 1.00e+01 1.00e-02 1.63e+01 dihedral pdb=" N PHE D 153 " pdb=" CA PHE D 153 " pdb=" CB PHE D 153 " pdb=" CG PHE D 153 " ideal model delta sinusoidal sigma weight residual -180.00 -137.33 -42.67 3 1.50e+01 4.44e-03 7.66e+00 dihedral pdb=" N PHE J 153 " pdb=" CA PHE J 153 " pdb=" CB PHE J 153 " pdb=" CG PHE J 153 " ideal model delta sinusoidal sigma weight residual -180.00 -137.33 -42.67 3 1.50e+01 4.44e-03 7.66e+00 ... (remaining 9810 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 1537 0.022 - 0.045: 654 0.045 - 0.067: 412 0.067 - 0.089: 112 0.089 - 0.111: 81 Chirality restraints: 2796 Sorted by residual: chirality pdb=" CA THR C 86 " pdb=" N THR C 86 " pdb=" C THR C 86 " pdb=" CB THR C 86 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.11 2.00e-01 2.50e+01 3.10e-01 chirality pdb=" CA THR K 86 " pdb=" N THR K 86 " pdb=" C THR K 86 " pdb=" CB THR K 86 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.11 2.00e-01 2.50e+01 3.02e-01 chirality pdb=" CA THR D 86 " pdb=" N THR D 86 " pdb=" C THR D 86 " pdb=" CB THR D 86 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.11 2.00e-01 2.50e+01 2.98e-01 ... (remaining 2793 not shown) Planarity restraints: 2784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 171 " -0.014 5.00e-02 4.00e+02 2.18e-02 7.60e-01 pdb=" N PRO B 172 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO B 172 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 172 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 171 " -0.014 5.00e-02 4.00e+02 2.17e-02 7.53e-01 pdb=" N PRO D 172 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO D 172 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 172 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 171 " -0.014 5.00e-02 4.00e+02 2.17e-02 7.52e-01 pdb=" N PRO H 172 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO H 172 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO H 172 " -0.011 5.00e-02 4.00e+02 ... (remaining 2781 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 261 2.60 - 3.18: 14129 3.18 - 3.75: 29076 3.75 - 4.33: 36100 4.33 - 4.90: 61413 Nonbonded interactions: 140979 Sorted by model distance: nonbonded pdb=" SG CYS H 60 " pdb=" SG CYS H 173 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS G 60 " pdb=" SG CYS G 173 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 60 " pdb=" SG CYS B 173 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS L 60 " pdb=" SG CYS L 173 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 60 " pdb=" SG CYS C 173 " model vdw 2.030 3.760 ... (remaining 140974 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' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 3.870 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: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 33.560 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 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 0.015 17052 Z= 0.113 Angle : 0.407 5.310 23316 Z= 0.204 Chirality : 0.036 0.111 2796 Planarity : 0.002 0.022 2784 Dihedral : 9.688 42.675 5796 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.29 % Allowed : 5.81 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.18), residues: 2028 helix: 3.36 (0.12), residues: 1392 sheet: 1.26 (0.48), residues: 132 loop : -1.33 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 77 HIS 0.001 0.000 HIS F 73 PHE 0.005 0.001 PHE E 180 TYR 0.004 0.001 TYR G 151 ARG 0.001 0.000 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 486 time to evaluate : 1.628 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: A 47 GLU cc_start: 0.8236 (pt0) cc_final: 0.7999 (pt0) REVERT: A 66 ASP cc_start: 0.8381 (t70) cc_final: 0.8039 (t0) REVERT: A 215 ARG cc_start: 0.8444 (tpp-160) cc_final: 0.8018 (tpt170) REVERT: B 30 ILE cc_start: 0.9400 (mt) cc_final: 0.9135 (mp) REVERT: B 47 GLU cc_start: 0.8248 (pt0) cc_final: 0.7971 (pt0) REVERT: B 66 ASP cc_start: 0.8315 (t70) cc_final: 0.8014 (t0) REVERT: B 142 ARG cc_start: 0.8744 (ttm170) cc_final: 0.7972 (ttm-80) REVERT: B 162 MET cc_start: 0.8610 (mmt) cc_final: 0.8211 (mmt) REVERT: B 215 ARG cc_start: 0.8413 (tpp-160) cc_final: 0.8057 (tpt170) REVERT: C 47 GLU cc_start: 0.8254 (pt0) cc_final: 0.8025 (pt0) REVERT: C 66 ASP cc_start: 0.8354 (t70) cc_final: 0.8069 (t0) REVERT: C 215 ARG cc_start: 0.8450 (tpp-160) cc_final: 0.8116 (tpt170) REVERT: D 47 GLU cc_start: 0.8208 (pt0) cc_final: 0.7986 (pt0) REVERT: D 66 ASP cc_start: 0.8355 (t70) cc_final: 0.8026 (t0) REVERT: D 215 ARG cc_start: 0.8403 (tpp-160) cc_final: 0.8076 (tpt170) REVERT: E 30 ILE cc_start: 0.9399 (mt) cc_final: 0.9135 (mp) REVERT: E 47 GLU cc_start: 0.8243 (pt0) cc_final: 0.7993 (pt0) REVERT: E 66 ASP cc_start: 0.8313 (t70) cc_final: 0.8010 (t0) REVERT: E 142 ARG cc_start: 0.8745 (ttm170) cc_final: 0.7977 (ttm-80) REVERT: E 162 MET cc_start: 0.8605 (mmt) cc_final: 0.8209 (mmt) REVERT: E 215 ARG cc_start: 0.8413 (tpp-160) cc_final: 0.8059 (tpt170) REVERT: F 47 GLU cc_start: 0.8262 (pt0) cc_final: 0.7971 (pt0) REVERT: F 66 ASP cc_start: 0.8355 (t70) cc_final: 0.8054 (t0) REVERT: F 162 MET cc_start: 0.8586 (mmt) cc_final: 0.8355 (mmt) REVERT: F 215 ARG cc_start: 0.8451 (tpp-160) cc_final: 0.8119 (tpt170) REVERT: G 47 GLU cc_start: 0.8228 (pt0) cc_final: 0.7984 (pt0) REVERT: G 66 ASP cc_start: 0.8355 (t70) cc_final: 0.8041 (t0) REVERT: G 215 ARG cc_start: 0.8405 (tpp-160) cc_final: 0.8082 (tpt170) REVERT: H 30 ILE cc_start: 0.9399 (mt) cc_final: 0.9134 (mp) REVERT: H 47 GLU cc_start: 0.8229 (pt0) cc_final: 0.7986 (pt0) REVERT: H 66 ASP cc_start: 0.8323 (t70) cc_final: 0.8007 (t0) REVERT: H 142 ARG cc_start: 0.8744 (ttm170) cc_final: 0.8072 (ttm-80) REVERT: H 162 MET cc_start: 0.8616 (mmt) cc_final: 0.8221 (mmt) REVERT: H 215 ARG cc_start: 0.8401 (tpp-160) cc_final: 0.8044 (tpt170) REVERT: I 47 GLU cc_start: 0.8244 (pt0) cc_final: 0.8020 (pt0) REVERT: I 66 ASP cc_start: 0.8362 (t70) cc_final: 0.8067 (t0) REVERT: I 162 MET cc_start: 0.8584 (mmt) cc_final: 0.8357 (mmt) REVERT: I 215 ARG cc_start: 0.8451 (tpp-160) cc_final: 0.8097 (tpt170) REVERT: J 47 GLU cc_start: 0.8230 (pt0) cc_final: 0.8005 (pt0) REVERT: J 66 ASP cc_start: 0.8369 (t70) cc_final: 0.8039 (t0) REVERT: J 215 ARG cc_start: 0.8411 (tpp-160) cc_final: 0.8071 (tpt170) REVERT: K 30 ILE cc_start: 0.9400 (mt) cc_final: 0.9130 (mp) REVERT: K 47 GLU cc_start: 0.8241 (pt0) cc_final: 0.7991 (pt0) REVERT: K 66 ASP cc_start: 0.8323 (t70) cc_final: 0.8010 (t0) REVERT: K 142 ARG cc_start: 0.8738 (ttm170) cc_final: 0.8061 (ttm-80) REVERT: K 162 MET cc_start: 0.8614 (mmt) cc_final: 0.8215 (mmt) REVERT: K 215 ARG cc_start: 0.8403 (tpp-160) cc_final: 0.8047 (tpt170) REVERT: L 47 GLU cc_start: 0.8246 (pt0) cc_final: 0.7989 (pt0) REVERT: L 66 ASP cc_start: 0.8374 (t70) cc_final: 0.8094 (t0) REVERT: L 133 TRP cc_start: 0.7959 (m100) cc_final: 0.7740 (m-10) REVERT: L 162 MET cc_start: 0.8581 (mmt) cc_final: 0.8348 (mmt) REVERT: L 215 ARG cc_start: 0.8461 (tpp-160) cc_final: 0.8104 (tpt170) outliers start: 24 outliers final: 0 residues processed: 498 average time/residue: 1.2151 time to fit residues: 674.6871 Evaluate side-chains 297 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN B 54 ASN B 175 ASN C 54 ASN C 175 ASN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN E 54 ASN E 175 ASN F 54 ASN F 175 ASN ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 ASN H 54 ASN H 175 ASN I 54 ASN I 175 ASN ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN K 54 ASN K 175 ASN L 54 ASN L 94 HIS L 175 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17052 Z= 0.314 Angle : 0.561 5.405 23316 Z= 0.298 Chirality : 0.044 0.203 2796 Planarity : 0.003 0.022 2784 Dihedral : 3.253 11.258 2232 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.46 % Allowed : 15.43 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.17), residues: 2028 helix: 3.24 (0.12), residues: 1404 sheet: 1.46 (0.46), residues: 132 loop : -1.67 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 44 HIS 0.004 0.001 HIS L 73 PHE 0.012 0.002 PHE E 180 TYR 0.014 0.001 TYR F 211 ARG 0.003 0.001 ARG J 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 311 time to evaluate : 1.931 Fit side-chains REVERT: A 47 GLU cc_start: 0.8440 (pt0) cc_final: 0.8236 (pt0) REVERT: A 66 ASP cc_start: 0.8738 (t70) cc_final: 0.8382 (t0) REVERT: A 133 TRP cc_start: 0.7432 (OUTLIER) cc_final: 0.7190 (m-10) REVERT: A 169 ASP cc_start: 0.8148 (p0) cc_final: 0.7923 (p0) REVERT: A 215 ARG cc_start: 0.8442 (tpp-160) cc_final: 0.8073 (tpt170) REVERT: B 47 GLU cc_start: 0.8415 (pt0) cc_final: 0.8119 (pt0) REVERT: B 66 ASP cc_start: 0.8736 (t70) cc_final: 0.8254 (t0) REVERT: B 133 TRP cc_start: 0.7409 (OUTLIER) cc_final: 0.7159 (m-10) REVERT: B 146 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8478 (mm-30) REVERT: B 162 MET cc_start: 0.8711 (mmt) cc_final: 0.8295 (mmt) REVERT: B 169 ASP cc_start: 0.8271 (p0) cc_final: 0.7890 (p0) REVERT: B 215 ARG cc_start: 0.8414 (tpp-160) cc_final: 0.8060 (tpt170) REVERT: C 30 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9260 (mp) REVERT: C 46 ASP cc_start: 0.8575 (p0) cc_final: 0.8276 (p0) REVERT: C 47 GLU cc_start: 0.8439 (pt0) cc_final: 0.8202 (pt0) REVERT: C 66 ASP cc_start: 0.8765 (t70) cc_final: 0.8364 (t0) REVERT: C 133 TRP cc_start: 0.7421 (OUTLIER) cc_final: 0.7205 (m-10) REVERT: C 203 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9086 (mp) REVERT: C 215 ARG cc_start: 0.8440 (tpp-160) cc_final: 0.8136 (tpt170) REVERT: D 66 ASP cc_start: 0.8736 (t70) cc_final: 0.8400 (t0) REVERT: D 133 TRP cc_start: 0.7388 (OUTLIER) cc_final: 0.7121 (m-10) REVERT: D 169 ASP cc_start: 0.8205 (p0) cc_final: 0.7903 (p0) REVERT: D 211 TYR cc_start: 0.8436 (t80) cc_final: 0.8196 (t80) REVERT: D 215 ARG cc_start: 0.8382 (tpp-160) cc_final: 0.8098 (tpt170) REVERT: E 47 GLU cc_start: 0.8412 (pt0) cc_final: 0.8112 (pt0) REVERT: E 66 ASP cc_start: 0.8739 (t70) cc_final: 0.8254 (t0) REVERT: E 133 TRP cc_start: 0.7413 (OUTLIER) cc_final: 0.7167 (m-10) REVERT: E 146 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8485 (mm-30) REVERT: E 162 MET cc_start: 0.8702 (mmt) cc_final: 0.8289 (mmt) REVERT: E 169 ASP cc_start: 0.8261 (p0) cc_final: 0.7879 (p0) REVERT: E 215 ARG cc_start: 0.8415 (tpp-160) cc_final: 0.8062 (tpt170) REVERT: F 30 ILE cc_start: 0.9470 (OUTLIER) cc_final: 0.9259 (mp) REVERT: F 46 ASP cc_start: 0.8572 (p0) cc_final: 0.8265 (p0) REVERT: F 47 GLU cc_start: 0.8431 (pt0) cc_final: 0.8139 (pt0) REVERT: F 66 ASP cc_start: 0.8762 (t70) cc_final: 0.8359 (t0) REVERT: F 93 MET cc_start: 0.9356 (OUTLIER) cc_final: 0.8894 (mmm) REVERT: F 133 TRP cc_start: 0.7407 (OUTLIER) cc_final: 0.7196 (m-10) REVERT: F 203 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.9064 (mp) REVERT: F 215 ARG cc_start: 0.8433 (tpp-160) cc_final: 0.8127 (tpt170) REVERT: G 66 ASP cc_start: 0.8734 (t70) cc_final: 0.8393 (t0) REVERT: G 133 TRP cc_start: 0.7397 (OUTLIER) cc_final: 0.7123 (m-10) REVERT: G 169 ASP cc_start: 0.8197 (p0) cc_final: 0.7895 (p0) REVERT: G 211 TYR cc_start: 0.8444 (t80) cc_final: 0.8204 (t80) REVERT: G 215 ARG cc_start: 0.8378 (tpp-160) cc_final: 0.8101 (tpt170) REVERT: H 47 GLU cc_start: 0.8409 (pt0) cc_final: 0.8121 (pt0) REVERT: H 66 ASP cc_start: 0.8751 (t70) cc_final: 0.8264 (t0) REVERT: H 133 TRP cc_start: 0.7414 (OUTLIER) cc_final: 0.7168 (m-10) REVERT: H 146 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8492 (mm-30) REVERT: H 169 ASP cc_start: 0.8280 (p0) cc_final: 0.7901 (p0) REVERT: H 215 ARG cc_start: 0.8415 (tpp-160) cc_final: 0.8052 (tpt170) REVERT: I 46 ASP cc_start: 0.8572 (p0) cc_final: 0.8305 (p0) REVERT: I 47 GLU cc_start: 0.8440 (pt0) cc_final: 0.8185 (pt0) REVERT: I 66 ASP cc_start: 0.8786 (t70) cc_final: 0.8376 (t0) REVERT: I 133 TRP cc_start: 0.7419 (OUTLIER) cc_final: 0.7208 (m-10) REVERT: I 215 ARG cc_start: 0.8426 (tpp-160) cc_final: 0.8119 (tpt170) REVERT: J 47 GLU cc_start: 0.8428 (pt0) cc_final: 0.8219 (pt0) REVERT: J 66 ASP cc_start: 0.8753 (t70) cc_final: 0.8404 (t0) REVERT: J 133 TRP cc_start: 0.7396 (OUTLIER) cc_final: 0.7148 (m-10) REVERT: J 169 ASP cc_start: 0.8201 (p0) cc_final: 0.7900 (p0) REVERT: J 211 TYR cc_start: 0.8434 (t80) cc_final: 0.8192 (t80) REVERT: J 215 ARG cc_start: 0.8380 (tpp-160) cc_final: 0.8097 (tpt170) REVERT: K 47 GLU cc_start: 0.8412 (pt0) cc_final: 0.8126 (pt0) REVERT: K 66 ASP cc_start: 0.8755 (t70) cc_final: 0.8267 (t0) REVERT: K 133 TRP cc_start: 0.7417 (OUTLIER) cc_final: 0.7172 (m-10) REVERT: K 146 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8446 (mm-30) REVERT: K 162 MET cc_start: 0.8703 (mmt) cc_final: 0.8285 (mmt) REVERT: K 169 ASP cc_start: 0.8270 (p0) cc_final: 0.7885 (p0) REVERT: K 215 ARG cc_start: 0.8411 (tpp-160) cc_final: 0.8050 (tpt170) REVERT: L 46 ASP cc_start: 0.8568 (p0) cc_final: 0.8293 (p0) REVERT: L 47 GLU cc_start: 0.8438 (pt0) cc_final: 0.8183 (pt0) REVERT: L 66 ASP cc_start: 0.8785 (t70) cc_final: 0.8373 (t0) REVERT: L 93 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.9036 (mmm) REVERT: L 94 HIS cc_start: 0.8718 (t70) cc_final: 0.8416 (t-90) REVERT: L 215 ARG cc_start: 0.8425 (tpp-160) cc_final: 0.8129 (tpt170) outliers start: 83 outliers final: 26 residues processed: 364 average time/residue: 1.2590 time to fit residues: 511.1501 Evaluate side-chains 316 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 273 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 133 TRP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 133 TRP Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 133 TRP Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 133 TRP Chi-restraints excluded: chain G residue 175 ASN Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 133 TRP Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 133 TRP Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 133 TRP Chi-restraints excluded: chain J residue 175 ASN Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 133 TRP Chi-restraints excluded: chain K residue 175 ASN Chi-restraints excluded: chain K residue 214 ILE Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 185 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 GLN ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN B 54 ASN B 61 ASN B 175 ASN ** C 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN C 94 HIS C 175 ASN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN ** E 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN E 61 ASN E 175 ASN F 54 ASN F 61 ASN F 97 HIS F 175 ASN ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 GLN G 175 ASN H 54 ASN H 61 ASN H 175 ASN ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 HIS I 175 ASN ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN ** K 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 57 GLN K 61 ASN K 175 ASN L 54 ASN L 175 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17052 Z= 0.211 Angle : 0.488 5.282 23316 Z= 0.258 Chirality : 0.042 0.222 2796 Planarity : 0.003 0.022 2784 Dihedral : 3.226 10.634 2232 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.66 % Allowed : 18.82 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.17), residues: 2028 helix: 3.16 (0.12), residues: 1404 sheet: 0.95 (0.43), residues: 132 loop : -1.40 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 133 HIS 0.003 0.001 HIS G 97 PHE 0.012 0.001 PHE F 180 TYR 0.008 0.001 TYR L 211 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 318 time to evaluate : 1.911 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8395 (pt0) cc_final: 0.8165 (pt0) REVERT: A 66 ASP cc_start: 0.8761 (t70) cc_final: 0.8409 (t0) REVERT: A 93 MET cc_start: 0.8899 (mmt) cc_final: 0.8694 (mmt) REVERT: A 133 TRP cc_start: 0.7389 (OUTLIER) cc_final: 0.7180 (m-10) REVERT: A 169 ASP cc_start: 0.8141 (p0) cc_final: 0.7905 (p0) REVERT: A 215 ARG cc_start: 0.8437 (tpp-160) cc_final: 0.8114 (tpt170) REVERT: B 47 GLU cc_start: 0.8401 (pt0) cc_final: 0.8176 (pt0) REVERT: B 66 ASP cc_start: 0.8738 (t70) cc_final: 0.8317 (t0) REVERT: B 93 MET cc_start: 0.9287 (tpp) cc_final: 0.8970 (mtp) REVERT: B 133 TRP cc_start: 0.7376 (OUTLIER) cc_final: 0.7132 (m-10) REVERT: B 169 ASP cc_start: 0.8185 (p0) cc_final: 0.7761 (p0) REVERT: B 215 ARG cc_start: 0.8391 (tpp-160) cc_final: 0.8048 (tpt170) REVERT: C 20 ILE cc_start: 0.8609 (mp) cc_final: 0.8257 (mp) REVERT: C 30 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9254 (mp) REVERT: C 46 ASP cc_start: 0.8596 (p0) cc_final: 0.8282 (p0) REVERT: C 47 GLU cc_start: 0.8384 (pt0) cc_final: 0.8154 (pt0) REVERT: C 66 ASP cc_start: 0.8777 (t70) cc_final: 0.8340 (t0) REVERT: C 133 TRP cc_start: 0.7388 (OUTLIER) cc_final: 0.7175 (m-10) REVERT: C 169 ASP cc_start: 0.8069 (p0) cc_final: 0.7821 (p0) REVERT: C 203 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9036 (mp) REVERT: C 215 ARG cc_start: 0.8427 (tpp-160) cc_final: 0.8139 (tpt170) REVERT: D 66 ASP cc_start: 0.8787 (t70) cc_final: 0.8421 (t0) REVERT: D 133 TRP cc_start: 0.7323 (OUTLIER) cc_final: 0.7087 (m-10) REVERT: D 169 ASP cc_start: 0.8209 (p0) cc_final: 0.7828 (p0) REVERT: D 211 TYR cc_start: 0.8426 (t80) cc_final: 0.8206 (t80) REVERT: D 215 ARG cc_start: 0.8367 (tpp-160) cc_final: 0.8097 (tpt170) REVERT: E 47 GLU cc_start: 0.8404 (pt0) cc_final: 0.8172 (pt0) REVERT: E 66 ASP cc_start: 0.8742 (t70) cc_final: 0.8319 (t0) REVERT: E 93 MET cc_start: 0.9277 (tpp) cc_final: 0.8964 (mtp) REVERT: E 133 TRP cc_start: 0.7377 (OUTLIER) cc_final: 0.7132 (m-10) REVERT: E 169 ASP cc_start: 0.8187 (p0) cc_final: 0.7760 (p0) REVERT: E 215 ARG cc_start: 0.8386 (tpp-160) cc_final: 0.8064 (tpt170) REVERT: F 30 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.9252 (mp) REVERT: F 46 ASP cc_start: 0.8590 (p0) cc_final: 0.8265 (p0) REVERT: F 47 GLU cc_start: 0.8376 (pt0) cc_final: 0.8130 (pt0) REVERT: F 66 ASP cc_start: 0.8777 (t70) cc_final: 0.8336 (t0) REVERT: F 93 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.8982 (mmm) REVERT: F 133 TRP cc_start: 0.7368 (OUTLIER) cc_final: 0.7161 (m-10) REVERT: F 169 ASP cc_start: 0.8057 (p0) cc_final: 0.7816 (p0) REVERT: F 203 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9033 (mp) REVERT: F 215 ARG cc_start: 0.8423 (tpp-160) cc_final: 0.8141 (tpt170) REVERT: G 66 ASP cc_start: 0.8775 (t70) cc_final: 0.8416 (t0) REVERT: G 133 TRP cc_start: 0.7323 (OUTLIER) cc_final: 0.7085 (m-10) REVERT: G 169 ASP cc_start: 0.8227 (p0) cc_final: 0.7844 (p0) REVERT: G 211 TYR cc_start: 0.8432 (t80) cc_final: 0.8206 (t80) REVERT: G 215 ARG cc_start: 0.8362 (tpp-160) cc_final: 0.8100 (tpt170) REVERT: H 47 GLU cc_start: 0.8402 (pt0) cc_final: 0.8194 (pt0) REVERT: H 66 ASP cc_start: 0.8755 (t70) cc_final: 0.8337 (t0) REVERT: H 133 TRP cc_start: 0.7382 (OUTLIER) cc_final: 0.7140 (m-10) REVERT: H 162 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8318 (mmt) REVERT: H 169 ASP cc_start: 0.8274 (p0) cc_final: 0.7842 (p0) REVERT: H 215 ARG cc_start: 0.8386 (tpp-160) cc_final: 0.8045 (tpt170) REVERT: I 20 ILE cc_start: 0.8599 (mp) cc_final: 0.8253 (mp) REVERT: I 46 ASP cc_start: 0.8594 (p0) cc_final: 0.8279 (p0) REVERT: I 66 ASP cc_start: 0.8796 (t70) cc_final: 0.8357 (t0) REVERT: I 133 TRP cc_start: 0.7348 (OUTLIER) cc_final: 0.7137 (m-10) REVERT: I 169 ASP cc_start: 0.8072 (p0) cc_final: 0.7815 (p0) REVERT: I 215 ARG cc_start: 0.8428 (tpp-160) cc_final: 0.8126 (tpt170) REVERT: J 66 ASP cc_start: 0.8783 (t70) cc_final: 0.8434 (t0) REVERT: J 133 TRP cc_start: 0.7350 (OUTLIER) cc_final: 0.7142 (m-10) REVERT: J 169 ASP cc_start: 0.8231 (p0) cc_final: 0.7870 (p0) REVERT: J 211 TYR cc_start: 0.8422 (t80) cc_final: 0.8200 (t80) REVERT: J 215 ARG cc_start: 0.8401 (tpp-160) cc_final: 0.8115 (tpt170) REVERT: K 47 GLU cc_start: 0.8400 (pt0) cc_final: 0.8182 (pt0) REVERT: K 66 ASP cc_start: 0.8759 (t70) cc_final: 0.8342 (t0) REVERT: K 133 TRP cc_start: 0.7399 (OUTLIER) cc_final: 0.7157 (m-10) REVERT: K 169 ASP cc_start: 0.8277 (p0) cc_final: 0.7850 (p0) REVERT: K 215 ARG cc_start: 0.8386 (tpp-160) cc_final: 0.8043 (tpt170) REVERT: L 20 ILE cc_start: 0.8617 (mp) cc_final: 0.8270 (mp) REVERT: L 46 ASP cc_start: 0.8583 (p0) cc_final: 0.8263 (p0) REVERT: L 66 ASP cc_start: 0.8794 (t70) cc_final: 0.8350 (t0) REVERT: L 93 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.9077 (mmt) REVERT: L 94 HIS cc_start: 0.8663 (t70) cc_final: 0.8428 (t70) REVERT: L 169 ASP cc_start: 0.8077 (p0) cc_final: 0.7820 (p0) REVERT: L 215 ARG cc_start: 0.8430 (tpp-160) cc_final: 0.8148 (tpt170) outliers start: 68 outliers final: 15 residues processed: 348 average time/residue: 1.2326 time to fit residues: 478.8697 Evaluate side-chains 320 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 287 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 133 TRP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 133 TRP Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 133 TRP Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain G residue 133 TRP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 133 TRP Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 162 MET Chi-restraints excluded: chain I residue 133 TRP Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 133 TRP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain K residue 133 TRP Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 chunk 197 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 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 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN A 205 ASN B 54 ASN B 57 GLN B 97 HIS B 175 ASN C 54 ASN C 175 ASN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS D 175 ASN D 205 ASN ** E 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS E 175 ASN F 54 ASN F 97 HIS F 175 ASN ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 HIS G 175 ASN G 205 ASN H 54 ASN ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 HIS H 175 ASN ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 GLN J 175 ASN J 205 ASN K 54 ASN K 97 HIS K 175 ASN L 54 ASN L 175 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17052 Z= 0.220 Angle : 0.482 5.265 23316 Z= 0.255 Chirality : 0.043 0.238 2796 Planarity : 0.003 0.028 2784 Dihedral : 3.185 10.590 2232 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.73 % Allowed : 18.92 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.17), residues: 2028 helix: 3.21 (0.12), residues: 1404 sheet: 1.02 (0.43), residues: 132 loop : -1.34 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 44 HIS 0.008 0.001 HIS I 97 PHE 0.011 0.001 PHE E 180 TYR 0.009 0.001 TYR G 65 ARG 0.008 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 317 time to evaluate : 2.025 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8609 (mp) cc_final: 0.8263 (mp) REVERT: A 66 ASP cc_start: 0.8795 (t70) cc_final: 0.8428 (t0) REVERT: A 93 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8624 (mmt) REVERT: A 133 TRP cc_start: 0.7362 (OUTLIER) cc_final: 0.7156 (m-10) REVERT: A 215 ARG cc_start: 0.8405 (tpp-160) cc_final: 0.8122 (tpt170) REVERT: B 66 ASP cc_start: 0.8761 (t70) cc_final: 0.8343 (t0) REVERT: B 93 MET cc_start: 0.9290 (tpp) cc_final: 0.8973 (mtp) REVERT: B 133 TRP cc_start: 0.7352 (OUTLIER) cc_final: 0.7143 (m-10) REVERT: B 169 ASP cc_start: 0.8146 (p0) cc_final: 0.7720 (p0) REVERT: B 215 ARG cc_start: 0.8376 (tpp-160) cc_final: 0.8052 (tpt170) REVERT: C 20 ILE cc_start: 0.8624 (mp) cc_final: 0.8293 (mp) REVERT: C 30 ILE cc_start: 0.9447 (OUTLIER) cc_final: 0.9246 (mp) REVERT: C 46 ASP cc_start: 0.8619 (p0) cc_final: 0.8338 (p0) REVERT: C 66 ASP cc_start: 0.8801 (t70) cc_final: 0.8368 (t0) REVERT: C 133 TRP cc_start: 0.7339 (OUTLIER) cc_final: 0.7128 (m-10) REVERT: C 169 ASP cc_start: 0.8076 (p0) cc_final: 0.7769 (p0) REVERT: C 203 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9035 (mp) REVERT: C 215 ARG cc_start: 0.8421 (tpp-160) cc_final: 0.8152 (tpt170) REVERT: D 66 ASP cc_start: 0.8840 (t70) cc_final: 0.8458 (t0) REVERT: D 133 TRP cc_start: 0.7315 (OUTLIER) cc_final: 0.7092 (m-10) REVERT: D 169 ASP cc_start: 0.8153 (p0) cc_final: 0.7801 (p0) REVERT: D 211 TYR cc_start: 0.8402 (t80) cc_final: 0.8173 (t80) REVERT: D 215 ARG cc_start: 0.8399 (tpp-160) cc_final: 0.8120 (tpt170) REVERT: E 47 GLU cc_start: 0.8410 (pt0) cc_final: 0.8192 (pt0) REVERT: E 66 ASP cc_start: 0.8764 (t70) cc_final: 0.8342 (t0) REVERT: E 93 MET cc_start: 0.9288 (tpp) cc_final: 0.8973 (mtp) REVERT: E 133 TRP cc_start: 0.7351 (OUTLIER) cc_final: 0.7141 (m-10) REVERT: E 169 ASP cc_start: 0.8147 (p0) cc_final: 0.7716 (p0) REVERT: E 215 ARG cc_start: 0.8374 (tpp-160) cc_final: 0.8065 (tpt170) REVERT: F 30 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.9248 (mp) REVERT: F 46 ASP cc_start: 0.8614 (p0) cc_final: 0.8326 (p0) REVERT: F 66 ASP cc_start: 0.8812 (t70) cc_final: 0.8377 (t0) REVERT: F 93 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.8977 (mmm) REVERT: F 133 TRP cc_start: 0.7339 (OUTLIER) cc_final: 0.7130 (m-10) REVERT: F 169 ASP cc_start: 0.8075 (p0) cc_final: 0.7774 (p0) REVERT: F 203 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9032 (mp) REVERT: F 215 ARG cc_start: 0.8410 (tpp-160) cc_final: 0.8147 (tpt170) REVERT: G 66 ASP cc_start: 0.8841 (t70) cc_final: 0.8462 (t0) REVERT: G 133 TRP cc_start: 0.7310 (OUTLIER) cc_final: 0.7078 (m-10) REVERT: G 169 ASP cc_start: 0.8149 (p0) cc_final: 0.7807 (p0) REVERT: G 211 TYR cc_start: 0.8408 (t80) cc_final: 0.8177 (t80) REVERT: G 215 ARG cc_start: 0.8401 (tpp-160) cc_final: 0.8128 (tpt170) REVERT: H 47 GLU cc_start: 0.8408 (pt0) cc_final: 0.8205 (pt0) REVERT: H 66 ASP cc_start: 0.8789 (t70) cc_final: 0.8368 (t0) REVERT: H 93 MET cc_start: 0.9313 (tpp) cc_final: 0.8946 (mtp) REVERT: H 133 TRP cc_start: 0.7348 (OUTLIER) cc_final: 0.7107 (m-10) REVERT: H 169 ASP cc_start: 0.8179 (p0) cc_final: 0.7734 (p0) REVERT: H 215 ARG cc_start: 0.8387 (tpp-160) cc_final: 0.8062 (tpt170) REVERT: I 20 ILE cc_start: 0.8621 (mp) cc_final: 0.8287 (mp) REVERT: I 46 ASP cc_start: 0.8571 (p0) cc_final: 0.8289 (p0) REVERT: I 47 GLU cc_start: 0.8362 (pt0) cc_final: 0.8129 (pt0) REVERT: I 66 ASP cc_start: 0.8832 (t70) cc_final: 0.8385 (t0) REVERT: I 133 TRP cc_start: 0.7333 (OUTLIER) cc_final: 0.7119 (m-10) REVERT: I 169 ASP cc_start: 0.8078 (p0) cc_final: 0.7779 (p0) REVERT: I 215 ARG cc_start: 0.8420 (tpp-160) cc_final: 0.8138 (tpt170) REVERT: J 66 ASP cc_start: 0.8838 (t70) cc_final: 0.8457 (t0) REVERT: J 133 TRP cc_start: 0.7341 (OUTLIER) cc_final: 0.7134 (m-10) REVERT: J 169 ASP cc_start: 0.8156 (p0) cc_final: 0.7813 (p0) REVERT: J 211 TYR cc_start: 0.8399 (t80) cc_final: 0.8165 (t80) REVERT: J 215 ARG cc_start: 0.8418 (tpp-160) cc_final: 0.8130 (tpt170) REVERT: K 47 GLU cc_start: 0.8413 (pt0) cc_final: 0.8210 (pt0) REVERT: K 66 ASP cc_start: 0.8790 (t70) cc_final: 0.8371 (t0) REVERT: K 93 MET cc_start: 0.9318 (tpp) cc_final: 0.8948 (mtp) REVERT: K 133 TRP cc_start: 0.7369 (OUTLIER) cc_final: 0.7126 (m-10) REVERT: K 169 ASP cc_start: 0.8200 (p0) cc_final: 0.7745 (p0) REVERT: K 215 ARG cc_start: 0.8377 (tpp-160) cc_final: 0.8057 (tpt170) REVERT: L 20 ILE cc_start: 0.8620 (mp) cc_final: 0.8284 (mp) REVERT: L 46 ASP cc_start: 0.8560 (p0) cc_final: 0.8278 (p0) REVERT: L 47 GLU cc_start: 0.8347 (pt0) cc_final: 0.8115 (pt0) REVERT: L 66 ASP cc_start: 0.8829 (t70) cc_final: 0.8380 (t0) REVERT: L 93 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.9029 (mmt) REVERT: L 94 HIS cc_start: 0.8657 (t70) cc_final: 0.8415 (t70) REVERT: L 169 ASP cc_start: 0.8076 (p0) cc_final: 0.7780 (p0) REVERT: L 215 ARG cc_start: 0.8416 (tpp-160) cc_final: 0.8142 (tpt170) outliers start: 88 outliers final: 25 residues processed: 371 average time/residue: 1.2234 time to fit residues: 506.5413 Evaluate side-chains 328 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 285 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 133 TRP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 133 TRP Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 133 TRP Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain G residue 133 TRP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 133 TRP Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 133 TRP Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 133 TRP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 133 TRP Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN C 54 ASN ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 ASN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 GLN D 97 HIS D 175 ASN E 54 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 ASN F 54 ASN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 ASN ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 HIS G 175 ASN H 54 ASN H 57 GLN ** H 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN I 54 ASN ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN K 54 ASN ** K 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 ASN L 54 ASN ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 17052 Z= 0.486 Angle : 0.581 5.501 23316 Z= 0.308 Chirality : 0.046 0.225 2796 Planarity : 0.003 0.020 2784 Dihedral : 3.367 10.568 2232 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.81 % Allowed : 19.19 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.17), residues: 2028 helix: 2.90 (0.12), residues: 1404 sheet: 1.58 (0.45), residues: 132 loop : -1.50 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 44 HIS 0.006 0.001 HIS I 73 PHE 0.019 0.002 PHE A 68 TYR 0.014 0.002 TYR G 65 ARG 0.007 0.001 ARG J 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 274 time to evaluate : 1.905 Fit side-chains REVERT: A 20 ILE cc_start: 0.8668 (mp) cc_final: 0.8380 (mp) REVERT: A 66 ASP cc_start: 0.8961 (t70) cc_final: 0.8544 (t0) REVERT: A 93 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8724 (mmt) REVERT: A 133 TRP cc_start: 0.7364 (OUTLIER) cc_final: 0.7145 (m-10) REVERT: A 169 ASP cc_start: 0.8244 (p0) cc_final: 0.7991 (p0) REVERT: A 215 ARG cc_start: 0.8404 (tpp-160) cc_final: 0.8131 (tpt170) REVERT: B 20 ILE cc_start: 0.8274 (mm) cc_final: 0.7815 (mp) REVERT: B 66 ASP cc_start: 0.8950 (t70) cc_final: 0.8492 (t0) REVERT: B 93 MET cc_start: 0.9328 (tpp) cc_final: 0.8985 (mtp) REVERT: B 97 HIS cc_start: 0.8196 (OUTLIER) cc_final: 0.7424 (t-90) REVERT: B 133 TRP cc_start: 0.7372 (OUTLIER) cc_final: 0.7143 (m-10) REVERT: B 169 ASP cc_start: 0.8321 (p0) cc_final: 0.7887 (p0) REVERT: B 215 ARG cc_start: 0.8401 (tpp-160) cc_final: 0.8058 (tpt170) REVERT: C 46 ASP cc_start: 0.8684 (p0) cc_final: 0.8436 (p0) REVERT: C 66 ASP cc_start: 0.8943 (t70) cc_final: 0.8480 (t0) REVERT: C 133 TRP cc_start: 0.7361 (OUTLIER) cc_final: 0.7127 (m-10) REVERT: C 169 ASP cc_start: 0.8213 (p0) cc_final: 0.7930 (p0) REVERT: C 203 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9038 (mp) REVERT: C 215 ARG cc_start: 0.8444 (tpp-160) cc_final: 0.8146 (tpt170) REVERT: D 66 ASP cc_start: 0.8961 (t70) cc_final: 0.8549 (t0) REVERT: D 133 TRP cc_start: 0.7294 (OUTLIER) cc_final: 0.7068 (m-10) REVERT: D 169 ASP cc_start: 0.8292 (p0) cc_final: 0.7892 (p0) REVERT: D 211 TYR cc_start: 0.8453 (t80) cc_final: 0.8250 (t80) REVERT: D 215 ARG cc_start: 0.8404 (tpp-160) cc_final: 0.8117 (tpt170) REVERT: E 47 GLU cc_start: 0.8482 (pt0) cc_final: 0.8160 (pt0) REVERT: E 66 ASP cc_start: 0.8946 (t70) cc_final: 0.8481 (t0) REVERT: E 93 MET cc_start: 0.9316 (tpp) cc_final: 0.8980 (mtp) REVERT: E 97 HIS cc_start: 0.8208 (OUTLIER) cc_final: 0.7439 (t-90) REVERT: E 133 TRP cc_start: 0.7371 (OUTLIER) cc_final: 0.7143 (m-10) REVERT: E 169 ASP cc_start: 0.8319 (p0) cc_final: 0.7877 (p0) REVERT: E 215 ARG cc_start: 0.8395 (tpp-160) cc_final: 0.8054 (tpt170) REVERT: F 46 ASP cc_start: 0.8668 (p0) cc_final: 0.8418 (p0) REVERT: F 66 ASP cc_start: 0.8946 (t70) cc_final: 0.8484 (t0) REVERT: F 93 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.9104 (mmt) REVERT: F 97 HIS cc_start: 0.8152 (OUTLIER) cc_final: 0.7449 (t-90) REVERT: F 133 TRP cc_start: 0.7343 (OUTLIER) cc_final: 0.7107 (m-10) REVERT: F 169 ASP cc_start: 0.8208 (p0) cc_final: 0.7931 (p0) REVERT: F 203 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9036 (mp) REVERT: F 215 ARG cc_start: 0.8438 (tpp-160) cc_final: 0.8143 (tpt170) REVERT: G 66 ASP cc_start: 0.8969 (t70) cc_final: 0.8562 (t0) REVERT: G 133 TRP cc_start: 0.7295 (OUTLIER) cc_final: 0.7066 (m-10) REVERT: G 169 ASP cc_start: 0.8302 (p0) cc_final: 0.7905 (p0) REVERT: G 215 ARG cc_start: 0.8398 (tpp-160) cc_final: 0.8126 (tpt170) REVERT: H 47 GLU cc_start: 0.8478 (pt0) cc_final: 0.8171 (pt0) REVERT: H 66 ASP cc_start: 0.8952 (t70) cc_final: 0.8479 (t0) REVERT: H 97 HIS cc_start: 0.8188 (OUTLIER) cc_final: 0.7414 (t-90) REVERT: H 133 TRP cc_start: 0.7373 (OUTLIER) cc_final: 0.7147 (m-10) REVERT: H 169 ASP cc_start: 0.8357 (p0) cc_final: 0.7896 (p0) REVERT: H 215 ARG cc_start: 0.8405 (tpp-160) cc_final: 0.8054 (tpt170) REVERT: I 46 ASP cc_start: 0.8687 (p0) cc_final: 0.8435 (p0) REVERT: I 66 ASP cc_start: 0.8955 (t70) cc_final: 0.8703 (t70) REVERT: I 133 TRP cc_start: 0.7350 (OUTLIER) cc_final: 0.7112 (m-10) REVERT: I 169 ASP cc_start: 0.8194 (p0) cc_final: 0.7922 (p0) REVERT: I 215 ARG cc_start: 0.8454 (tpp-160) cc_final: 0.8153 (tpt170) REVERT: J 66 ASP cc_start: 0.8964 (t70) cc_final: 0.8553 (t0) REVERT: J 133 TRP cc_start: 0.7316 (OUTLIER) cc_final: 0.7083 (m-10) REVERT: J 169 ASP cc_start: 0.8309 (p0) cc_final: 0.7932 (p0) REVERT: J 211 TYR cc_start: 0.8453 (t80) cc_final: 0.8252 (t80) REVERT: J 215 ARG cc_start: 0.8415 (tpp-160) cc_final: 0.8131 (tpt170) REVERT: K 20 ILE cc_start: 0.8293 (mm) cc_final: 0.7843 (mp) REVERT: K 47 GLU cc_start: 0.8477 (pt0) cc_final: 0.8166 (pt0) REVERT: K 66 ASP cc_start: 0.8951 (t70) cc_final: 0.8482 (t0) REVERT: K 97 HIS cc_start: 0.8174 (OUTLIER) cc_final: 0.7408 (t-90) REVERT: K 133 TRP cc_start: 0.7378 (OUTLIER) cc_final: 0.7148 (m-10) REVERT: K 167 LYS cc_start: 0.9194 (mptm) cc_final: 0.8964 (mmtt) REVERT: K 169 ASP cc_start: 0.8361 (p0) cc_final: 0.7920 (p0) REVERT: K 215 ARG cc_start: 0.8406 (tpp-160) cc_final: 0.8048 (tpt170) REVERT: L 46 ASP cc_start: 0.8682 (p0) cc_final: 0.8425 (p0) REVERT: L 66 ASP cc_start: 0.8952 (t70) cc_final: 0.8696 (t70) REVERT: L 93 MET cc_start: 0.9311 (OUTLIER) cc_final: 0.9075 (mmt) REVERT: L 94 HIS cc_start: 0.8644 (t70) cc_final: 0.8390 (t70) REVERT: L 169 ASP cc_start: 0.8190 (p0) cc_final: 0.7920 (p0) REVERT: L 215 ARG cc_start: 0.8444 (tpp-160) cc_final: 0.8162 (tpt170) outliers start: 108 outliers final: 30 residues processed: 346 average time/residue: 1.1788 time to fit residues: 459.2802 Evaluate side-chains 303 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 252 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 133 TRP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 133 TRP Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 133 TRP Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 133 TRP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 133 TRP Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 133 TRP Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 133 TRP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 133 TRP Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 214 ILE Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 ASN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS D 175 ASN ** E 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 ASN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS F 175 ASN ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 HIS G 175 ASN ** H 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN ** K 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 ASN L 54 ASN ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17052 Z= 0.180 Angle : 0.476 5.217 23316 Z= 0.253 Chirality : 0.042 0.209 2796 Planarity : 0.003 0.021 2784 Dihedral : 3.291 10.482 2232 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.60 % Allowed : 20.91 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.17), residues: 2028 helix: 3.10 (0.12), residues: 1404 sheet: 1.22 (0.43), residues: 132 loop : -1.58 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 133 HIS 0.002 0.000 HIS H 73 PHE 0.012 0.001 PHE H 180 TYR 0.008 0.001 TYR G 211 ARG 0.006 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 329 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8586 (mp) cc_final: 0.8321 (mp) REVERT: A 66 ASP cc_start: 0.8858 (t70) cc_final: 0.8443 (t0) REVERT: A 93 MET cc_start: 0.8924 (mmt) cc_final: 0.8695 (mmt) REVERT: A 133 TRP cc_start: 0.7266 (OUTLIER) cc_final: 0.7046 (m-10) REVERT: A 215 ARG cc_start: 0.8355 (tpp-160) cc_final: 0.8123 (tpt170) REVERT: B 66 ASP cc_start: 0.8862 (t70) cc_final: 0.8438 (t0) REVERT: B 93 MET cc_start: 0.9334 (tpp) cc_final: 0.9029 (mtp) REVERT: B 133 TRP cc_start: 0.7266 (OUTLIER) cc_final: 0.7037 (m-10) REVERT: B 169 ASP cc_start: 0.8072 (p0) cc_final: 0.7665 (p0) REVERT: B 215 ARG cc_start: 0.8363 (tpp-160) cc_final: 0.8054 (tpt170) REVERT: C 20 ILE cc_start: 0.8596 (mp) cc_final: 0.8310 (mp) REVERT: C 66 ASP cc_start: 0.8867 (t70) cc_final: 0.8584 (t70) REVERT: C 133 TRP cc_start: 0.7222 (OUTLIER) cc_final: 0.6992 (m-10) REVERT: C 169 ASP cc_start: 0.8014 (p0) cc_final: 0.7784 (p0) REVERT: C 203 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.8996 (mp) REVERT: C 215 ARG cc_start: 0.8405 (tpp-160) cc_final: 0.8142 (tpt170) REVERT: D 66 ASP cc_start: 0.8862 (t70) cc_final: 0.8429 (t0) REVERT: D 133 TRP cc_start: 0.7205 (OUTLIER) cc_final: 0.6988 (m-10) REVERT: D 169 ASP cc_start: 0.8021 (p0) cc_final: 0.7714 (p0) REVERT: D 211 TYR cc_start: 0.8398 (t80) cc_final: 0.8168 (t80) REVERT: D 215 ARG cc_start: 0.8422 (tpp-160) cc_final: 0.8152 (tpt170) REVERT: E 46 ASP cc_start: 0.8542 (p0) cc_final: 0.8335 (p0) REVERT: E 66 ASP cc_start: 0.8857 (t70) cc_final: 0.8415 (t0) REVERT: E 93 MET cc_start: 0.9322 (tpp) cc_final: 0.9024 (mtp) REVERT: E 133 TRP cc_start: 0.7266 (OUTLIER) cc_final: 0.7038 (m-10) REVERT: E 169 ASP cc_start: 0.8082 (p0) cc_final: 0.7667 (p0) REVERT: E 215 ARG cc_start: 0.8372 (tpp-160) cc_final: 0.8049 (tpt170) REVERT: F 46 ASP cc_start: 0.8531 (p0) cc_final: 0.8315 (p0) REVERT: F 66 ASP cc_start: 0.8863 (t70) cc_final: 0.8580 (t70) REVERT: F 133 TRP cc_start: 0.7224 (OUTLIER) cc_final: 0.6988 (m-10) REVERT: F 169 ASP cc_start: 0.8013 (p0) cc_final: 0.7783 (p0) REVERT: F 203 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.8992 (mp) REVERT: F 215 ARG cc_start: 0.8400 (tpp-160) cc_final: 0.8141 (tpt170) REVERT: G 66 ASP cc_start: 0.8883 (t70) cc_final: 0.8458 (t0) REVERT: G 133 TRP cc_start: 0.7189 (OUTLIER) cc_final: 0.6973 (m-10) REVERT: G 169 ASP cc_start: 0.8044 (p0) cc_final: 0.7755 (p0) REVERT: G 215 ARG cc_start: 0.8405 (tpp-160) cc_final: 0.8169 (tpt170) REVERT: H 46 ASP cc_start: 0.8547 (p0) cc_final: 0.8339 (p0) REVERT: H 66 ASP cc_start: 0.8864 (t70) cc_final: 0.8413 (t0) REVERT: H 133 TRP cc_start: 0.7259 (OUTLIER) cc_final: 0.7028 (m-10) REVERT: H 169 ASP cc_start: 0.8084 (p0) cc_final: 0.7673 (p0) REVERT: H 215 ARG cc_start: 0.8371 (tpp-160) cc_final: 0.8057 (tpt170) REVERT: I 46 ASP cc_start: 0.8522 (p0) cc_final: 0.8300 (p0) REVERT: I 66 ASP cc_start: 0.8869 (t70) cc_final: 0.8589 (t70) REVERT: I 133 TRP cc_start: 0.7230 (OUTLIER) cc_final: 0.6994 (m-10) REVERT: I 169 ASP cc_start: 0.7996 (p0) cc_final: 0.7772 (p0) REVERT: I 215 ARG cc_start: 0.8405 (tpp-160) cc_final: 0.8128 (tpt170) REVERT: J 66 ASP cc_start: 0.8867 (t70) cc_final: 0.8441 (t0) REVERT: J 133 TRP cc_start: 0.7218 (OUTLIER) cc_final: 0.6994 (m-10) REVERT: J 169 ASP cc_start: 0.8033 (p0) cc_final: 0.7742 (p0) REVERT: J 211 TYR cc_start: 0.8401 (t80) cc_final: 0.8172 (t80) REVERT: J 215 ARG cc_start: 0.8432 (tpp-160) cc_final: 0.8149 (tpt170) REVERT: K 46 ASP cc_start: 0.8546 (p0) cc_final: 0.8343 (p0) REVERT: K 66 ASP cc_start: 0.8863 (t70) cc_final: 0.8423 (t0) REVERT: K 133 TRP cc_start: 0.7269 (OUTLIER) cc_final: 0.7038 (m-10) REVERT: K 167 LYS cc_start: 0.9034 (mptm) cc_final: 0.8823 (mmtt) REVERT: K 169 ASP cc_start: 0.8102 (p0) cc_final: 0.7687 (p0) REVERT: K 215 ARG cc_start: 0.8370 (tpp-160) cc_final: 0.8046 (tpt170) REVERT: L 46 ASP cc_start: 0.8511 (p0) cc_final: 0.8279 (p0) REVERT: L 66 ASP cc_start: 0.8863 (t70) cc_final: 0.8581 (t70) REVERT: L 93 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.9095 (mmt) REVERT: L 169 ASP cc_start: 0.7996 (p0) cc_final: 0.7774 (p0) REVERT: L 215 ARG cc_start: 0.8402 (tpp-160) cc_final: 0.8132 (tpt170) outliers start: 67 outliers final: 16 residues processed: 368 average time/residue: 1.2329 time to fit residues: 506.0449 Evaluate side-chains 318 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 288 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 133 TRP Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 133 TRP Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 133 TRP Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain G residue 133 TRP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 133 TRP Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain I residue 133 TRP Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 133 TRP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain K residue 133 TRP Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 134 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 0.4980 chunk 110 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 175 ASN A 205 ASN B 97 HIS B 175 ASN ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 ASN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 ASN F 54 ASN F 57 GLN F 97 HIS F 175 ASN G 54 ASN G 61 ASN ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 ASN H 97 HIS H 175 ASN I 54 ASN ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN J 175 ASN K 54 ASN K 97 HIS K 175 ASN L 54 ASN L 61 ASN L 175 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17052 Z= 0.237 Angle : 0.491 5.247 23316 Z= 0.262 Chirality : 0.042 0.223 2796 Planarity : 0.003 0.023 2784 Dihedral : 3.239 10.327 2232 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.03 % Allowed : 21.24 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.17), residues: 2028 helix: 3.09 (0.12), residues: 1404 sheet: 1.39 (0.45), residues: 132 loop : -1.58 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 44 HIS 0.010 0.001 HIS L 94 PHE 0.013 0.001 PHE B 180 TYR 0.009 0.001 TYR F 65 ARG 0.004 0.000 ARG H 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 301 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8597 (mp) cc_final: 0.8350 (mp) REVERT: A 54 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8649 (t0) REVERT: A 66 ASP cc_start: 0.8863 (t70) cc_final: 0.8461 (t0) REVERT: A 93 MET cc_start: 0.8910 (mmt) cc_final: 0.8681 (mmt) REVERT: A 133 TRP cc_start: 0.7268 (OUTLIER) cc_final: 0.7053 (m-10) REVERT: A 169 ASP cc_start: 0.8240 (p0) cc_final: 0.7988 (p0) REVERT: A 215 ARG cc_start: 0.8371 (tpp-160) cc_final: 0.8140 (tpt170) REVERT: B 93 MET cc_start: 0.9347 (tpp) cc_final: 0.9015 (mtp) REVERT: B 133 TRP cc_start: 0.7239 (OUTLIER) cc_final: 0.7018 (m-10) REVERT: B 169 ASP cc_start: 0.8121 (p0) cc_final: 0.7685 (p0) REVERT: B 215 ARG cc_start: 0.8378 (tpp-160) cc_final: 0.8049 (tpt170) REVERT: C 133 TRP cc_start: 0.7215 (OUTLIER) cc_final: 0.6989 (m-10) REVERT: C 169 ASP cc_start: 0.8041 (p0) cc_final: 0.7788 (p0) REVERT: C 203 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9011 (mp) REVERT: C 215 ARG cc_start: 0.8403 (tpp-160) cc_final: 0.8147 (tpt170) REVERT: D 66 ASP cc_start: 0.8850 (t70) cc_final: 0.8427 (t0) REVERT: D 133 TRP cc_start: 0.7191 (OUTLIER) cc_final: 0.6979 (m-10) REVERT: D 169 ASP cc_start: 0.8095 (p0) cc_final: 0.7758 (p0) REVERT: D 211 TYR cc_start: 0.8420 (t80) cc_final: 0.8218 (t80) REVERT: D 215 ARG cc_start: 0.8407 (tpp-160) cc_final: 0.8143 (tpt170) REVERT: E 46 ASP cc_start: 0.8491 (p0) cc_final: 0.8289 (p0) REVERT: E 66 ASP cc_start: 0.8868 (t70) cc_final: 0.8446 (t0) REVERT: E 93 MET cc_start: 0.9338 (tpp) cc_final: 0.9015 (mtp) REVERT: E 133 TRP cc_start: 0.7253 (OUTLIER) cc_final: 0.7026 (m-10) REVERT: E 169 ASP cc_start: 0.8132 (p0) cc_final: 0.7697 (p0) REVERT: E 215 ARG cc_start: 0.8375 (tpp-160) cc_final: 0.8057 (tpt170) REVERT: F 133 TRP cc_start: 0.7217 (OUTLIER) cc_final: 0.6986 (m-10) REVERT: F 169 ASP cc_start: 0.8053 (p0) cc_final: 0.7803 (p0) REVERT: F 203 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9001 (mp) REVERT: F 215 ARG cc_start: 0.8393 (tpp-160) cc_final: 0.8144 (tpt170) REVERT: G 20 ILE cc_start: 0.8570 (mp) cc_final: 0.8290 (mp) REVERT: G 66 ASP cc_start: 0.8866 (t70) cc_final: 0.8446 (t0) REVERT: G 133 TRP cc_start: 0.7183 (OUTLIER) cc_final: 0.6968 (m-10) REVERT: G 169 ASP cc_start: 0.8069 (p0) cc_final: 0.7731 (p0) REVERT: G 215 ARG cc_start: 0.8391 (tpp-160) cc_final: 0.8175 (tpt170) REVERT: H 66 ASP cc_start: 0.8888 (t70) cc_final: 0.8463 (t0) REVERT: H 133 TRP cc_start: 0.7222 (OUTLIER) cc_final: 0.6997 (m-10) REVERT: H 169 ASP cc_start: 0.8119 (p0) cc_final: 0.7670 (p0) REVERT: H 215 ARG cc_start: 0.8388 (tpp-160) cc_final: 0.8057 (tpt170) REVERT: I 133 TRP cc_start: 0.7194 (OUTLIER) cc_final: 0.6962 (m-10) REVERT: I 169 ASP cc_start: 0.8039 (p0) cc_final: 0.7795 (p0) REVERT: I 215 ARG cc_start: 0.8400 (tpp-160) cc_final: 0.8129 (tpt170) REVERT: J 66 ASP cc_start: 0.8863 (t70) cc_final: 0.8453 (t0) REVERT: J 133 TRP cc_start: 0.7213 (OUTLIER) cc_final: 0.6993 (m-10) REVERT: J 169 ASP cc_start: 0.8071 (p0) cc_final: 0.7736 (p0) REVERT: J 211 TYR cc_start: 0.8419 (t80) cc_final: 0.8216 (t80) REVERT: J 215 ARG cc_start: 0.8414 (tpp-160) cc_final: 0.8137 (tpt170) REVERT: K 66 ASP cc_start: 0.8885 (t70) cc_final: 0.8465 (t0) REVERT: K 80 GLN cc_start: 0.9156 (tt0) cc_final: 0.8932 (tt0) REVERT: K 133 TRP cc_start: 0.7257 (OUTLIER) cc_final: 0.7035 (m-10) REVERT: K 169 ASP cc_start: 0.8139 (p0) cc_final: 0.7701 (p0) REVERT: K 215 ARG cc_start: 0.8392 (tpp-160) cc_final: 0.8052 (tpt170) REVERT: L 46 ASP cc_start: 0.8523 (p0) cc_final: 0.8318 (p0) REVERT: L 93 MET cc_start: 0.9320 (OUTLIER) cc_final: 0.9089 (mmt) REVERT: L 169 ASP cc_start: 0.8022 (p0) cc_final: 0.7775 (p0) REVERT: L 215 ARG cc_start: 0.8405 (tpp-160) cc_final: 0.8144 (tpt170) outliers start: 75 outliers final: 18 residues processed: 346 average time/residue: 1.2430 time to fit residues: 480.1468 Evaluate side-chains 312 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 279 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain C residue 133 TRP Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 133 TRP Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain F residue 133 TRP Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain G residue 133 TRP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 133 TRP Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain I residue 133 TRP Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 133 TRP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain K residue 133 TRP Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 134 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 175 ASN B 97 HIS B 175 ASN C 175 ASN D 54 ASN D 97 HIS D 175 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 ASN F 54 ASN F 97 HIS F 175 ASN G 54 ASN G 97 HIS G 175 ASN H 97 HIS H 175 ASN I 54 ASN I 61 ASN I 175 ASN J 54 ASN J 175 ASN K 97 HIS K 175 ASN L 54 ASN L 97 HIS L 175 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17052 Z= 0.193 Angle : 0.483 5.181 23316 Z= 0.258 Chirality : 0.041 0.203 2796 Planarity : 0.003 0.022 2784 Dihedral : 3.258 10.116 2232 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.49 % Allowed : 21.67 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.17), residues: 2028 helix: 3.09 (0.12), residues: 1404 sheet: 1.37 (0.43), residues: 132 loop : -1.58 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 44 HIS 0.005 0.001 HIS I 94 PHE 0.012 0.001 PHE B 180 TYR 0.009 0.001 TYR E 65 ARG 0.005 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 292 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8585 (mp) cc_final: 0.8336 (mp) REVERT: A 66 ASP cc_start: 0.8844 (t70) cc_final: 0.8437 (t0) REVERT: A 93 MET cc_start: 0.8916 (mmt) cc_final: 0.8694 (mmt) REVERT: A 133 TRP cc_start: 0.7215 (OUTLIER) cc_final: 0.7001 (m-10) REVERT: A 169 ASP cc_start: 0.8218 (p0) cc_final: 0.7914 (p0) REVERT: A 215 ARG cc_start: 0.8351 (tpp-160) cc_final: 0.8130 (tpt170) REVERT: B 93 MET cc_start: 0.9338 (tpp) cc_final: 0.8995 (mtp) REVERT: B 133 TRP cc_start: 0.7196 (OUTLIER) cc_final: 0.6973 (m-10) REVERT: B 169 ASP cc_start: 0.8027 (p0) cc_final: 0.7616 (p0) REVERT: B 215 ARG cc_start: 0.8371 (tpp-160) cc_final: 0.8048 (tpt170) REVERT: C 133 TRP cc_start: 0.7156 (OUTLIER) cc_final: 0.6927 (m-10) REVERT: C 169 ASP cc_start: 0.7958 (p0) cc_final: 0.7742 (p0) REVERT: C 203 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9001 (mp) REVERT: C 215 ARG cc_start: 0.8403 (tpp-160) cc_final: 0.8140 (tpt170) REVERT: D 66 ASP cc_start: 0.8833 (t70) cc_final: 0.8415 (t0) REVERT: D 133 TRP cc_start: 0.7162 (OUTLIER) cc_final: 0.6952 (m-10) REVERT: D 169 ASP cc_start: 0.8019 (p0) cc_final: 0.7702 (p0) REVERT: D 211 TYR cc_start: 0.8406 (t80) cc_final: 0.8196 (t80) REVERT: D 215 ARG cc_start: 0.8406 (tpp-160) cc_final: 0.8146 (tpt170) REVERT: E 66 ASP cc_start: 0.8868 (t70) cc_final: 0.8441 (t0) REVERT: E 93 MET cc_start: 0.9335 (tpp) cc_final: 0.8994 (mtp) REVERT: E 133 TRP cc_start: 0.7192 (OUTLIER) cc_final: 0.6968 (m-10) REVERT: E 169 ASP cc_start: 0.8050 (p0) cc_final: 0.7639 (p0) REVERT: E 215 ARG cc_start: 0.8377 (tpp-160) cc_final: 0.8047 (tpt170) REVERT: F 93 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8925 (mmm) REVERT: F 133 TRP cc_start: 0.7162 (OUTLIER) cc_final: 0.6930 (m-10) REVERT: F 169 ASP cc_start: 0.7965 (p0) cc_final: 0.7749 (p0) REVERT: F 203 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.8997 (mp) REVERT: F 215 ARG cc_start: 0.8395 (tpp-160) cc_final: 0.8143 (tpt170) REVERT: G 20 ILE cc_start: 0.8541 (mp) cc_final: 0.8273 (mp) REVERT: G 66 ASP cc_start: 0.8852 (t70) cc_final: 0.8433 (t0) REVERT: G 133 TRP cc_start: 0.7147 (OUTLIER) cc_final: 0.6935 (m-10) REVERT: G 169 ASP cc_start: 0.7963 (p0) cc_final: 0.7687 (p0) REVERT: H 133 TRP cc_start: 0.7191 (OUTLIER) cc_final: 0.6969 (m-10) REVERT: H 169 ASP cc_start: 0.8037 (p0) cc_final: 0.7623 (p0) REVERT: H 215 ARG cc_start: 0.8371 (tpp-160) cc_final: 0.8050 (tpt170) REVERT: I 133 TRP cc_start: 0.7166 (OUTLIER) cc_final: 0.6932 (m-10) REVERT: I 215 ARG cc_start: 0.8386 (tpp-160) cc_final: 0.8127 (tpt170) REVERT: J 66 ASP cc_start: 0.8851 (t70) cc_final: 0.8435 (t0) REVERT: J 133 TRP cc_start: 0.7175 (OUTLIER) cc_final: 0.6956 (m-10) REVERT: J 169 ASP cc_start: 0.7967 (p0) cc_final: 0.7692 (p0) REVERT: J 211 TYR cc_start: 0.8405 (t80) cc_final: 0.8194 (t80) REVERT: J 215 ARG cc_start: 0.8399 (tpp-160) cc_final: 0.8150 (tpt170) REVERT: K 133 TRP cc_start: 0.7203 (OUTLIER) cc_final: 0.6982 (m-10) REVERT: K 169 ASP cc_start: 0.8066 (p0) cc_final: 0.7647 (p0) REVERT: K 215 ARG cc_start: 0.8376 (tpp-160) cc_final: 0.8048 (tpt170) REVERT: L 93 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.9101 (mmt) REVERT: L 215 ARG cc_start: 0.8386 (tpp-160) cc_final: 0.8129 (tpt170) outliers start: 65 outliers final: 15 residues processed: 329 average time/residue: 1.2331 time to fit residues: 453.6785 Evaluate side-chains 306 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain C residue 133 TRP Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 133 TRP Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 133 TRP Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain G residue 133 TRP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 133 TRP Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain I residue 133 TRP Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 133 TRP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain K residue 133 TRP Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 134 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.9980 chunk 171 optimal weight: 7.9990 chunk 183 optimal weight: 0.0570 chunk 110 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 175 ASN B 61 ASN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN C 175 ASN D 54 ASN D 97 HIS D 175 ASN E 61 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 ASN F 54 ASN F 97 HIS F 175 ASN G 54 ASN G 97 HIS G 175 ASN H 61 ASN ** H 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN I 54 ASN I 175 ASN J 54 ASN J 175 ASN ** K 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 ASN L 54 ASN L 175 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17052 Z= 0.167 Angle : 0.477 8.119 23316 Z= 0.255 Chirality : 0.040 0.162 2796 Planarity : 0.003 0.026 2784 Dihedral : 3.237 10.073 2232 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.33 % Allowed : 21.67 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.17), residues: 2028 helix: 3.13 (0.12), residues: 1404 sheet: 1.19 (0.42), residues: 132 loop : -1.46 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 44 HIS 0.005 0.001 HIS I 94 PHE 0.014 0.001 PHE H 180 TYR 0.007 0.001 TYR E 65 ARG 0.004 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 313 time to evaluate : 2.191 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8552 (mp) cc_final: 0.8314 (mp) REVERT: A 66 ASP cc_start: 0.8794 (t70) cc_final: 0.8389 (t0) REVERT: A 93 MET cc_start: 0.8913 (mmt) cc_final: 0.8698 (mmt) REVERT: A 169 ASP cc_start: 0.8187 (p0) cc_final: 0.7901 (p0) REVERT: A 215 ARG cc_start: 0.8335 (tpp-160) cc_final: 0.8120 (tpt170) REVERT: B 93 MET cc_start: 0.9320 (tpp) cc_final: 0.8956 (mtp) REVERT: B 169 ASP cc_start: 0.7946 (p0) cc_final: 0.7561 (p0) REVERT: B 215 ARG cc_start: 0.8360 (tpp-160) cc_final: 0.8046 (tpt170) REVERT: C 20 ILE cc_start: 0.8590 (mp) cc_final: 0.8362 (mp) REVERT: C 169 ASP cc_start: 0.7817 (p0) cc_final: 0.7594 (p0) REVERT: C 203 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.8990 (mp) REVERT: C 215 ARG cc_start: 0.8377 (tpp-160) cc_final: 0.8126 (tpt170) REVERT: D 66 ASP cc_start: 0.8798 (t70) cc_final: 0.8381 (t0) REVERT: D 133 TRP cc_start: 0.7126 (OUTLIER) cc_final: 0.6910 (m-10) REVERT: D 169 ASP cc_start: 0.7977 (p0) cc_final: 0.7668 (p0) REVERT: D 211 TYR cc_start: 0.8407 (t80) cc_final: 0.8180 (t80) REVERT: D 215 ARG cc_start: 0.8395 (tpp-160) cc_final: 0.8148 (tpt170) REVERT: E 66 ASP cc_start: 0.8817 (t70) cc_final: 0.8371 (t0) REVERT: E 93 MET cc_start: 0.9329 (tpp) cc_final: 0.8971 (mtp) REVERT: E 169 ASP cc_start: 0.7952 (p0) cc_final: 0.7561 (p0) REVERT: E 215 ARG cc_start: 0.8353 (tpp-160) cc_final: 0.8042 (tpt170) REVERT: F 93 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8946 (mmm) REVERT: F 169 ASP cc_start: 0.7837 (p0) cc_final: 0.7616 (p0) REVERT: F 203 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.8990 (mp) REVERT: F 215 ARG cc_start: 0.8362 (tpp-160) cc_final: 0.8129 (tpt170) REVERT: G 20 ILE cc_start: 0.8481 (mp) cc_final: 0.8199 (mp) REVERT: G 66 ASP cc_start: 0.8826 (t70) cc_final: 0.8414 (t0) REVERT: G 133 TRP cc_start: 0.7118 (OUTLIER) cc_final: 0.6901 (m-10) REVERT: G 169 ASP cc_start: 0.7876 (p0) cc_final: 0.7615 (p0) REVERT: H 169 ASP cc_start: 0.7952 (p0) cc_final: 0.7563 (p0) REVERT: H 215 ARG cc_start: 0.8376 (tpp-160) cc_final: 0.8059 (tpt170) REVERT: I 215 ARG cc_start: 0.8371 (tpp-160) cc_final: 0.8128 (tpt170) REVERT: J 66 ASP cc_start: 0.8816 (t70) cc_final: 0.8410 (t0) REVERT: J 169 ASP cc_start: 0.7878 (p0) cc_final: 0.7622 (p0) REVERT: J 211 TYR cc_start: 0.8408 (t80) cc_final: 0.8181 (t80) REVERT: J 215 ARG cc_start: 0.8397 (tpp-160) cc_final: 0.8164 (tpt170) REVERT: K 169 ASP cc_start: 0.7971 (p0) cc_final: 0.7580 (p0) REVERT: K 215 ARG cc_start: 0.8375 (tpp-160) cc_final: 0.8054 (tpt170) REVERT: L 93 MET cc_start: 0.9337 (OUTLIER) cc_final: 0.8994 (mmm) REVERT: L 215 ARG cc_start: 0.8365 (tpp-160) cc_final: 0.8131 (tpt170) outliers start: 62 outliers final: 15 residues processed: 351 average time/residue: 1.2967 time to fit residues: 507.1973 Evaluate side-chains 299 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 278 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain G residue 133 TRP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 214 ILE Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 214 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 161 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 175 ASN B 80 GLN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN C 99 GLN C 175 ASN D 54 ASN D 97 HIS D 175 ASN E 97 HIS E 175 ASN F 54 ASN F 97 HIS F 175 ASN G 54 ASN ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 ASN H 80 GLN H 97 HIS H 175 ASN I 54 ASN I 99 GLN I 175 ASN J 54 ASN J 175 ASN K 80 GLN K 97 HIS K 175 ASN L 54 ASN L 175 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17052 Z= 0.186 Angle : 0.478 5.494 23316 Z= 0.255 Chirality : 0.040 0.138 2796 Planarity : 0.003 0.034 2784 Dihedral : 3.253 10.089 2232 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.01 % Allowed : 22.15 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.17), residues: 2028 helix: 3.12 (0.12), residues: 1404 sheet: 1.27 (0.42), residues: 132 loop : -1.30 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 132 HIS 0.009 0.001 HIS L 94 PHE 0.011 0.001 PHE B 180 TYR 0.008 0.001 TYR L 65 ARG 0.006 0.001 ARG H 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 295 time to evaluate : 1.889 Fit side-chains REVERT: A 20 ILE cc_start: 0.8548 (mp) cc_final: 0.8329 (mp) REVERT: A 66 ASP cc_start: 0.8781 (t70) cc_final: 0.8374 (t0) REVERT: A 169 ASP cc_start: 0.8152 (p0) cc_final: 0.7884 (p0) REVERT: A 215 ARG cc_start: 0.8328 (tpp-160) cc_final: 0.8123 (tpt170) REVERT: B 80 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8936 (tt0) REVERT: B 93 MET cc_start: 0.9332 (tpp) cc_final: 0.9005 (mtp) REVERT: B 169 ASP cc_start: 0.7914 (p0) cc_final: 0.7545 (p0) REVERT: B 215 ARG cc_start: 0.8372 (tpp-160) cc_final: 0.8060 (tpt170) REVERT: C 20 ILE cc_start: 0.8558 (mp) cc_final: 0.8321 (mp) REVERT: C 203 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9013 (mp) REVERT: C 215 ARG cc_start: 0.8368 (tpp-160) cc_final: 0.8130 (tpt170) REVERT: D 66 ASP cc_start: 0.8804 (t70) cc_final: 0.8387 (t0) REVERT: D 169 ASP cc_start: 0.7935 (p0) cc_final: 0.7658 (p0) REVERT: D 211 TYR cc_start: 0.8415 (t80) cc_final: 0.8181 (t80) REVERT: D 215 ARG cc_start: 0.8404 (tpp-160) cc_final: 0.8165 (tpt170) REVERT: E 93 MET cc_start: 0.9331 (tpp) cc_final: 0.8951 (mtp) REVERT: E 169 ASP cc_start: 0.7942 (p0) cc_final: 0.7575 (p0) REVERT: E 215 ARG cc_start: 0.8362 (tpp-160) cc_final: 0.8050 (tpt170) REVERT: F 93 MET cc_start: 0.9346 (OUTLIER) cc_final: 0.8942 (mmm) REVERT: F 203 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9011 (mp) REVERT: F 215 ARG cc_start: 0.8352 (tpp-160) cc_final: 0.8125 (tpt170) REVERT: G 20 ILE cc_start: 0.8469 (mp) cc_final: 0.8196 (mp) REVERT: G 169 ASP cc_start: 0.7850 (p0) cc_final: 0.7597 (p0) REVERT: H 169 ASP cc_start: 0.7916 (p0) cc_final: 0.7544 (p0) REVERT: H 215 ARG cc_start: 0.8375 (tpp-160) cc_final: 0.8060 (tpt170) REVERT: I 20 ILE cc_start: 0.8588 (mp) cc_final: 0.8345 (mp) REVERT: I 215 ARG cc_start: 0.8362 (tpp-160) cc_final: 0.8121 (tpt170) REVERT: J 66 ASP cc_start: 0.8818 (t70) cc_final: 0.8408 (t0) REVERT: J 169 ASP cc_start: 0.7856 (p0) cc_final: 0.7606 (p0) REVERT: J 211 TYR cc_start: 0.8411 (t80) cc_final: 0.8180 (t80) REVERT: J 215 ARG cc_start: 0.8391 (tpp-160) cc_final: 0.8159 (tpt170) REVERT: K 80 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8805 (tt0) REVERT: K 169 ASP cc_start: 0.7953 (p0) cc_final: 0.7577 (p0) REVERT: K 215 ARG cc_start: 0.8371 (tpp-160) cc_final: 0.8055 (tpt170) REVERT: L 20 ILE cc_start: 0.8600 (mp) cc_final: 0.8357 (mp) REVERT: L 93 MET cc_start: 0.9326 (OUTLIER) cc_final: 0.8984 (mmm) REVERT: L 133 TRP cc_start: 0.7728 (m100) cc_final: 0.7521 (m-10) REVERT: L 215 ARG cc_start: 0.8354 (tpp-160) cc_final: 0.8113 (tpt170) outliers start: 56 outliers final: 14 residues processed: 332 average time/residue: 1.2210 time to fit residues: 453.3459 Evaluate side-chains 307 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 287 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 214 ILE Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain K residue 80 GLN Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 214 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 175 ASN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN C 99 GLN C 175 ASN D 54 ASN ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN E 97 HIS E 175 ASN F 54 ASN F 97 HIS F 175 ASN G 54 ASN ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 ASN ** H 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN I 54 ASN ** I 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN I 175 ASN J 54 ASN ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN K 97 HIS K 175 ASN L 54 ASN ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.095750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.074584 restraints weight = 31913.209| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.28 r_work: 0.2927 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.214 17052 Z= 0.299 Angle : 0.728 59.199 23316 Z= 0.431 Chirality : 0.054 1.875 2796 Planarity : 0.004 0.172 2784 Dihedral : 3.332 28.707 2232 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.43 % Favored : 98.52 % Rotamer: Outliers : 2.63 % Allowed : 22.63 % Favored : 74.73 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.17), residues: 2028 helix: 3.09 (0.12), residues: 1404 sheet: 1.30 (0.42), residues: 132 loop : -1.23 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 132 HIS 0.009 0.001 HIS L 94 PHE 0.011 0.001 PHE B 180 TYR 0.008 0.001 TYR F 65 ARG 0.005 0.001 ARG E 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7222.75 seconds wall clock time: 130 minutes 17.86 seconds (7817.86 seconds total)