Starting phenix.real_space_refine on Fri Aug 22 14:46:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7umq_26607/08_2025/7umq_26607.cif Found real_map, /net/cci-nas-00/data/ceres_data/7umq_26607/08_2025/7umq_26607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7umq_26607/08_2025/7umq_26607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7umq_26607/08_2025/7umq_26607.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7umq_26607/08_2025/7umq_26607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7umq_26607/08_2025/7umq_26607.map" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 30 5.16 5 C 2760 2.51 5 N 850 2.21 5 O 740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4380 Number of models: 1 Model: "" Number of chains: 1 Chain: "J" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Restraints were copied for chains: H, D, B, F, I, G, C, A, E Time building chain proxies: 0.66, per 1000 atoms: 0.15 Number of scatterers: 4380 At special positions: 0 Unit cell: (89.474, 123.97, 42.042, 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 30 16.00 O 740 8.00 N 850 7.00 C 2760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 181.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'J' and resid 89 through 91 removed outlier: 6.118A pdb=" N TRP J 89 " --> pdb=" O GLY H 90 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TRP H 89 " --> pdb=" O GLY F 90 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TRP D 89 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 95 through 100 removed outlier: 6.321A pdb=" N THR D 95 " --> pdb=" O HIS F 96 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLN F 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER D 97 " --> pdb=" O GLN F 98 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASN F 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP D 99 " --> pdb=" O ASN F 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 106 through 107 removed outlier: 6.655A pdb=" N LYS D 106 " --> pdb=" O THR F 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 115 through 117 removed outlier: 6.522A pdb=" N ALA D 115 " --> pdb=" O ALA F 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 120 through 122 removed outlier: 6.965A pdb=" N VAL J 121 " --> pdb=" O VAL H 122 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL H 121 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL D 121 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 125 through 130 removed outlier: 6.891A pdb=" N GLY J 126 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY H 127 " --> pdb=" O GLY J 126 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR J 128 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY H 126 " --> pdb=" O LEU F 125 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY F 127 " --> pdb=" O GLY H 126 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR H 128 " --> pdb=" O GLY F 127 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N LEU D 125 " --> pdb=" O GLY F 126 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N TYR F 128 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLY D 127 " --> pdb=" O TYR F 128 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU F 130 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL D 129 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY D 126 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY B 127 " --> pdb=" O GLY D 126 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR D 128 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 138 through 139 removed outlier: 6.539A pdb=" N ILE J 138 " --> pdb=" O ILE H 139 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE H 138 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE D 138 " --> pdb=" O ILE B 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 89 through 91 removed outlier: 6.118A pdb=" N TRP I 89 " --> pdb=" O GLY G 90 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TRP G 89 " --> pdb=" O GLY E 90 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TRP C 89 " --> pdb=" O GLY A 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 95 through 100 removed outlier: 6.322A pdb=" N THR C 95 " --> pdb=" O HIS E 96 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLN E 98 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER C 97 " --> pdb=" O GLN E 98 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASN E 100 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP C 99 " --> pdb=" O ASN E 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 106 through 107 removed outlier: 6.654A pdb=" N LYS C 106 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 115 through 117 removed outlier: 6.522A pdb=" N ALA C 115 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 120 through 122 removed outlier: 6.965A pdb=" N VAL I 121 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL G 121 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL C 121 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 125 through 130 removed outlier: 6.891A pdb=" N GLY I 126 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY G 127 " --> pdb=" O GLY I 126 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR I 128 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY G 126 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY E 127 " --> pdb=" O GLY G 126 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR G 128 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N LEU C 125 " --> pdb=" O GLY E 126 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N TYR E 128 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLY C 127 " --> pdb=" O TYR E 128 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU E 130 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL C 129 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY C 126 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY A 127 " --> pdb=" O GLY C 126 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR C 128 " --> pdb=" O GLY A 127 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 138 through 139 removed outlier: 6.539A pdb=" N ILE I 138 " --> pdb=" O ILE G 139 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE G 138 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE C 138 " --> pdb=" O ILE A 139 " (cutoff:3.500A) 70 hydrogen bonds defined for protein. 210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.47 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1403 1.33 - 1.45: 1147 1.45 - 1.57: 1910 1.57 - 1.69: 10 1.69 - 1.81: 60 Bond restraints: 4530 Sorted by residual: bond pdb=" CG HIS D 111 " pdb=" CD2 HIS D 111 " ideal model delta sigma weight residual 1.354 1.271 0.083 1.10e-02 8.26e+03 5.63e+01 bond pdb=" CG HIS I 111 " pdb=" CD2 HIS I 111 " ideal model delta sigma weight residual 1.354 1.272 0.082 1.10e-02 8.26e+03 5.61e+01 bond pdb=" CG HIS F 111 " pdb=" CD2 HIS F 111 " ideal model delta sigma weight residual 1.354 1.272 0.082 1.10e-02 8.26e+03 5.60e+01 bond pdb=" CG HIS J 111 " pdb=" CD2 HIS J 111 " ideal model delta sigma weight residual 1.354 1.272 0.082 1.10e-02 8.26e+03 5.59e+01 bond pdb=" CG HIS B 111 " pdb=" CD2 HIS B 111 " ideal model delta sigma weight residual 1.354 1.272 0.082 1.10e-02 8.26e+03 5.59e+01 ... (remaining 4525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 3646 1.45 - 2.89: 1494 2.89 - 4.34: 644 4.34 - 5.78: 202 5.78 - 7.23: 124 Bond angle restraints: 6110 Sorted by residual: angle pdb=" C ARG E 136 " pdb=" N PRO E 137 " pdb=" CA PRO E 137 " ideal model delta sigma weight residual 119.85 126.78 -6.93 1.01e+00 9.80e-01 4.71e+01 angle pdb=" C ARG I 136 " pdb=" N PRO I 137 " pdb=" CA PRO I 137 " ideal model delta sigma weight residual 119.85 126.75 -6.90 1.01e+00 9.80e-01 4.66e+01 angle pdb=" C ARG J 136 " pdb=" N PRO J 137 " pdb=" CA PRO J 137 " ideal model delta sigma weight residual 119.85 126.74 -6.89 1.01e+00 9.80e-01 4.66e+01 angle pdb=" C ARG F 136 " pdb=" N PRO F 137 " pdb=" CA PRO F 137 " ideal model delta sigma weight residual 119.85 126.73 -6.88 1.01e+00 9.80e-01 4.64e+01 angle pdb=" C ARG B 136 " pdb=" N PRO B 137 " pdb=" CA PRO B 137 " ideal model delta sigma weight residual 119.85 126.73 -6.88 1.01e+00 9.80e-01 4.64e+01 ... (remaining 6105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.45: 2240 10.45 - 20.91: 110 20.91 - 31.36: 90 31.36 - 41.81: 10 41.81 - 52.26: 10 Dihedral angle restraints: 2460 sinusoidal: 900 harmonic: 1560 Sorted by residual: dihedral pdb=" C TRP A 89 " pdb=" N TRP A 89 " pdb=" CA TRP A 89 " pdb=" CB TRP A 89 " ideal model delta harmonic sigma weight residual -122.60 -129.47 6.87 0 2.50e+00 1.60e-01 7.56e+00 dihedral pdb=" C TRP B 89 " pdb=" N TRP B 89 " pdb=" CA TRP B 89 " pdb=" CB TRP B 89 " ideal model delta harmonic sigma weight residual -122.60 -129.46 6.86 0 2.50e+00 1.60e-01 7.52e+00 dihedral pdb=" C TRP E 89 " pdb=" N TRP E 89 " pdb=" CA TRP E 89 " pdb=" CB TRP E 89 " ideal model delta harmonic sigma weight residual -122.60 -129.45 6.85 0 2.50e+00 1.60e-01 7.50e+00 ... (remaining 2457 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.066: 309 0.066 - 0.129: 147 0.129 - 0.192: 64 0.192 - 0.255: 22 0.255 - 0.319: 18 Chirality restraints: 560 Sorted by residual: chirality pdb=" CA TRP D 89 " pdb=" N TRP D 89 " pdb=" C TRP D 89 " pdb=" CB TRP D 89 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA TRP E 89 " pdb=" N TRP E 89 " pdb=" C TRP E 89 " pdb=" CB TRP E 89 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA TRP J 89 " pdb=" N TRP J 89 " pdb=" C TRP J 89 " pdb=" CB TRP J 89 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 557 not shown) Planarity restraints: 800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 81 " -0.032 2.00e-02 2.50e+03 1.63e-02 6.62e+00 pdb=" CG TRP F 81 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP F 81 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP F 81 " 0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP F 81 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP F 81 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP F 81 " 0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 81 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 81 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F 81 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 81 " 0.032 2.00e-02 2.50e+03 1.62e-02 6.59e+00 pdb=" CG TRP E 81 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP E 81 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP E 81 " -0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP E 81 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP E 81 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP E 81 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 81 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 81 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 81 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 81 " 0.032 2.00e-02 2.50e+03 1.62e-02 6.54e+00 pdb=" CG TRP I 81 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP I 81 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP I 81 " -0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP I 81 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP I 81 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP I 81 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 81 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 81 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP I 81 " 0.021 2.00e-02 2.50e+03 ... (remaining 797 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 2414 3.01 - 3.48: 4106 3.48 - 3.96: 6913 3.96 - 4.43: 8233 4.43 - 4.90: 15076 Nonbonded interactions: 36742 Sorted by model distance: nonbonded pdb=" N GLY G 93 " pdb=" O GLY G 93 " model vdw 2.540 2.496 nonbonded pdb=" N GLY E 93 " pdb=" O GLY E 93 " model vdw 2.541 2.496 nonbonded pdb=" N GLY H 93 " pdb=" O GLY H 93 " model vdw 2.541 2.496 nonbonded pdb=" N GLY F 93 " pdb=" O GLY F 93 " model vdw 2.541 2.496 nonbonded pdb=" N GLY D 93 " pdb=" O GLY D 93 " model vdw 2.541 2.496 ... (remaining 36737 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: 0.02 Found NCS groups: ncs_group { reference = chain 'J' selection = chain 'H' selection = chain 'D' selection = chain 'B' selection = chain 'F' selection = chain 'I' selection = chain 'G' selection = chain 'C' selection = chain 'A' selection = chain 'E' } 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: 1.090 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.180 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 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 : 0.023 0.101 4530 Z= 1.352 Angle : 2.110 7.226 6110 Z= 1.387 Chirality : 0.102 0.319 560 Planarity : 0.009 0.024 800 Dihedral : 9.850 52.261 1520 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.35 (0.24), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 136 TYR 0.012 0.007 TYR D 128 PHE 0.010 0.005 PHE B 141 TRP 0.032 0.007 TRP F 81 HIS 0.017 0.004 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.02296 ( 4530) covalent geometry : angle 2.11033 ( 6110) hydrogen bonds : bond 0.13240 ( 70) hydrogen bonds : angle 9.52741 ( 210) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.137 Fit side-chains REVERT: B 91 GLN cc_start: 0.5935 (tt0) cc_final: 0.4892 (pm20) REVERT: A 91 GLN cc_start: 0.5723 (tt0) cc_final: 0.4867 (pm20) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.0527 time to fit residues: 11.5684 Evaluate side-chains 110 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 100 ASN ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.158824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.149762 restraints weight = 8583.069| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 3.19 r_work: 0.4356 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4530 Z= 0.256 Angle : 0.799 4.745 6110 Z= 0.421 Chirality : 0.045 0.163 560 Planarity : 0.005 0.056 800 Dihedral : 5.287 14.247 630 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.67 % Favored : 93.17 % Rotamer: Outliers : 5.13 % Allowed : 12.56 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.90 (0.22), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.17), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 136 TYR 0.005 0.002 TYR F 128 PHE 0.009 0.002 PHE D 141 TRP 0.027 0.003 TRP B 81 HIS 0.004 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 4530) covalent geometry : angle 0.79935 ( 6110) hydrogen bonds : bond 0.03307 ( 70) hydrogen bonds : angle 6.95427 ( 210) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 103 SER cc_start: 0.8683 (t) cc_final: 0.8474 (p) REVERT: J 141 PHE cc_start: 0.7347 (t80) cc_final: 0.6342 (p90) REVERT: H 112 MET cc_start: 0.8816 (mpp) cc_final: 0.8463 (mpp) REVERT: D 112 MET cc_start: 0.8934 (mpp) cc_final: 0.8687 (mpp) REVERT: F 85 HIS cc_start: 0.7995 (m90) cc_final: 0.7653 (m-70) REVERT: I 81 TRP cc_start: 0.7219 (m-10) cc_final: 0.6496 (m100) REVERT: I 103 SER cc_start: 0.8704 (t) cc_final: 0.8492 (p) REVERT: I 141 PHE cc_start: 0.7256 (t80) cc_final: 0.6240 (p90) REVERT: G 81 TRP cc_start: 0.8583 (m-10) cc_final: 0.8371 (m-10) REVERT: G 100 ASN cc_start: 0.9090 (t0) cc_final: 0.8855 (t0) REVERT: G 112 MET cc_start: 0.8836 (mpp) cc_final: 0.8457 (mpp) REVERT: C 112 MET cc_start: 0.8956 (mpp) cc_final: 0.8698 (mpp) REVERT: C 134 MET cc_start: 0.7928 (mtt) cc_final: 0.7654 (mtt) REVERT: A 134 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7422 (mtt) outliers start: 20 outliers final: 14 residues processed: 134 average time/residue: 0.0337 time to fit residues: 6.6957 Evaluate side-chains 134 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain E residue 122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 140 HIS H 140 HIS ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS B 83 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS ** F 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 HIS I 140 HIS G 140 HIS ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS A 83 GLN ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.148140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.139840 restraints weight = 9041.805| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 3.07 r_work: 0.4253 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 4530 Z= 0.343 Angle : 0.869 6.134 6110 Z= 0.453 Chirality : 0.047 0.167 560 Planarity : 0.005 0.043 800 Dihedral : 5.615 17.032 630 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.33 % Favored : 85.50 % Rotamer: Outliers : 7.95 % Allowed : 16.67 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.21 (0.23), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.17), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 136 TYR 0.010 0.002 TYR H 128 PHE 0.013 0.003 PHE A 141 TRP 0.043 0.004 TRP C 99 HIS 0.006 0.001 HIS I 85 Details of bonding type rmsd covalent geometry : bond 0.00766 ( 4530) covalent geometry : angle 0.86905 ( 6110) hydrogen bonds : bond 0.03426 ( 70) hydrogen bonds : angle 5.92479 ( 210) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.144 Fit side-chains REVERT: J 103 SER cc_start: 0.8735 (t) cc_final: 0.8533 (p) REVERT: J 141 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6124 (p90) REVERT: D 134 MET cc_start: 0.8129 (mtt) cc_final: 0.7801 (mtt) REVERT: F 85 HIS cc_start: 0.8068 (m90) cc_final: 0.7786 (m-70) REVERT: I 103 SER cc_start: 0.8754 (t) cc_final: 0.8514 (p) REVERT: I 141 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.6015 (p90) REVERT: G 81 TRP cc_start: 0.8687 (m-10) cc_final: 0.8346 (m-10) REVERT: C 112 MET cc_start: 0.8953 (mpp) cc_final: 0.8684 (mpp) REVERT: A 99 TRP cc_start: 0.7955 (m-10) cc_final: 0.7704 (m-10) REVERT: A 134 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7437 (mtt) REVERT: E 85 HIS cc_start: 0.8189 (m-70) cc_final: 0.7710 (m-70) outliers start: 31 outliers final: 20 residues processed: 132 average time/residue: 0.0384 time to fit residues: 7.3225 Evaluate side-chains 139 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 141 PHE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 141 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.148642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.140306 restraints weight = 8811.493| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 3.15 r_work: 0.4238 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.5838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4530 Z= 0.261 Angle : 0.768 5.838 6110 Z= 0.395 Chirality : 0.045 0.118 560 Planarity : 0.005 0.034 800 Dihedral : 5.159 15.180 630 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 6.67 % Allowed : 20.00 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.48 (0.22), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.17), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 136 TYR 0.031 0.004 TYR H 128 PHE 0.009 0.002 PHE E 141 TRP 0.032 0.003 TRP C 99 HIS 0.004 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00585 ( 4530) covalent geometry : angle 0.76771 ( 6110) hydrogen bonds : bond 0.03018 ( 70) hydrogen bonds : angle 5.47430 ( 210) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.169 Fit side-chains REVERT: J 81 TRP cc_start: 0.5082 (OUTLIER) cc_final: 0.4073 (m100) REVERT: J 141 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.6180 (p90) REVERT: H 85 HIS cc_start: 0.8251 (m-70) cc_final: 0.7984 (m-70) REVERT: H 112 MET cc_start: 0.8613 (mpp) cc_final: 0.8384 (mpp) REVERT: H 122 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8350 (p) REVERT: H 136 ARG cc_start: 0.8445 (ttm170) cc_final: 0.7881 (mtp180) REVERT: D 112 MET cc_start: 0.8852 (mpp) cc_final: 0.8605 (mpp) REVERT: B 112 MET cc_start: 0.8643 (mpp) cc_final: 0.8396 (mpp) REVERT: F 81 TRP cc_start: 0.9071 (m-10) cc_final: 0.8128 (m-10) REVERT: I 81 TRP cc_start: 0.7045 (m-10) cc_final: 0.5933 (m100) REVERT: I 141 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.6153 (p90) REVERT: G 81 TRP cc_start: 0.8654 (m-10) cc_final: 0.8205 (m-10) REVERT: G 100 ASN cc_start: 0.8996 (t0) cc_final: 0.8627 (t0) REVERT: G 112 MET cc_start: 0.8574 (mpp) cc_final: 0.8343 (mpp) REVERT: G 122 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8264 (p) REVERT: C 112 MET cc_start: 0.8923 (mpp) cc_final: 0.8651 (mpp) REVERT: A 81 TRP cc_start: 0.8658 (m-10) cc_final: 0.8406 (m-10) REVERT: A 134 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7317 (mtt) REVERT: E 81 TRP cc_start: 0.9041 (m-10) cc_final: 0.8284 (m-10) outliers start: 26 outliers final: 19 residues processed: 125 average time/residue: 0.0410 time to fit residues: 7.3465 Evaluate side-chains 135 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 81 TRP Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 141 PHE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 141 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 30.0000 chunk 55 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.153642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.145089 restraints weight = 8722.348| |-----------------------------------------------------------------------------| r_work (start): 0.4412 rms_B_bonded: 3.17 r_work: 0.4311 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4530 Z= 0.171 Angle : 0.684 5.351 6110 Z= 0.346 Chirality : 0.044 0.172 560 Planarity : 0.004 0.031 800 Dihedral : 4.699 13.160 630 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 6.92 % Allowed : 17.95 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.64 (0.21), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.16), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 136 TYR 0.026 0.003 TYR G 128 PHE 0.006 0.001 PHE I 141 TRP 0.019 0.002 TRP C 99 HIS 0.003 0.001 HIS I 85 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 4530) covalent geometry : angle 0.68362 ( 6110) hydrogen bonds : bond 0.02812 ( 70) hydrogen bonds : angle 5.03786 ( 210) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.152 Fit side-chains REVERT: J 141 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.6264 (p90) REVERT: H 121 VAL cc_start: 0.9230 (t) cc_final: 0.8698 (m) REVERT: H 122 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8252 (p) REVERT: H 136 ARG cc_start: 0.8473 (ttm170) cc_final: 0.8055 (mtp180) REVERT: D 81 TRP cc_start: 0.8694 (m-10) cc_final: 0.8057 (m-10) REVERT: D 112 MET cc_start: 0.8788 (mpp) cc_final: 0.8555 (mpp) REVERT: F 81 TRP cc_start: 0.8984 (m-10) cc_final: 0.8164 (m-10) REVERT: F 134 MET cc_start: 0.7576 (mtt) cc_final: 0.7350 (mmt) REVERT: I 81 TRP cc_start: 0.7007 (m-10) cc_final: 0.6003 (m100) REVERT: I 141 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.6228 (p90) REVERT: G 81 TRP cc_start: 0.8659 (m-10) cc_final: 0.8285 (m-10) REVERT: G 100 ASN cc_start: 0.8968 (t0) cc_final: 0.8525 (t0) REVERT: G 121 VAL cc_start: 0.9208 (t) cc_final: 0.8698 (m) REVERT: G 122 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8161 (p) REVERT: G 136 ARG cc_start: 0.8513 (ttm170) cc_final: 0.8156 (mtt180) REVERT: C 112 MET cc_start: 0.8824 (mpp) cc_final: 0.8518 (mpp) REVERT: A 81 TRP cc_start: 0.8595 (m-10) cc_final: 0.8318 (m-10) REVERT: E 81 TRP cc_start: 0.8996 (m-10) cc_final: 0.8476 (m-10) outliers start: 27 outliers final: 16 residues processed: 122 average time/residue: 0.0408 time to fit residues: 6.9786 Evaluate side-chains 126 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 141 PHE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain E residue 122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 37 optimal weight: 30.0000 chunk 16 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.147904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.139689 restraints weight = 9162.224| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 3.11 r_work: 0.4249 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 4530 Z= 0.254 Angle : 0.779 9.279 6110 Z= 0.391 Chirality : 0.045 0.177 560 Planarity : 0.004 0.031 800 Dihedral : 4.974 15.255 630 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 5.90 % Allowed : 21.28 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.87 (0.21), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.16), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 136 TYR 0.031 0.004 TYR H 128 PHE 0.009 0.002 PHE J 141 TRP 0.034 0.003 TRP H 99 HIS 0.005 0.001 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 4530) covalent geometry : angle 0.77935 ( 6110) hydrogen bonds : bond 0.02861 ( 70) hydrogen bonds : angle 5.36948 ( 210) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.141 Fit side-chains REVERT: J 81 TRP cc_start: 0.4897 (OUTLIER) cc_final: 0.3291 (m100) REVERT: J 141 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6259 (p90) REVERT: H 122 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8236 (p) REVERT: H 136 ARG cc_start: 0.8447 (ttm170) cc_final: 0.8229 (mtp180) REVERT: D 81 TRP cc_start: 0.8785 (m-10) cc_final: 0.8518 (m-10) REVERT: B 112 MET cc_start: 0.8568 (mpp) cc_final: 0.8217 (mpp) REVERT: F 85 HIS cc_start: 0.8254 (m90) cc_final: 0.7867 (m90) REVERT: F 128 TYR cc_start: 0.9118 (m-80) cc_final: 0.8454 (m-10) REVERT: I 141 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.6235 (p90) REVERT: G 122 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8187 (p) REVERT: A 81 TRP cc_start: 0.8713 (m-10) cc_final: 0.8402 (m-10) outliers start: 23 outliers final: 16 residues processed: 117 average time/residue: 0.0384 time to fit residues: 6.3793 Evaluate side-chains 127 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 81 TRP Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 141 PHE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain E residue 122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 27 optimal weight: 30.0000 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.145187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.137126 restraints weight = 9114.894| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 3.09 r_work: 0.4225 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.6429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 4530 Z= 0.314 Angle : 0.832 6.655 6110 Z= 0.423 Chirality : 0.047 0.180 560 Planarity : 0.005 0.030 800 Dihedral : 5.208 15.895 630 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 6.67 % Allowed : 22.82 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.05 (0.20), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.15), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 136 TYR 0.035 0.004 TYR H 128 PHE 0.011 0.002 PHE I 141 TRP 0.042 0.003 TRP G 99 HIS 0.006 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00710 ( 4530) covalent geometry : angle 0.83243 ( 6110) hydrogen bonds : bond 0.02958 ( 70) hydrogen bonds : angle 5.68040 ( 210) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.100 Fit side-chains REVERT: J 81 TRP cc_start: 0.4890 (OUTLIER) cc_final: 0.4160 (m100) REVERT: J 141 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.6133 (p90) REVERT: H 122 VAL cc_start: 0.8762 (OUTLIER) cc_final: 0.8229 (p) REVERT: B 112 MET cc_start: 0.8615 (mpp) cc_final: 0.8409 (mpp) REVERT: F 85 HIS cc_start: 0.8313 (m90) cc_final: 0.7890 (m90) REVERT: F 128 TYR cc_start: 0.9118 (m-80) cc_final: 0.8415 (m-10) REVERT: I 141 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6106 (p90) REVERT: G 122 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8218 (p) REVERT: A 112 MET cc_start: 0.8436 (mpp) cc_final: 0.8229 (mpp) outliers start: 26 outliers final: 17 residues processed: 108 average time/residue: 0.0398 time to fit residues: 6.0738 Evaluate side-chains 122 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 81 TRP Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 141 PHE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain E residue 122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 44 optimal weight: 0.0020 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 0.0670 chunk 35 optimal weight: 10.0000 overall best weight: 3.4132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.152731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.144311 restraints weight = 8786.828| |-----------------------------------------------------------------------------| r_work (start): 0.4420 rms_B_bonded: 3.16 r_work: 0.4323 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.6544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4530 Z= 0.160 Angle : 0.684 6.161 6110 Z= 0.339 Chirality : 0.045 0.179 560 Planarity : 0.004 0.030 800 Dihedral : 4.611 13.987 630 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 5.90 % Allowed : 24.62 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.03 (0.21), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.16), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG J 136 TYR 0.028 0.003 TYR H 128 PHE 0.006 0.001 PHE I 141 TRP 0.020 0.002 TRP G 99 HIS 0.003 0.001 HIS I 85 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 4530) covalent geometry : angle 0.68412 ( 6110) hydrogen bonds : bond 0.02597 ( 70) hydrogen bonds : angle 4.99384 ( 210) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.154 Fit side-chains REVERT: J 81 TRP cc_start: 0.4831 (OUTLIER) cc_final: 0.3120 (m100) REVERT: J 141 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.6292 (p90) REVERT: H 100 ASN cc_start: 0.9066 (t0) cc_final: 0.8485 (t0) REVERT: H 136 ARG cc_start: 0.8427 (ttm170) cc_final: 0.8118 (mtp180) REVERT: D 81 TRP cc_start: 0.8831 (m-10) cc_final: 0.8581 (m-10) REVERT: I 141 PHE cc_start: 0.7415 (OUTLIER) cc_final: 0.6273 (p90) REVERT: G 100 ASN cc_start: 0.9027 (t0) cc_final: 0.8703 (t0) REVERT: G 136 ARG cc_start: 0.8467 (ttm170) cc_final: 0.8212 (mtp180) outliers start: 23 outliers final: 16 residues processed: 111 average time/residue: 0.0447 time to fit residues: 6.8499 Evaluate side-chains 118 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 81 TRP Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 141 PHE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain E residue 122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.151794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.143255 restraints weight = 8911.774| |-----------------------------------------------------------------------------| r_work (start): 0.4412 rms_B_bonded: 3.23 r_work: 0.4313 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.6577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4530 Z= 0.185 Angle : 0.692 5.541 6110 Z= 0.345 Chirality : 0.045 0.136 560 Planarity : 0.004 0.032 800 Dihedral : 4.560 13.982 630 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 5.13 % Allowed : 22.82 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.07 (0.21), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.16), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 136 TYR 0.031 0.003 TYR H 128 PHE 0.008 0.002 PHE J 141 TRP 0.025 0.002 TRP G 99 HIS 0.003 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 4530) covalent geometry : angle 0.69180 ( 6110) hydrogen bonds : bond 0.02100 ( 70) hydrogen bonds : angle 4.83565 ( 210) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.101 Fit side-chains REVERT: J 81 TRP cc_start: 0.4840 (OUTLIER) cc_final: 0.3198 (m100) REVERT: J 141 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.6143 (p90) REVERT: H 136 ARG cc_start: 0.8452 (ttm170) cc_final: 0.8080 (mtp180) REVERT: D 81 TRP cc_start: 0.8780 (m-10) cc_final: 0.8552 (m-10) REVERT: B 112 MET cc_start: 0.8692 (mpp) cc_final: 0.8135 (mpp) REVERT: I 141 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.6106 (p90) REVERT: G 136 ARG cc_start: 0.8458 (ttm170) cc_final: 0.8200 (mtp180) outliers start: 20 outliers final: 16 residues processed: 112 average time/residue: 0.0475 time to fit residues: 7.1473 Evaluate side-chains 126 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 81 TRP Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 141 PHE Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.4980 chunk 46 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.152822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.144397 restraints weight = 8886.842| |-----------------------------------------------------------------------------| r_work (start): 0.4428 rms_B_bonded: 3.19 r_work: 0.4331 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.6660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4530 Z= 0.160 Angle : 0.691 9.979 6110 Z= 0.336 Chirality : 0.044 0.144 560 Planarity : 0.004 0.031 800 Dihedral : 4.423 13.557 630 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 5.13 % Allowed : 23.33 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.09 (0.20), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.16), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG J 136 TYR 0.028 0.003 TYR H 128 PHE 0.006 0.001 PHE J 141 TRP 0.023 0.002 TRP G 99 HIS 0.003 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 4530) covalent geometry : angle 0.69082 ( 6110) hydrogen bonds : bond 0.01962 ( 70) hydrogen bonds : angle 4.62325 ( 210) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.161 Fit side-chains REVERT: J 81 TRP cc_start: 0.4806 (OUTLIER) cc_final: 0.3109 (m100) REVERT: J 141 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6170 (p90) REVERT: H 100 ASN cc_start: 0.9026 (t0) cc_final: 0.8511 (t0) REVERT: H 125 LEU cc_start: 0.8956 (pp) cc_final: 0.8741 (pt) REVERT: H 136 ARG cc_start: 0.8456 (ttm170) cc_final: 0.8168 (mtp180) REVERT: D 81 TRP cc_start: 0.8761 (m-10) cc_final: 0.8484 (m-10) REVERT: I 141 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.6139 (p90) REVERT: G 100 ASN cc_start: 0.9028 (t0) cc_final: 0.8566 (t0) REVERT: G 136 ARG cc_start: 0.8450 (ttm170) cc_final: 0.8212 (mtp180) outliers start: 20 outliers final: 16 residues processed: 113 average time/residue: 0.0517 time to fit residues: 7.7621 Evaluate side-chains 124 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 81 TRP Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 141 PHE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain E residue 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.144844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.136675 restraints weight = 9229.885| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 3.20 r_work: 0.4225 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.6631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 4530 Z= 0.314 Angle : 0.830 8.434 6110 Z= 0.420 Chirality : 0.047 0.155 560 Planarity : 0.004 0.027 800 Dihedral : 5.028 15.131 630 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 15.00 % Favored : 84.83 % Rotamer: Outliers : 5.13 % Allowed : 23.59 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.24 (0.20), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.15), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 136 TYR 0.031 0.003 TYR H 128 PHE 0.012 0.002 PHE I 141 TRP 0.041 0.003 TRP G 99 HIS 0.006 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00711 ( 4530) covalent geometry : angle 0.83008 ( 6110) hydrogen bonds : bond 0.02406 ( 70) hydrogen bonds : angle 5.32115 ( 210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 816.58 seconds wall clock time: 14 minutes 49.13 seconds (889.13 seconds total)