Starting phenix.real_space_refine on Thu Mar 6 01:40:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7umq_26607/03_2025/7umq_26607.cif Found real_map, /net/cci-nas-00/data/ceres_data/7umq_26607/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7umq_26607/03_2025/7umq_26607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7umq_26607/03_2025/7umq_26607.map" model { file = "/net/cci-nas-00/data/ceres_data/7umq_26607/03_2025/7umq_26607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7umq_26607/03_2025/7umq_26607.cif" } resolution = 3.29 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= 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4380 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.82, per 1000 atoms: 0.42 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: 1.06 Conformation dependent library (CDL) restraints added in 543.0 milliseconds 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: 0.74 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: 1.03 Time building geometry restraints manager: 1.27 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 1.020 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.460 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.810 ------------------------------------------------------------------------------- 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= 1.595 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 (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: -3.35 (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 TRP 0.032 0.007 TRP F 81 HIS 0.017 0.004 HIS B 111 PHE 0.010 0.005 PHE B 141 TYR 0.012 0.007 TYR D 128 ARG 0.001 0.000 ARG J 136 *********************** 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 : 0.464 Fit side-chains REVERT: B 91 GLN cc_start: 0.5935 (tt0) cc_final: 0.4891 (pm20) REVERT: A 91 GLN cc_start: 0.5723 (tt0) cc_final: 0.4869 (pm20) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1498 time to fit residues: 32.2711 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 : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.160583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.151293 restraints weight = 8339.599| |-----------------------------------------------------------------------------| r_work (start): 0.4449 rms_B_bonded: 3.18 r_work: 0.4357 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4530 Z= 0.380 Angle : 0.807 5.048 6110 Z= 0.424 Chirality : 0.046 0.164 560 Planarity : 0.005 0.055 800 Dihedral : 5.174 13.688 630 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.67 % Favored : 93.17 % Rotamer: Outliers : 4.36 % Allowed : 13.08 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.22), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.17), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 81 HIS 0.003 0.001 HIS D 140 PHE 0.006 0.001 PHE D 141 TYR 0.005 0.002 TYR I 128 ARG 0.007 0.001 ARG C 136 *********************** 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 149 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 141 PHE cc_start: 0.7247 (t80) cc_final: 0.6192 (p90) REVERT: H 85 HIS cc_start: 0.7927 (m-70) cc_final: 0.7652 (m-70) REVERT: H 100 ASN cc_start: 0.9136 (t0) cc_final: 0.8808 (t0) REVERT: H 112 MET cc_start: 0.8789 (mpp) cc_final: 0.8403 (mpp) REVERT: H 134 MET cc_start: 0.7952 (mtt) cc_final: 0.7722 (mtt) REVERT: D 112 MET cc_start: 0.8865 (mpp) cc_final: 0.8645 (mpp) REVERT: D 134 MET cc_start: 0.7965 (mtt) cc_final: 0.7695 (mtt) REVERT: I 81 TRP cc_start: 0.7253 (m-10) cc_final: 0.6531 (m100) REVERT: I 141 PHE cc_start: 0.7476 (t80) cc_final: 0.6035 (p90) REVERT: G 85 HIS cc_start: 0.8141 (m-70) cc_final: 0.7895 (m90) REVERT: G 100 ASN cc_start: 0.9140 (t0) cc_final: 0.8827 (t0) REVERT: G 112 MET cc_start: 0.8783 (mpp) cc_final: 0.8371 (mpp) REVERT: C 112 MET cc_start: 0.8907 (mpp) cc_final: 0.8675 (mpp) REVERT: C 121 VAL cc_start: 0.9210 (t) cc_final: 0.9009 (m) REVERT: E 85 HIS cc_start: 0.8015 (m90) cc_final: 0.7629 (m-70) outliers start: 17 outliers final: 14 residues processed: 134 average time/residue: 0.0938 time to fit residues: 17.8729 Evaluate side-chains 129 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 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 44 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 100 ASN J 140 HIS ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 HIS I 100 ASN 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 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.147932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.139689 restraints weight = 9029.719| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 3.10 r_work: 0.4269 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 4530 Z= 0.554 Angle : 0.886 7.877 6110 Z= 0.462 Chirality : 0.047 0.164 560 Planarity : 0.005 0.036 800 Dihedral : 5.736 17.123 630 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.00 % Favored : 85.83 % Rotamer: Outliers : 8.21 % Allowed : 14.62 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.23), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.17), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP C 99 HIS 0.005 0.001 HIS B 85 PHE 0.014 0.004 PHE E 141 TYR 0.010 0.002 TYR H 128 ARG 0.005 0.001 ARG J 136 *********************** 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 156 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.489 Fit side-chains REVERT: J 81 TRP cc_start: 0.5301 (OUTLIER) cc_final: 0.3977 (m100) REVERT: J 141 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6087 (p90) REVERT: H 85 HIS cc_start: 0.8263 (m-70) cc_final: 0.7999 (m-70) REVERT: D 112 MET cc_start: 0.8943 (mpp) cc_final: 0.8737 (mpp) REVERT: D 136 ARG cc_start: 0.6721 (ptt180) cc_final: 0.5879 (mtm180) REVERT: B 81 TRP cc_start: 0.8413 (m-10) cc_final: 0.7526 (m-10) REVERT: F 85 HIS cc_start: 0.8360 (m-70) cc_final: 0.7847 (m-70) REVERT: I 81 TRP cc_start: 0.7170 (m-10) cc_final: 0.6119 (m100) REVERT: I 141 PHE cc_start: 0.7287 (OUTLIER) cc_final: 0.6035 (p90) REVERT: C 112 MET cc_start: 0.8973 (mpp) cc_final: 0.8773 (mpp) REVERT: A 134 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7457 (mtt) REVERT: E 85 HIS cc_start: 0.8130 (m90) cc_final: 0.7898 (m-70) outliers start: 32 outliers final: 22 residues processed: 130 average time/residue: 0.0978 time to fit residues: 17.8662 Evaluate side-chains 139 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 B residue 125 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain F residue 122 VAL 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 125 LEU 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 27 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** 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** ** A 100 ASN ** 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 = 0.4454 r_free = 0.4454 target = 0.150687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.142410 restraints weight = 8880.145| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 3.17 r_work: 0.4290 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4530 Z= 0.317 Angle : 0.719 7.107 6110 Z= 0.366 Chirality : 0.043 0.118 560 Planarity : 0.004 0.033 800 Dihedral : 4.942 13.744 630 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 7.18 % Allowed : 18.72 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.22), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.17), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 99 HIS 0.003 0.001 HIS A 85 PHE 0.008 0.002 PHE E 141 TYR 0.028 0.003 TYR G 128 ARG 0.003 0.001 ARG J 136 *********************** 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: 28 poor density : 118 time to evaluate : 0.468 Fit side-chains REVERT: J 81 TRP cc_start: 0.4952 (OUTLIER) cc_final: 0.3832 (m100) REVERT: J 141 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.6195 (p90) REVERT: H 100 ASN cc_start: 0.9037 (t0) cc_final: 0.8798 (t0) REVERT: H 112 MET cc_start: 0.8574 (mpp) cc_final: 0.8344 (mpp) REVERT: H 122 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8286 (p) REVERT: H 136 ARG cc_start: 0.8507 (ttm170) cc_final: 0.8286 (mtp180) REVERT: D 112 MET cc_start: 0.8854 (mpp) cc_final: 0.8618 (mpp) REVERT: B 81 TRP cc_start: 0.8470 (m-10) cc_final: 0.8235 (m-10) REVERT: F 85 HIS cc_start: 0.8300 (m-70) cc_final: 0.7856 (m-70) REVERT: F 134 MET cc_start: 0.7661 (mtt) cc_final: 0.7450 (mmt) REVERT: I 81 TRP cc_start: 0.7048 (m-10) cc_final: 0.5912 (m100) REVERT: I 141 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.6303 (p90) REVERT: G 100 ASN cc_start: 0.8964 (t0) cc_final: 0.8628 (t0) REVERT: G 112 MET cc_start: 0.8557 (mpp) cc_final: 0.8300 (mpp) REVERT: G 122 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8330 (p) REVERT: C 112 MET cc_start: 0.8905 (mpp) cc_final: 0.8656 (mpp) REVERT: A 134 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7562 (mtt) REVERT: E 81 TRP cc_start: 0.8977 (m-10) cc_final: 0.8113 (m-10) REVERT: E 85 HIS cc_start: 0.8061 (m90) cc_final: 0.7673 (m90) outliers start: 28 outliers final: 19 residues processed: 123 average time/residue: 0.1046 time to fit residues: 18.0435 Evaluate side-chains 138 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 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 125 LEU 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 53 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 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 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 = 0.4385 r_free = 0.4385 target = 0.143794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.135711 restraints weight = 9399.019| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 3.14 r_work: 0.4205 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.6127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 4530 Z= 0.545 Angle : 0.853 5.463 6110 Z= 0.443 Chirality : 0.047 0.176 560 Planarity : 0.005 0.034 800 Dihedral : 5.478 17.280 630 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.33 % Allowed : 15.33 % Favored : 84.33 % Rotamer: Outliers : 7.95 % Allowed : 17.18 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.71 (0.21), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.16), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP H 99 HIS 0.005 0.002 HIS A 85 PHE 0.014 0.003 PHE E 141 TYR 0.028 0.004 TYR G 128 ARG 0.004 0.001 ARG I 136 *********************** 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 147 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.447 Fit side-chains REVERT: J 81 TRP cc_start: 0.4974 (OUTLIER) cc_final: 0.4078 (m100) REVERT: J 141 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6163 (p90) REVERT: H 122 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8271 (p) REVERT: D 81 TRP cc_start: 0.8721 (m-10) cc_final: 0.8451 (m-10) REVERT: B 81 TRP cc_start: 0.8675 (m-10) cc_final: 0.8296 (m-10) REVERT: F 85 HIS cc_start: 0.8398 (m-70) cc_final: 0.8081 (m-70) REVERT: F 128 TYR cc_start: 0.9069 (m-80) cc_final: 0.8588 (m-10) REVERT: I 81 TRP cc_start: 0.7100 (m-10) cc_final: 0.5904 (m100) REVERT: G 100 ASN cc_start: 0.9087 (t0) cc_final: 0.8882 (t0) REVERT: G 122 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8397 (p) REVERT: C 81 TRP cc_start: 0.8803 (m-10) cc_final: 0.8490 (m-10) REVERT: A 128 TYR cc_start: 0.8508 (m-80) cc_final: 0.8229 (m-80) REVERT: A 134 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7447 (mtt) REVERT: E 128 TYR cc_start: 0.9061 (m-80) cc_final: 0.8592 (m-10) outliers start: 31 outliers final: 23 residues processed: 123 average time/residue: 0.1024 time to fit residues: 18.0391 Evaluate side-chains 135 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 81 TRP Chi-restraints excluded: chain J residue 103 SER 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 B residue 129 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain G residue 121 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 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 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 = 0.4448 r_free = 0.4448 target = 0.149443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.141040 restraints weight = 8945.158| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 3.21 r_work: 0.4249 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.6292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4530 Z= 0.349 Angle : 0.732 5.812 6110 Z= 0.372 Chirality : 0.045 0.171 560 Planarity : 0.005 0.033 800 Dihedral : 4.967 14.366 630 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.83 % Favored : 88.83 % Rotamer: Outliers : 6.92 % Allowed : 20.77 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.88 (0.20), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.16), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 99 HIS 0.004 0.001 HIS A 85 PHE 0.010 0.002 PHE E 141 TYR 0.023 0.003 TYR H 128 ARG 0.003 0.001 ARG I 136 *********************** 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 137 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.469 Fit side-chains REVERT: J 81 TRP cc_start: 0.4892 (OUTLIER) cc_final: 0.4166 (m100) REVERT: J 141 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6230 (p90) REVERT: H 122 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8107 (p) REVERT: D 81 TRP cc_start: 0.8741 (m-10) cc_final: 0.8418 (m-10) REVERT: B 81 TRP cc_start: 0.8641 (m-10) cc_final: 0.8334 (m-10) REVERT: B 112 MET cc_start: 0.8538 (mpp) cc_final: 0.8197 (mpp) REVERT: F 85 HIS cc_start: 0.8262 (m-70) cc_final: 0.7978 (m-70) REVERT: I 81 TRP cc_start: 0.7058 (m-10) cc_final: 0.5781 (m100) REVERT: G 122 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8143 (p) REVERT: C 81 TRP cc_start: 0.8846 (m-10) cc_final: 0.8549 (m-10) REVERT: A 112 MET cc_start: 0.8561 (mpp) cc_final: 0.8219 (mpp) REVERT: A 134 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7232 (mtt) REVERT: E 85 HIS cc_start: 0.8305 (m90) cc_final: 0.7853 (m90) outliers start: 27 outliers final: 21 residues processed: 116 average time/residue: 0.0993 time to fit residues: 16.6346 Evaluate side-chains 132 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 81 TRP Chi-restraints excluded: chain J residue 103 SER 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 129 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 122 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 9.9990 chunk 15 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 111 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 83 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 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 = 0.4413 r_free = 0.4413 target = 0.145758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.137576 restraints weight = 9013.296| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 3.21 r_work: 0.4230 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.6398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 4530 Z= 0.481 Angle : 0.805 5.509 6110 Z= 0.415 Chirality : 0.047 0.168 560 Planarity : 0.005 0.033 800 Dihedral : 5.193 15.922 630 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.33 % Allowed : 14.83 % Favored : 84.83 % Rotamer: Outliers : 7.69 % Allowed : 18.97 % 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 (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: -5.08 (0.20), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.15), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP G 99 HIS 0.006 0.001 HIS A 85 PHE 0.015 0.003 PHE E 141 TYR 0.022 0.003 TYR H 128 ARG 0.004 0.001 ARG I 136 *********************** 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 139 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.438 Fit side-chains REVERT: J 81 TRP cc_start: 0.4896 (OUTLIER) cc_final: 0.4252 (m100) REVERT: J 125 LEU cc_start: 0.8872 (pp) cc_final: 0.8652 (pp) REVERT: J 141 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.6112 (p90) REVERT: H 122 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8145 (p) REVERT: D 81 TRP cc_start: 0.8739 (m-10) cc_final: 0.8403 (m-10) REVERT: B 81 TRP cc_start: 0.8695 (m-10) cc_final: 0.8351 (m-10) REVERT: B 112 MET cc_start: 0.8591 (mpp) cc_final: 0.8319 (mpp) REVERT: F 128 TYR cc_start: 0.9091 (m-80) cc_final: 0.8551 (m-10) REVERT: I 81 TRP cc_start: 0.7092 (m-10) cc_final: 0.5802 (m100) REVERT: G 122 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8245 (p) REVERT: A 112 MET cc_start: 0.8603 (mpp) cc_final: 0.8327 (mpp) REVERT: A 134 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7320 (mtt) REVERT: E 85 HIS cc_start: 0.8390 (m90) cc_final: 0.7994 (m90) REVERT: E 128 TYR cc_start: 0.9057 (m-80) cc_final: 0.8640 (m-10) outliers start: 30 outliers final: 22 residues processed: 117 average time/residue: 0.1023 time to fit residues: 16.7226 Evaluate side-chains 131 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 81 TRP Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain H residue 109 MET 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 129 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain G residue 109 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 30.0000 chunk 59 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 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 = 0.152207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.143765 restraints weight = 8802.766| |-----------------------------------------------------------------------------| r_work (start): 0.4412 rms_B_bonded: 3.24 r_work: 0.4316 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4530 Z= 0.253 Angle : 0.666 5.518 6110 Z= 0.336 Chirality : 0.044 0.166 560 Planarity : 0.004 0.033 800 Dihedral : 4.636 13.915 630 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 7.18 % Allowed : 20.51 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.06 (0.20), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.15), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 99 HIS 0.003 0.001 HIS I 85 PHE 0.008 0.002 PHE E 141 TYR 0.022 0.003 TYR H 128 ARG 0.002 0.001 ARG G 136 *********************** 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 137 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.475 Fit side-chains REVERT: J 141 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.6284 (p90) REVERT: H 122 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8049 (p) REVERT: H 136 ARG cc_start: 0.8463 (ttm170) cc_final: 0.8200 (mtp180) REVERT: D 81 TRP cc_start: 0.8809 (m-10) cc_final: 0.8560 (m-10) REVERT: B 81 TRP cc_start: 0.8613 (m-10) cc_final: 0.8302 (m-10) REVERT: I 81 TRP cc_start: 0.6845 (m-10) cc_final: 0.5826 (m100) REVERT: G 122 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8056 (p) REVERT: C 81 TRP cc_start: 0.8784 (m-10) cc_final: 0.8401 (m-10) REVERT: E 81 TRP cc_start: 0.8870 (m-10) cc_final: 0.8607 (m-10) outliers start: 28 outliers final: 21 residues processed: 114 average time/residue: 0.1134 time to fit residues: 18.2019 Evaluate side-chains 129 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain H residue 109 MET 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 129 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain I residue 103 SER 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 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 Chi-restraints excluded: chain E residue 141 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 GLN ** 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 85 HIS ** 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 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 = 0.4436 r_free = 0.4436 target = 0.146273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.138001 restraints weight = 8985.224| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 3.21 r_work: 0.4244 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 4530 Z= 0.442 Angle : 0.801 10.313 6110 Z= 0.404 Chirality : 0.047 0.150 560 Planarity : 0.005 0.030 800 Dihedral : 4.992 14.772 630 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 15.00 % Favored : 84.67 % Rotamer: Outliers : 6.92 % Allowed : 19.23 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.18 (0.20), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.15), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP G 99 HIS 0.005 0.001 HIS A 85 PHE 0.014 0.002 PHE E 141 TYR 0.022 0.003 TYR G 128 ARG 0.003 0.001 ARG J 136 *********************** 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 136 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.447 Fit side-chains REVERT: H 122 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8234 (p) REVERT: D 81 TRP cc_start: 0.8783 (m-10) cc_final: 0.8489 (m-10) REVERT: B 81 TRP cc_start: 0.8653 (m-10) cc_final: 0.8328 (m-10) REVERT: F 128 TYR cc_start: 0.9065 (m-80) cc_final: 0.8642 (m-10) REVERT: I 81 TRP cc_start: 0.7090 (m-10) cc_final: 0.5711 (m100) REVERT: G 122 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8239 (p) REVERT: C 81 TRP cc_start: 0.8809 (m-10) cc_final: 0.8443 (m-10) REVERT: E 85 HIS cc_start: 0.8343 (m90) cc_final: 0.7976 (m90) REVERT: E 128 TYR cc_start: 0.9080 (m-80) cc_final: 0.8642 (m-10) outliers start: 27 outliers final: 21 residues processed: 115 average time/residue: 0.1047 time to fit residues: 16.9414 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 : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 122 VAL 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 B residue 129 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain I residue 103 SER 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 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 Chi-restraints excluded: chain E residue 141 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 0.0570 overall best weight: 3.4106 ------------------------------------------------------------------------------- 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 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** 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 = 0.4501 r_free = 0.4501 target = 0.152064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.143446 restraints weight = 8750.598| |-----------------------------------------------------------------------------| r_work (start): 0.4409 rms_B_bonded: 3.23 r_work: 0.4308 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.6682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4530 Z= 0.256 Angle : 0.692 8.160 6110 Z= 0.342 Chirality : 0.045 0.130 560 Planarity : 0.004 0.033 800 Dihedral : 4.563 13.479 630 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 5.64 % Allowed : 20.26 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.17 (0.20), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.15), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 99 HIS 0.003 0.001 HIS I 85 PHE 0.008 0.001 PHE E 141 TYR 0.025 0.003 TYR H 128 ARG 0.002 0.001 ARG I 136 ********************** 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 130 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.437 Fit side-chains REVERT: H 100 ASN cc_start: 0.9033 (t0) cc_final: 0.8507 (t0) REVERT: H 122 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8089 (p) REVERT: D 81 TRP cc_start: 0.8742 (m-10) cc_final: 0.8452 (m-10) REVERT: B 81 TRP cc_start: 0.8615 (m-10) cc_final: 0.8317 (m-10) REVERT: I 81 TRP cc_start: 0.6880 (m-10) cc_final: 0.5830 (m100) REVERT: G 100 ASN cc_start: 0.9024 (t0) cc_final: 0.8476 (t0) REVERT: G 122 VAL cc_start: 0.8669 (OUTLIER) cc_final: 0.8058 (p) REVERT: C 81 TRP cc_start: 0.8751 (m-10) cc_final: 0.8436 (m-10) outliers start: 22 outliers final: 20 residues processed: 113 average time/residue: 0.1188 time to fit residues: 18.9164 Evaluate side-chains 127 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 122 VAL 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 129 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain I residue 103 SER 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 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 Chi-restraints excluded: chain E residue 141 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 58 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 33 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** 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 = 0.4420 r_free = 0.4420 target = 0.144896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.136687 restraints weight = 9131.575| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 3.22 r_work: 0.4233 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.6672 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= 0.486 Angle : 0.833 7.125 6110 Z= 0.425 Chirality : 0.048 0.141 560 Planarity : 0.005 0.029 800 Dihedral : 5.086 14.638 630 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.33 % Allowed : 15.83 % Favored : 83.83 % Rotamer: Outliers : 6.15 % Allowed : 20.51 % 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 (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: -5.30 (0.19), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.15), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP G 99 HIS 0.006 0.001 HIS A 85 PHE 0.014 0.002 PHE E 141 TYR 0.021 0.003 TYR H 128 ARG 0.004 0.001 ARG J 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1772.21 seconds wall clock time: 31 minutes 46.34 seconds (1906.34 seconds total)