Starting phenix.real_space_refine on Mon Sep 23 18:14:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umq_26607/09_2024/7umq_26607.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umq_26607/09_2024/7umq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umq_26607/09_2024/7umq_26607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umq_26607/09_2024/7umq_26607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umq_26607/09_2024/7umq_26607.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umq_26607/09_2024/7umq_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-5461/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: 1.79, per 1000 atoms: 0.41 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: 0.98 Conformation dependent library (CDL) restraints added in 609.1 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: 0.78 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: 1.11 Time building geometry restraints manager: 1.13 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.560 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.710 Find NCS groups from input model: 0.160 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.650 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.565 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: 0.1577 time to fit residues: 33.8096 Evaluate side-chains 110 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 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 fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 141 PHE cc_start: 0.6398 (t80) cc_final: 0.6014 (p90) REVERT: H 85 HIS cc_start: 0.7699 (m-70) cc_final: 0.7377 (m-70) REVERT: H 100 ASN cc_start: 0.7848 (t0) cc_final: 0.7617 (t0) REVERT: I 141 PHE cc_start: 0.6597 (t80) cc_final: 0.5934 (p90) REVERT: G 100 ASN cc_start: 0.7887 (t0) cc_final: 0.7668 (t0) outliers start: 17 outliers final: 14 residues processed: 134 average time/residue: 0.1077 time to fit residues: 20.1566 Evaluate side-chains 129 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 30 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 30.0000 chunk 37 optimal weight: 0.0370 chunk 15 optimal weight: 30.0000 chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 overall best weight: 6.2068 ------------------------------------------------------------------------------- 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** B 83 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN G 140 HIS ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 4530 Z= 0.414 Angle : 0.789 7.513 6110 Z= 0.406 Chirality : 0.044 0.162 560 Planarity : 0.005 0.032 800 Dihedral : 5.196 15.239 630 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 8.21 % Allowed : 15.38 % Favored : 76.41 % 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: -4.15 (0.23), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.17), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 99 HIS 0.006 0.001 HIS I 85 PHE 0.011 0.003 PHE J 141 TYR 0.011 0.002 TYR H 128 ARG 0.004 0.001 ARG I 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 155 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 123 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: J 81 TRP cc_start: 0.5603 (OUTLIER) cc_final: 0.4229 (m100) REVERT: J 141 PHE cc_start: 0.6997 (OUTLIER) cc_final: 0.6210 (p90) REVERT: I 81 TRP cc_start: 0.5516 (OUTLIER) cc_final: 0.4372 (m100) REVERT: I 141 PHE cc_start: 0.6885 (OUTLIER) cc_final: 0.6146 (p90) REVERT: A 134 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6551 (mtt) REVERT: E 81 TRP cc_start: 0.8168 (m-10) cc_final: 0.7935 (m-10) outliers start: 32 outliers final: 20 residues processed: 127 average time/residue: 0.1211 time to fit residues: 21.1668 Evaluate side-chains 138 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 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 81 TRP 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 41 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 48 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 140 HIS ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 HIS I 140 HIS ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4530 Z= 0.330 Angle : 0.725 6.736 6110 Z= 0.368 Chirality : 0.044 0.150 560 Planarity : 0.004 0.031 800 Dihedral : 4.901 14.274 630 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 7.69 % Allowed : 17.69 % Favored : 74.62 % 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: -4.32 (0.22), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.17), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 81 HIS 0.004 0.001 HIS I 85 PHE 0.008 0.002 PHE E 141 TYR 0.009 0.002 TYR G 128 ARG 0.008 0.001 ARG D 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 149 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 119 time to evaluate : 0.501 Fit side-chains REVERT: J 81 TRP cc_start: 0.5463 (OUTLIER) cc_final: 0.4142 (m100) REVERT: J 141 PHE cc_start: 0.6927 (OUTLIER) cc_final: 0.6148 (p90) REVERT: I 81 TRP cc_start: 0.5401 (OUTLIER) cc_final: 0.4396 (m100) REVERT: I 141 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6284 (p90) REVERT: A 134 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6849 (mtt) outliers start: 30 outliers final: 18 residues processed: 124 average time/residue: 0.1105 time to fit residues: 18.7137 Evaluate side-chains 135 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 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 141 PHE Chi-restraints excluded: chain I residue 81 TRP Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 141 PHE 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 0 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.6106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4530 Z= 0.328 Angle : 0.719 5.931 6110 Z= 0.365 Chirality : 0.044 0.152 560 Planarity : 0.004 0.033 800 Dihedral : 4.792 13.572 630 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 7.18 % Allowed : 20.00 % 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 (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: -4.56 (0.21), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.16), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 99 HIS 0.004 0.001 HIS A 85 PHE 0.008 0.002 PHE E 141 TYR 0.010 0.002 TYR J 128 ARG 0.003 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 148 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 0.514 Fit side-chains REVERT: J 81 TRP cc_start: 0.5402 (OUTLIER) cc_final: 0.4186 (m100) REVERT: J 141 PHE cc_start: 0.6981 (OUTLIER) cc_final: 0.6202 (p90) REVERT: H 112 MET cc_start: 0.8007 (mpp) cc_final: 0.7752 (mpp) REVERT: B 112 MET cc_start: 0.7741 (mpp) cc_final: 0.7348 (mpp) REVERT: I 81 TRP cc_start: 0.5503 (OUTLIER) cc_final: 0.3719 (m100) REVERT: I 141 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.6127 (p90) REVERT: G 112 MET cc_start: 0.7999 (mpp) cc_final: 0.7715 (mpp) REVERT: A 112 MET cc_start: 0.7713 (mpp) cc_final: 0.7337 (mpp) REVERT: A 134 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6608 (mtt) outliers start: 28 outliers final: 19 residues processed: 126 average time/residue: 0.0953 time to fit residues: 17.1644 Evaluate side-chains 137 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 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 81 TRP Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 141 PHE 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 14 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 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 83 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.6317 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= 0.390 Angle : 0.770 6.236 6110 Z= 0.392 Chirality : 0.046 0.175 560 Planarity : 0.004 0.033 800 Dihedral : 5.022 14.522 630 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.33 % Favored : 88.50 % Rotamer: Outliers : 8.21 % Allowed : 20.51 % 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 (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: -4.78 (0.21), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.16), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP H 99 HIS 0.005 0.001 HIS A 85 PHE 0.011 0.002 PHE E 141 TYR 0.010 0.002 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 146 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 114 time to evaluate : 0.484 Fit side-chains REVERT: J 81 TRP cc_start: 0.5430 (OUTLIER) cc_final: 0.4335 (m100) REVERT: J 141 PHE cc_start: 0.7011 (OUTLIER) cc_final: 0.6248 (p90) REVERT: D 112 MET cc_start: 0.8065 (mpp) cc_final: 0.7728 (mpp) REVERT: I 81 TRP cc_start: 0.5485 (OUTLIER) cc_final: 0.3724 (m100) REVERT: I 141 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.6126 (p90) REVERT: C 112 MET cc_start: 0.8086 (mpp) cc_final: 0.7723 (mpp) REVERT: A 134 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6708 (mtt) outliers start: 32 outliers final: 24 residues processed: 124 average time/residue: 0.1031 time to fit residues: 17.7263 Evaluate side-chains 139 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 130 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 81 TRP Chi-restraints excluded: chain I residue 103 SER 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 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 32 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 0.0870 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- 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** ** G 83 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.6497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4530 Z= 0.208 Angle : 0.634 5.590 6110 Z= 0.313 Chirality : 0.044 0.171 560 Planarity : 0.004 0.034 800 Dihedral : 4.427 12.044 630 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.00 % Favored : 89.83 % Rotamer: Outliers : 5.90 % Allowed : 22.82 % 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 (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: -4.73 (0.21), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.16), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 81 HIS 0.003 0.001 HIS I 85 PHE 0.005 0.001 PHE E 141 TYR 0.014 0.002 TYR J 128 ARG 0.002 0.000 ARG J 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 133 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 0.520 Fit side-chains REVERT: J 141 PHE cc_start: 0.6853 (OUTLIER) cc_final: 0.6284 (p90) REVERT: D 112 MET cc_start: 0.7942 (mpp) cc_final: 0.7690 (mpp) REVERT: I 141 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.6149 (p90) REVERT: C 112 MET cc_start: 0.7896 (mpp) cc_final: 0.7634 (mpp) outliers start: 23 outliers final: 19 residues processed: 119 average time/residue: 0.1078 time to fit residues: 17.6239 Evaluate side-chains 126 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 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 141 PHE Chi-restraints excluded: chain I residue 103 SER 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 45 optimal weight: 30.0000 chunk 52 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 83 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.6470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4530 Z= 0.374 Angle : 0.743 9.793 6110 Z= 0.373 Chirality : 0.045 0.154 560 Planarity : 0.004 0.031 800 Dihedral : 4.765 14.438 630 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.50 % Favored : 87.33 % Rotamer: Outliers : 6.41 % Allowed : 22.05 % 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 (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: -4.89 (0.21), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.16), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP H 99 HIS 0.005 0.001 HIS A 85 PHE 0.012 0.002 PHE E 141 TYR 0.011 0.002 TYR H 128 ARG 0.004 0.001 ARG E 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 133 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 0.591 Fit side-chains REVERT: J 141 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.6456 (p90) REVERT: D 112 MET cc_start: 0.7998 (mpp) cc_final: 0.7776 (mpp) REVERT: I 141 PHE cc_start: 0.6960 (OUTLIER) cc_final: 0.6146 (p90) outliers start: 25 outliers final: 20 residues processed: 115 average time/residue: 0.1292 time to fit residues: 20.6734 Evaluate side-chains 125 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 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 I residue 103 SER 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 141 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 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** ** G 85 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.6572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 4530 Z= 0.476 Angle : 0.830 10.622 6110 Z= 0.420 Chirality : 0.047 0.159 560 Planarity : 0.004 0.029 800 Dihedral : 5.141 15.601 630 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.00 % Favored : 87.67 % Rotamer: Outliers : 6.41 % Allowed : 21.54 % 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 (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 0.046 0.004 TRP G 99 HIS 0.007 0.001 HIS A 85 PHE 0.015 0.003 PHE E 141 TYR 0.011 0.002 TYR H 128 ARG 0.004 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 132 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.490 Fit side-chains REVERT: J 141 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6553 (p90) REVERT: H 100 ASN cc_start: 0.7854 (t0) cc_final: 0.7571 (t0) REVERT: I 141 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6068 (p90) outliers start: 25 outliers final: 20 residues processed: 115 average time/residue: 0.1131 time to fit residues: 18.0178 Evaluate side-chains 125 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 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 I residue 103 SER 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 141 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 30.0000 chunk 37 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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** ** 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** ** G 85 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.6636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 4530 Z= 0.502 Angle : 0.831 6.515 6110 Z= 0.428 Chirality : 0.048 0.162 560 Planarity : 0.005 0.032 800 Dihedral : 5.233 15.183 630 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.33 % Allowed : 14.67 % Favored : 85.00 % Rotamer: Outliers : 6.41 % Allowed : 23.33 % Favored : 70.26 % 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: -5.19 (0.20), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.15), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP G 99 HIS 0.007 0.001 HIS A 85 PHE 0.016 0.003 PHE E 141 TYR 0.009 0.002 TYR G 128 ARG 0.004 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 134 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 0.497 Fit side-chains REVERT: I 141 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.6053 (p90) outliers start: 25 outliers final: 19 residues processed: 117 average time/residue: 0.1152 time to fit residues: 18.4447 Evaluate side-chains 119 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 I residue 103 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 = 0.4524 r_free = 0.4524 target = 0.152622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.143976 restraints weight = 8609.336| |-----------------------------------------------------------------------------| r_work (start): 0.4442 rms_B_bonded: 3.27 r_work: 0.4338 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.6778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4530 Z= 0.245 Angle : 0.686 10.349 6110 Z= 0.339 Chirality : 0.045 0.145 560 Planarity : 0.004 0.031 800 Dihedral : 4.581 13.458 630 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 6.15 % Allowed : 24.10 % Favored : 69.74 % 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: -5.09 (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 TRP 0.025 0.002 TRP C 81 HIS 0.003 0.001 HIS A 85 PHE 0.006 0.001 PHE E 141 TYR 0.024 0.004 TYR E 128 ARG 0.002 0.001 ARG I 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1175.55 seconds wall clock time: 21 minutes 51.47 seconds (1311.47 seconds total)