Starting phenix.real_space_refine on Sun Mar 10 19:36:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umq_26607/03_2024/7umq_26607.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umq_26607/03_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_26607/03_2024/7umq_26607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umq_26607/03_2024/7umq_26607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umq_26607/03_2024/7umq_26607.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umq_26607/03_2024/7umq_26607.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4380 Number of models: 1 Model: "" Number of chains: 10 Chain: "J" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "H" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "D" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "B" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "F" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "I" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} 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} Chain: "E" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Time building chain proxies: 2.74, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 1.75 Conformation dependent library (CDL) restraints added in 772.7 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: 0.65 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: 1.12 Time building geometry restraints manager: 1.89 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: 98.29 - 105.45: 190 105.45 - 112.62: 2086 112.62 - 119.78: 1831 119.78 - 126.95: 1863 126.95 - 134.11: 140 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 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: 0.010 Extract box with map and model: 3.040 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.610 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.450 ------------------------------------------------------------------------------- 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 : 0.524 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: 0.1534 time to fit residues: 32.9566 Evaluate side-chains 110 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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: 5.9990 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 100 ASN ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4256 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= 0.374 Angle : 0.794 4.550 6110 Z= 0.413 Chirality : 0.045 0.157 560 Planarity : 0.004 0.052 800 Dihedral : 5.116 14.101 630 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.50 % Favored : 92.33 % Rotamer: Outliers : 4.87 % Allowed : 11.03 % Favored : 84.10 % 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: -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 0.025 0.003 TRP B 81 HIS 0.004 0.001 HIS C 111 PHE 0.008 0.002 PHE D 141 TYR 0.006 0.002 TYR F 128 ARG 0.005 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 151 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 141 PHE cc_start: 0.6417 (t80) cc_final: 0.6048 (p90) REVERT: I 141 PHE cc_start: 0.6506 (t80) cc_final: 0.6035 (p90) outliers start: 19 outliers final: 14 residues processed: 134 average time/residue: 0.0954 time to fit residues: 18.1803 Evaluate side-chains 127 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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: 20.0000 chunk 45 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- 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** J 140 HIS 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 140 HIS F 140 HIS ** I 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 HIS G 140 HIS ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS E 140 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 4530 Z= 0.562 Angle : 0.894 7.965 6110 Z= 0.461 Chirality : 0.047 0.163 560 Planarity : 0.005 0.035 800 Dihedral : 5.717 17.217 630 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.67 % Favored : 86.17 % Rotamer: Outliers : 8.21 % Allowed : 18.21 % Favored : 73.59 % 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 (0.18), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP A 81 HIS 0.006 0.002 HIS J 85 PHE 0.014 0.004 PHE E 141 TYR 0.009 0.002 TYR G 128 ARG 0.005 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 158 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 0.467 Fit side-chains REVERT: J 81 TRP cc_start: 0.5720 (OUTLIER) cc_final: 0.4509 (m100) REVERT: J 141 PHE cc_start: 0.7062 (OUTLIER) cc_final: 0.6068 (p90) REVERT: I 81 TRP cc_start: 0.5436 (OUTLIER) cc_final: 0.4384 (m100) REVERT: I 141 PHE cc_start: 0.7011 (OUTLIER) cc_final: 0.6127 (p90) REVERT: A 134 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6793 (mtt) outliers start: 32 outliers final: 20 residues processed: 130 average time/residue: 0.1203 time to fit residues: 21.0617 Evaluate side-chains 133 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 28 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** B 83 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4530 Z= 0.281 Angle : 0.700 7.066 6110 Z= 0.349 Chirality : 0.043 0.118 560 Planarity : 0.004 0.024 800 Dihedral : 4.845 14.043 630 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 7.95 % Allowed : 20.51 % 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: -4.44 (0.22), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.17), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 81 HIS 0.004 0.001 HIS J 85 PHE 0.007 0.002 PHE E 141 TYR 0.028 0.003 TYR H 128 ARG 0.006 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: 31 poor density : 118 time to evaluate : 0.524 Fit side-chains REVERT: J 81 TRP cc_start: 0.5403 (OUTLIER) cc_final: 0.4161 (m100) REVERT: J 141 PHE cc_start: 0.6834 (OUTLIER) cc_final: 0.6079 (p90) REVERT: I 81 TRP cc_start: 0.5398 (OUTLIER) cc_final: 0.4268 (m100) REVERT: I 141 PHE cc_start: 0.6930 (OUTLIER) cc_final: 0.6229 (p90) outliers start: 31 outliers final: 20 residues processed: 122 average time/residue: 0.1070 time to fit residues: 18.2480 Evaluate side-chains 132 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 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 95 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 125 LEU 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: 10.0000 chunk 49 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 overall best weight: 6.9788 ------------------------------------------------------------------------------- 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** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.6069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4530 Z= 0.450 Angle : 0.804 6.486 6110 Z= 0.409 Chirality : 0.046 0.167 560 Planarity : 0.004 0.024 800 Dihedral : 5.179 14.794 630 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.50 % Favored : 85.50 % Rotamer: Outliers : 7.69 % Allowed : 22.05 % 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: -4.68 (0.22), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.16), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP H 99 HIS 0.008 0.002 HIS E 85 PHE 0.012 0.002 PHE E 141 TYR 0.024 0.003 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 142 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 112 time to evaluate : 0.484 Fit side-chains REVERT: J 81 TRP cc_start: 0.5422 (OUTLIER) cc_final: 0.4407 (m100) REVERT: J 141 PHE cc_start: 0.7012 (OUTLIER) cc_final: 0.6153 (p90) REVERT: I 81 TRP cc_start: 0.5376 (OUTLIER) cc_final: 0.3675 (m100) REVERT: I 141 PHE cc_start: 0.6981 (OUTLIER) cc_final: 0.6135 (p90) outliers start: 30 outliers final: 20 residues processed: 116 average time/residue: 0.0976 time to fit residues: 16.0704 Evaluate side-chains 128 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 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 125 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 125 LEU 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 121 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 125 LEU 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: 9.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 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** ** I 111 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 4530 Z= 0.514 Angle : 0.856 5.529 6110 Z= 0.439 Chirality : 0.047 0.171 560 Planarity : 0.004 0.022 800 Dihedral : 5.409 15.462 630 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.83 % Favored : 86.17 % Rotamer: Outliers : 8.72 % Allowed : 20.26 % Favored : 71.03 % 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: -4.98 (0.21), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.16), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP D 99 HIS 0.008 0.002 HIS E 85 PHE 0.014 0.003 PHE E 141 TYR 0.025 0.004 TYR F 128 ARG 0.004 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 142 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 108 time to evaluate : 0.493 Fit side-chains REVERT: J 81 TRP cc_start: 0.5491 (OUTLIER) cc_final: 0.4368 (m100) REVERT: J 141 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.6186 (p90) REVERT: I 81 TRP cc_start: 0.5325 (OUTLIER) cc_final: 0.4353 (m100) REVERT: I 141 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6174 (p90) outliers start: 34 outliers final: 25 residues processed: 116 average time/residue: 0.0976 time to fit residues: 16.0614 Evaluate side-chains 126 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 121 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 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 121 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 125 LEU 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: 8.9990 chunk 48 optimal weight: 8.9990 chunk 57 optimal weight: 30.0000 chunk 36 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.6440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4530 Z= 0.419 Angle : 0.789 5.893 6110 Z= 0.400 Chirality : 0.046 0.188 560 Planarity : 0.004 0.026 800 Dihedral : 5.106 15.172 630 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.33 % Favored : 86.50 % Rotamer: Outliers : 7.44 % Allowed : 23.08 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.033 0.003 TRP C 99 HIS 0.006 0.001 HIS F 85 PHE 0.014 0.002 PHE E 141 TYR 0.039 0.005 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 131 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 0.486 Fit side-chains REVERT: J 81 TRP cc_start: 0.5443 (OUTLIER) cc_final: 0.3668 (m100) REVERT: J 141 PHE cc_start: 0.6971 (OUTLIER) cc_final: 0.6201 (p90) REVERT: B 112 MET cc_start: 0.7550 (mpp) cc_final: 0.6627 (mpp) REVERT: I 81 TRP cc_start: 0.5278 (OUTLIER) cc_final: 0.3539 (m100) REVERT: I 141 PHE cc_start: 0.7013 (OUTLIER) cc_final: 0.6187 (p90) REVERT: A 112 MET cc_start: 0.7556 (mpp) cc_final: 0.6634 (mpp) outliers start: 29 outliers final: 21 residues processed: 110 average time/residue: 0.0964 time to fit residues: 15.1672 Evaluate side-chains 123 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 141 PHE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain 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 109 MET 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 125 LEU 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 28 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 32 optimal weight: 0.0040 chunk 23 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 4.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4530 Z= 0.327 Angle : 0.734 10.118 6110 Z= 0.366 Chirality : 0.045 0.185 560 Planarity : 0.004 0.028 800 Dihedral : 4.827 15.177 630 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.50 % Favored : 88.33 % Rotamer: Outliers : 7.18 % Allowed : 24.10 % Favored : 68.72 % 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 (0.16), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 99 HIS 0.005 0.001 HIS F 85 PHE 0.010 0.002 PHE E 141 TYR 0.026 0.004 TYR F 128 ARG 0.002 0.001 ARG I 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 132 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 0.441 Fit side-chains REVERT: J 81 TRP cc_start: 0.5297 (OUTLIER) cc_final: 0.3686 (m100) REVERT: J 141 PHE cc_start: 0.6909 (OUTLIER) cc_final: 0.6193 (p90) REVERT: I 81 TRP cc_start: 0.5191 (OUTLIER) cc_final: 0.3501 (m100) REVERT: I 141 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.6146 (p90) outliers start: 28 outliers final: 17 residues processed: 112 average time/residue: 0.1016 time to fit residues: 15.8717 Evaluate side-chains 121 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 D residue 122 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain 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 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: 10.0000 chunk 50 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 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** ** I 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 4530 Z= 0.520 Angle : 0.864 7.716 6110 Z= 0.439 Chirality : 0.048 0.205 560 Planarity : 0.004 0.024 800 Dihedral : 5.314 15.766 630 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 0.33 % Allowed : 15.67 % Favored : 84.00 % Rotamer: Outliers : 6.67 % Allowed : 23.59 % 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: -5.25 (0.20), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.15), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP C 99 HIS 0.007 0.002 HIS F 85 PHE 0.016 0.003 PHE E 141 TYR 0.035 0.005 TYR H 128 ARG 0.004 0.001 ARG I 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 126 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 100 time to evaluate : 0.459 Fit side-chains REVERT: J 81 TRP cc_start: 0.5297 (OUTLIER) cc_final: 0.4467 (m100) REVERT: I 81 TRP cc_start: 0.5268 (OUTLIER) cc_final: 0.4508 (m100) outliers start: 26 outliers final: 20 residues processed: 111 average time/residue: 0.1107 time to fit residues: 17.3241 Evaluate side-chains 111 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 H residue 122 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain I residue 81 TRP 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 125 LEU 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: 5.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- 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** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.6683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4530 Z= 0.354 Angle : 0.767 10.922 6110 Z= 0.382 Chirality : 0.046 0.183 560 Planarity : 0.004 0.027 800 Dihedral : 4.954 15.041 630 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.00 % Favored : 88.83 % Rotamer: Outliers : 6.41 % Allowed : 24.36 % Favored : 69.23 % 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: -5.24 (0.20), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.15), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP G 99 HIS 0.005 0.001 HIS F 85 PHE 0.012 0.002 PHE E 141 TYR 0.031 0.006 TYR E 128 ARG 0.003 0.001 ARG J 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 123 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 0.478 Fit side-chains REVERT: J 81 TRP cc_start: 0.5210 (OUTLIER) cc_final: 0.3532 (m100) REVERT: H 100 ASN cc_start: 0.7768 (t0) cc_final: 0.7495 (t0) REVERT: I 81 TRP cc_start: 0.5195 (OUTLIER) cc_final: 0.3497 (m100) outliers start: 25 outliers final: 21 residues processed: 109 average time/residue: 0.1037 time to fit residues: 15.7506 Evaluate side-chains 118 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 H residue 109 MET Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain I residue 81 TRP 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 125 LEU 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 48 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 2 optimal weight: 0.0010 chunk 34 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 32 optimal weight: 0.0970 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.4592 r_free = 0.4592 target = 0.159512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.150521 restraints weight = 8396.571| |-----------------------------------------------------------------------------| r_work (start): 0.4517 rms_B_bonded: 3.24 r_work: 0.4418 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4530 Z= 0.171 Angle : 0.623 10.361 6110 Z= 0.301 Chirality : 0.044 0.189 560 Planarity : 0.004 0.034 800 Dihedral : 4.351 15.755 630 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 3.08 % Allowed : 27.18 % 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: -5.07 (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 0.013 0.001 TRP C 81 HIS 0.002 0.001 HIS F 85 PHE 0.004 0.001 PHE E 141 TYR 0.034 0.006 TYR E 128 ARG 0.001 0.000 ARG D 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1115.28 seconds wall clock time: 21 minutes 4.18 seconds (1264.18 seconds total)