Starting phenix.real_space_refine on Sun Dec 10 06:31:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l08_8300/12_2023/5l08_8300.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l08_8300/12_2023/5l08_8300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l08_8300/12_2023/5l08_8300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l08_8300/12_2023/5l08_8300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l08_8300/12_2023/5l08_8300.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l08_8300/12_2023/5l08_8300.pdb" } resolution = 4.6 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 ------------------------------------------------------------------------------- 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= -31.220 sd= 18.086 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 72 5.16 5 C 8658 2.51 5 N 2286 2.21 5 O 2601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 56": "OE1" <-> "OE2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "F GLU 12": "OE1" <-> "OE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "G GLU 50": "OE1" <-> "OE2" Residue "G GLU 85": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13617 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "B" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "C" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "D" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "E" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "F" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "G" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "H" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "I" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Time building chain proxies: 7.50, per 1000 atoms: 0.55 Number of scatterers: 13617 At special positions: 0 Unit cell: (102.92, 103.54, 125.24, 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 72 16.00 O 2601 8.00 N 2286 7.00 C 8658 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: 5.25 Conformation dependent library (CDL) restraints added in 2.2 seconds 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3186 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 0 sheets defined 75.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 8 through 13 removed outlier: 3.655A pdb=" N GLY A 11 " --> pdb=" O TYR A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 27 Processing helix chain 'A' and resid 40 through 51 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 82 through 91 removed outlier: 3.619A pdb=" N ARG A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 removed outlier: 3.603A pdb=" N VAL A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 128 Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 159 through 168 removed outlier: 4.294A pdb=" N VAL A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 178 removed outlier: 3.990A pdb=" N LYS A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'B' and resid 2 through 2 No H-bonds generated for 'chain 'B' and resid 2 through 2' Processing helix chain 'B' and resid 3 through 12 removed outlier: 3.807A pdb=" N ASP B 9 " --> pdb=" O ARG B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 40 through 51 Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.535A pdb=" N ILE B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 99 through 111 Processing helix chain 'B' and resid 113 through 128 removed outlier: 4.761A pdb=" N GLU B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 156 through 159 Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'C' and resid 3 through 6 Processing helix chain 'C' and resid 7 through 12 removed outlier: 3.874A pdb=" N GLY C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 12 " --> pdb=" O TYR C 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 12' Processing helix chain 'C' and resid 15 through 27 Processing helix chain 'C' and resid 40 through 51 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 83 through 91 removed outlier: 4.117A pdb=" N GLU C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 115 through 128 removed outlier: 3.972A pdb=" N SER C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 156 through 165 removed outlier: 3.685A pdb=" N LYS C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 8 through 14 removed outlier: 4.576A pdb=" N GLY D 11 " --> pdb=" O TYR D 8 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU D 12 " --> pdb=" O ASP D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 27 through 29 No H-bonds generated for 'chain 'D' and resid 27 through 29' Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 40 through 51 Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 71 through 78 removed outlier: 3.520A pdb=" N LEU D 75 " --> pdb=" O ARG D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 113 through 128 Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 156 through 166 removed outlier: 3.525A pdb=" N LEU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 removed outlier: 3.719A pdb=" N LEU D 172 " --> pdb=" O ASN D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'E' and resid 2 through 2 No H-bonds generated for 'chain 'E' and resid 2 through 2' Processing helix chain 'E' and resid 3 through 12 removed outlier: 3.844A pdb=" N ASP E 9 " --> pdb=" O ARG E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 27 Processing helix chain 'E' and resid 40 through 51 Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 71 through 78 Processing helix chain 'E' and resid 83 through 90 Processing helix chain 'E' and resid 99 through 112 Processing helix chain 'E' and resid 113 through 128 Processing helix chain 'E' and resid 138 through 149 Processing helix chain 'E' and resid 156 through 166 removed outlier: 3.605A pdb=" N LEU E 160 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 177 removed outlier: 3.796A pdb=" N LEU E 172 " --> pdb=" O ASN E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'F' and resid 2 through 2 No H-bonds generated for 'chain 'F' and resid 2 through 2' Processing helix chain 'F' and resid 3 through 12 Processing helix chain 'F' and resid 15 through 26 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 40 through 51 Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 71 through 76 Processing helix chain 'F' and resid 82 through 88 removed outlier: 3.576A pdb=" N MET F 86 " --> pdb=" O ARG F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 92 removed outlier: 3.655A pdb=" N THR F 92 " --> pdb=" O GLU F 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 89 through 92' Processing helix chain 'F' and resid 99 through 112 Processing helix chain 'F' and resid 113 through 128 Processing helix chain 'F' and resid 138 through 149 Processing helix chain 'F' and resid 156 through 166 removed outlier: 4.166A pdb=" N LEU F 160 " --> pdb=" O LYS F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 170 removed outlier: 6.968A pdb=" N SER F 170 " --> pdb=" O ILE F 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 167 through 170' Processing helix chain 'F' and resid 171 through 176 Processing helix chain 'F' and resid 177 through 182 Processing helix chain 'G' and resid 2 through 2 No H-bonds generated for 'chain 'G' and resid 2 through 2' Processing helix chain 'G' and resid 3 through 8 Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 15 through 26 Processing helix chain 'G' and resid 27 through 29 No H-bonds generated for 'chain 'G' and resid 27 through 29' Processing helix chain 'G' and resid 31 through 36 Processing helix chain 'G' and resid 40 through 51 removed outlier: 4.120A pdb=" N LYS G 51 " --> pdb=" O ARG G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 71 through 78 removed outlier: 3.579A pdb=" N LEU G 75 " --> pdb=" O ARG G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 90 removed outlier: 4.338A pdb=" N MET G 86 " --> pdb=" O ARG G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 112 Processing helix chain 'G' and resid 113 through 128 removed outlier: 3.518A pdb=" N SER G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 148 Processing helix chain 'G' and resid 153 through 157 Processing helix chain 'G' and resid 158 through 159 No H-bonds generated for 'chain 'G' and resid 158 through 159' Processing helix chain 'G' and resid 160 through 165 Processing helix chain 'G' and resid 168 through 176 removed outlier: 3.677A pdb=" N LEU G 172 " --> pdb=" O ASN G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 182 removed outlier: 4.692A pdb=" N GLU G 180 " --> pdb=" O ASP G 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 14 removed outlier: 3.861A pdb=" N TYR H 8 " --> pdb=" O SER H 4 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP H 9 " --> pdb=" O ARG H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 26 removed outlier: 4.064A pdb=" N ALA H 20 " --> pdb=" O SER H 16 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER H 21 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 29 No H-bonds generated for 'chain 'H' and resid 27 through 29' Processing helix chain 'H' and resid 31 through 36 Processing helix chain 'H' and resid 40 through 51 Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 71 through 78 removed outlier: 3.544A pdb=" N LEU H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 91 removed outlier: 3.675A pdb=" N GLU H 89 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 112 Processing helix chain 'H' and resid 113 through 128 Processing helix chain 'H' and resid 138 through 149 Processing helix chain 'H' and resid 156 through 159 Processing helix chain 'H' and resid 160 through 165 Processing helix chain 'H' and resid 168 through 176 removed outlier: 3.609A pdb=" N LEU H 172 " --> pdb=" O ASN H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 182 Processing helix chain 'I' and resid 2 through 8 removed outlier: 3.537A pdb=" N TYR I 8 " --> pdb=" O ARG I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 14 removed outlier: 4.169A pdb=" N GLN I 13 " --> pdb=" O ASP I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 26 Processing helix chain 'I' and resid 27 through 29 No H-bonds generated for 'chain 'I' and resid 27 through 29' Processing helix chain 'I' and resid 31 through 36 Processing helix chain 'I' and resid 40 through 51 Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 71 through 77 removed outlier: 3.975A pdb=" N ILE I 76 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 91 Processing helix chain 'I' and resid 99 through 112 Processing helix chain 'I' and resid 116 through 128 Processing helix chain 'I' and resid 138 through 149 Processing helix chain 'I' and resid 156 through 159 Processing helix chain 'I' and resid 160 through 165 Processing helix chain 'I' and resid 168 through 176 removed outlier: 3.613A pdb=" N LEU I 172 " --> pdb=" O ASN I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 182 668 hydrogen bonds defined for protein. 1806 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: 3.60 Time building geometry restraints manager: 5.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2473 1.31 - 1.44: 3098 1.44 - 1.56: 8073 1.56 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 13770 Sorted by residual: bond pdb=" C TYR E 8 " pdb=" O TYR E 8 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.15e-02 7.56e+03 1.67e+01 bond pdb=" C TYR B 8 " pdb=" O TYR B 8 " ideal model delta sigma weight residual 1.236 1.190 0.047 1.15e-02 7.56e+03 1.67e+01 bond pdb=" C TYR H 8 " pdb=" O TYR H 8 " ideal model delta sigma weight residual 1.236 1.190 0.047 1.15e-02 7.56e+03 1.66e+01 bond pdb=" C TYR F 8 " pdb=" O TYR F 8 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.15e-02 7.56e+03 1.61e+01 bond pdb=" C TYR C 8 " pdb=" O TYR C 8 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.15e-02 7.56e+03 1.58e+01 ... (remaining 13765 not shown) Histogram of bond angle deviations from ideal: 100.85 - 108.00: 180 108.00 - 115.14: 8414 115.14 - 122.29: 7333 122.29 - 129.43: 2478 129.43 - 136.58: 9 Bond angle restraints: 18414 Sorted by residual: angle pdb=" C GLU F 36 " pdb=" N PRO F 37 " pdb=" CA PRO F 37 " ideal model delta sigma weight residual 120.83 114.92 5.91 1.02e+00 9.61e-01 3.35e+01 angle pdb=" O LEU H 7 " pdb=" C LEU H 7 " pdb=" N TYR H 8 " ideal model delta sigma weight residual 122.12 127.51 -5.39 1.06e+00 8.90e-01 2.59e+01 angle pdb=" O LEU E 7 " pdb=" C LEU E 7 " pdb=" N TYR E 8 " ideal model delta sigma weight residual 122.12 127.46 -5.34 1.06e+00 8.90e-01 2.54e+01 angle pdb=" O LEU F 7 " pdb=" C LEU F 7 " pdb=" N TYR F 8 " ideal model delta sigma weight residual 122.12 127.45 -5.33 1.06e+00 8.90e-01 2.53e+01 angle pdb=" O LEU B 7 " pdb=" C LEU B 7 " pdb=" N TYR B 8 " ideal model delta sigma weight residual 122.12 127.43 -5.31 1.06e+00 8.90e-01 2.51e+01 ... (remaining 18409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 8342 17.69 - 35.37: 253 35.37 - 53.06: 95 53.06 - 70.75: 39 70.75 - 88.44: 10 Dihedral angle restraints: 8739 sinusoidal: 3879 harmonic: 4860 Sorted by residual: dihedral pdb=" CB GLU F 55 " pdb=" CG GLU F 55 " pdb=" CD GLU F 55 " pdb=" OE1 GLU F 55 " ideal model delta sinusoidal sigma weight residual 0.00 88.44 -88.44 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA ASP C 15 " pdb=" CB ASP C 15 " pdb=" CG ASP C 15 " pdb=" OD1 ASP C 15 " ideal model delta sinusoidal sigma weight residual -30.00 -84.87 54.87 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CB GLU A 89 " pdb=" CG GLU A 89 " pdb=" CD GLU A 89 " pdb=" OE1 GLU A 89 " ideal model delta sinusoidal sigma weight residual 0.00 86.06 -86.06 1 3.00e+01 1.11e-03 9.93e+00 ... (remaining 8736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1200 0.028 - 0.055: 343 0.055 - 0.083: 86 0.083 - 0.110: 352 0.110 - 0.138: 89 Chirality restraints: 2070 Sorted by residual: chirality pdb=" CA VAL C 150 " pdb=" N VAL C 150 " pdb=" C VAL C 150 " pdb=" CB VAL C 150 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA VAL H 150 " pdb=" N VAL H 150 " pdb=" C VAL H 150 " pdb=" CB VAL H 150 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA VAL E 150 " pdb=" N VAL E 150 " pdb=" C VAL E 150 " pdb=" CB VAL E 150 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 2067 not shown) Planarity restraints: 2367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 32 " 0.014 2.00e-02 2.50e+03 3.00e-02 9.02e+00 pdb=" C GLN F 32 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN F 32 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG F 33 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 32 " 0.014 2.00e-02 2.50e+03 2.99e-02 8.93e+00 pdb=" C GLN A 32 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN A 32 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 33 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 32 " -0.014 2.00e-02 2.50e+03 2.99e-02 8.91e+00 pdb=" C GLN B 32 " 0.052 2.00e-02 2.50e+03 pdb=" O GLN B 32 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG B 33 " -0.018 2.00e-02 2.50e+03 ... (remaining 2364 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 102 2.61 - 3.18: 13739 3.18 - 3.76: 20829 3.76 - 4.33: 32333 4.33 - 4.90: 48222 Nonbonded interactions: 115225 Sorted by model distance: nonbonded pdb=" CE1 PHE A 122 " pdb=" O LEU B 42 " model vdw 2.041 3.340 nonbonded pdb=" O GLU F 127 " pdb=" CG1 ILE F 128 " model vdw 2.236 3.440 nonbonded pdb=" O ARG F 118 " pdb=" CD2 PHE F 122 " model vdw 2.239 3.340 nonbonded pdb=" O GLU C 127 " pdb=" CG1 ILE C 128 " model vdw 2.257 3.440 nonbonded pdb=" O GLU A 127 " pdb=" CG1 ILE A 128 " model vdw 2.259 3.440 ... (remaining 115220 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' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.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' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.150 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 36.840 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.070 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 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 : 0.011 0.053 13770 Z= 0.694 Angle : 1.031 11.579 18414 Z= 0.757 Chirality : 0.051 0.138 2070 Planarity : 0.003 0.030 2367 Dihedral : 11.660 88.436 5553 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.04 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: -0.41 (0.22), residues: 1611 helix: -1.38 (0.15), residues: 952 sheet: None (None), residues: 0 loop : 1.97 (0.29), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE F 45 TYR 0.007 0.000 TYR D 29 ARG 0.003 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2129 time to fit residues: 24.4185 Evaluate side-chains 68 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.172 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.0070 chunk 122 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 82 optimal weight: 0.0270 chunk 65 optimal weight: 2.9990 chunk 126 optimal weight: 30.0000 chunk 49 optimal weight: 20.0000 chunk 77 optimal weight: 0.7980 chunk 94 optimal weight: 20.0000 chunk 147 optimal weight: 0.9980 overall best weight: 0.9658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 1.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 13770 Z= 0.395 Angle : 1.209 15.262 18414 Z= 0.626 Chirality : 0.061 0.332 2070 Planarity : 0.013 0.171 2367 Dihedral : 7.108 21.781 1800 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 35.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.74 % Allowed : 4.07 % Favored : 94.19 % 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: -1.86 (0.19), residues: 1611 helix: -1.60 (0.13), residues: 1179 sheet: None (None), residues: 0 loop : 0.58 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.002 PHE G 120 TYR 0.018 0.003 TYR F 106 ARG 0.009 0.001 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 115 average time/residue: 0.1990 time to fit residues: 24.6885 Evaluate side-chains 84 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.188 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 0.0970 chunk 45 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 147 optimal weight: 8.9990 chunk 159 optimal weight: 0.0670 chunk 131 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 chunk 50 optimal weight: 0.0470 chunk 118 optimal weight: 0.0370 overall best weight: 0.1692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN F 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 1.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13770 Z= 0.348 Angle : 1.144 11.623 18414 Z= 0.596 Chirality : 0.058 0.237 2070 Planarity : 0.008 0.083 2367 Dihedral : 7.108 26.766 1800 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 40.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.16 % Allowed : 6.98 % Favored : 91.86 % 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: -2.45 (0.20), residues: 1611 helix: -1.94 (0.14), residues: 1134 sheet: None (None), residues: 0 loop : -0.18 (0.31), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.003 PHE C 122 TYR 0.035 0.004 TYR G 8 ARG 0.006 0.001 ARG E 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 97 average time/residue: 0.1865 time to fit residues: 19.5937 Evaluate side-chains 75 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.168 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 8.9990 chunk 110 optimal weight: 0.0670 chunk 76 optimal weight: 20.0000 chunk 16 optimal weight: 0.0270 chunk 70 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 42 optimal weight: 0.0470 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 1.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13770 Z= 0.307 Angle : 1.069 9.958 18414 Z= 0.558 Chirality : 0.058 0.181 2070 Planarity : 0.011 0.141 2367 Dihedral : 6.956 23.981 1800 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 40.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % 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: -2.20 (0.21), residues: 1611 helix: -1.96 (0.14), residues: 1143 sheet: None (None), residues: 0 loop : 0.58 (0.34), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.003 PHE A 24 TYR 0.024 0.003 TYR B 8 ARG 0.006 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1906 time to fit residues: 18.8633 Evaluate side-chains 66 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.186 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 20.0000 chunk 88 optimal weight: 0.0470 chunk 2 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 108 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 79 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 39 optimal weight: 0.0980 overall best weight: 4.2284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 1.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13770 Z= 0.304 Angle : 1.031 10.032 18414 Z= 0.531 Chirality : 0.053 0.165 2070 Planarity : 0.007 0.062 2367 Dihedral : 6.561 25.360 1800 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 37.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % 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: -1.69 (0.22), residues: 1611 helix: -1.51 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : 0.64 (0.35), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHE E 24 TYR 0.015 0.002 TYR H 78 ARG 0.017 0.002 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2261 time to fit residues: 23.2935 Evaluate side-chains 73 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.203 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 8.9990 chunk 141 optimal weight: 30.0000 chunk 30 optimal weight: 0.0070 chunk 91 optimal weight: 0.0370 chunk 38 optimal weight: 0.0670 chunk 156 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 72 optimal weight: 40.0000 chunk 13 optimal weight: 0.0770 chunk 51 optimal weight: 30.0000 chunk 82 optimal weight: 5.9990 overall best weight: 0.6374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 1.6332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13770 Z= 0.386 Angle : 1.124 10.188 18414 Z= 0.580 Chirality : 0.056 0.174 2070 Planarity : 0.008 0.083 2367 Dihedral : 7.035 28.467 1800 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 40.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % 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: -2.31 (0.20), residues: 1611 helix: -1.91 (0.14), residues: 1143 sheet: None (None), residues: 0 loop : 0.14 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHE G 120 TYR 0.032 0.004 TYR G 178 ARG 0.013 0.002 ARG I 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2084 time to fit residues: 17.9801 Evaluate side-chains 62 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.188 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 87 optimal weight: 0.0170 chunk 156 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 95 optimal weight: 0.0270 chunk 72 optimal weight: 50.0000 overall best weight: 1.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 ASN ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 1.6749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13770 Z= 0.322 Angle : 1.121 11.201 18414 Z= 0.591 Chirality : 0.051 0.165 2070 Planarity : 0.006 0.041 2367 Dihedral : 7.096 26.121 1800 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 36.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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: -2.44 (0.20), residues: 1611 helix: -2.00 (0.12), residues: 1125 sheet: None (None), residues: 0 loop : -0.02 (0.33), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE H 24 TYR 0.017 0.003 TYR C 78 ARG 0.015 0.002 ARG D 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1930 time to fit residues: 17.0545 Evaluate side-chains 64 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.163 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 0.0270 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 30 optimal weight: 20.0000 chunk 99 optimal weight: 30.0000 chunk 106 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 142 optimal weight: 20.0000 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 1.7274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13770 Z= 0.353 Angle : 1.195 12.538 18414 Z= 0.596 Chirality : 0.056 0.202 2070 Planarity : 0.006 0.048 2367 Dihedral : 7.451 28.749 1800 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 38.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.58 % Allowed : 2.91 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.20), residues: 1611 helix: -2.07 (0.13), residues: 1161 sheet: None (None), residues: 0 loop : 0.05 (0.35), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.003 PHE H 181 TYR 0.017 0.002 TYR D 78 ARG 0.009 0.001 ARG G 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.2028 time to fit residues: 18.7008 Evaluate side-chains 66 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.236 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 30.0000 chunk 136 optimal weight: 20.0000 chunk 145 optimal weight: 4.9990 chunk 87 optimal weight: 40.0000 chunk 63 optimal weight: 50.0000 chunk 114 optimal weight: 0.2980 chunk 44 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 137 optimal weight: 0.3980 chunk 144 optimal weight: 30.0000 chunk 95 optimal weight: 0.0040 overall best weight: 2.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 GLN E 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 1.7782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13770 Z= 0.371 Angle : 1.178 12.012 18414 Z= 0.604 Chirality : 0.058 0.197 2070 Planarity : 0.007 0.047 2367 Dihedral : 7.449 25.942 1800 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 39.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: -2.65 (0.19), residues: 1611 helix: -2.10 (0.13), residues: 1134 sheet: None (None), residues: 0 loop : -0.23 (0.32), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.003 PHE G 122 TYR 0.024 0.003 TYR F 78 ARG 0.019 0.003 ARG G 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1814 time to fit residues: 15.6308 Evaluate side-chains 59 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.186 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 0.6980 chunk 93 optimal weight: 0.2980 chunk 72 optimal weight: 40.0000 chunk 106 optimal weight: 2.9990 chunk 161 optimal weight: 0.4980 chunk 148 optimal weight: 20.0000 chunk 128 optimal weight: 0.0670 chunk 13 optimal weight: 30.0000 chunk 99 optimal weight: 0.0370 chunk 78 optimal weight: 30.0000 chunk 102 optimal weight: 4.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 1.8407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13770 Z= 0.306 Angle : 1.164 12.993 18414 Z= 0.582 Chirality : 0.058 0.185 2070 Planarity : 0.007 0.047 2367 Dihedral : 7.578 28.309 1800 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 39.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.84 (0.19), residues: 1611 helix: -2.31 (0.12), residues: 1170 sheet: None (None), residues: 0 loop : 0.15 (0.34), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE F 24 TYR 0.020 0.003 TYR H 78 ARG 0.017 0.002 ARG H 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1928 time to fit residues: 17.5920 Evaluate side-chains 60 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.182 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 18 optimal weight: 30.0000 chunk 35 optimal weight: 30.0000 chunk 128 optimal weight: 7.9990 chunk 53 optimal weight: 30.0000 chunk 132 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 113 optimal weight: 0.9980 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.133499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.113289 restraints weight = 4960.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.115953 restraints weight = 3546.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.117613 restraints weight = 2736.298| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 1.8692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 13770 Z= 0.371 Angle : 1.231 11.459 18414 Z= 0.623 Chirality : 0.062 0.262 2070 Planarity : 0.009 0.084 2367 Dihedral : 7.584 27.076 1800 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 43.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -2.70 (0.20), residues: 1611 helix: -2.24 (0.12), residues: 1179 sheet: None (None), residues: 0 loop : 0.37 (0.36), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.004 PHE A 67 TYR 0.020 0.002 TYR I 78 ARG 0.016 0.002 ARG C 71 =============================================================================== Job complete usr+sys time: 2494.09 seconds wall clock time: 46 minutes 13.74 seconds (2773.74 seconds total)