Starting phenix.real_space_refine on Sat Mar 16 04:13:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l08_8300/03_2024/5l08_8300.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l08_8300/03_2024/5l08_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_8300/03_2024/5l08_8300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l08_8300/03_2024/5l08_8300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l08_8300/03_2024/5l08_8300.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l08_8300/03_2024/5l08_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.25, per 1000 atoms: 0.53 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: 5.07 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: 1.40 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: 3.29 Time building geometry restraints manager: 5.52 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: 0.260 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: 1.900 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 35.300 Find NCS groups from input model: 0.820 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.300 ------------------------------------------------------------------------------- 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 : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.7137 (mt) cc_final: 0.6885 (mt) REVERT: A 40 ASP cc_start: 0.8831 (p0) cc_final: 0.8541 (p0) REVERT: A 51 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8632 (mmtm) REVERT: A 61 PHE cc_start: 0.8366 (t80) cc_final: 0.7560 (t80) REVERT: A 62 LEU cc_start: 0.9136 (tp) cc_final: 0.8875 (tp) REVERT: A 69 ILE cc_start: 0.9271 (pt) cc_final: 0.9019 (mp) REVERT: A 74 LEU cc_start: 0.9180 (mt) cc_final: 0.8972 (mt) REVERT: A 97 GLN cc_start: 0.7430 (mm-40) cc_final: 0.7018 (mt0) REVERT: A 103 VAL cc_start: 0.8960 (p) cc_final: 0.8383 (m) REVERT: A 106 TYR cc_start: 0.8451 (t80) cc_final: 0.8054 (t80) REVERT: A 151 ILE cc_start: 0.8064 (pt) cc_final: 0.7769 (pt) REVERT: A 152 LEU cc_start: 0.7996 (tp) cc_final: 0.7624 (tp) REVERT: A 160 LEU cc_start: 0.8948 (mt) cc_final: 0.8563 (mt) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2198 time to fit residues: 25.1691 Evaluate side-chains 68 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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: 0.0570 chunk 122 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 126 optimal weight: 30.0000 chunk 49 optimal weight: 0.7980 chunk 77 optimal weight: 0.0470 chunk 94 optimal weight: 7.9990 chunk 147 optimal weight: 0.0980 overall best weight: 0.7998 ------------------------------------------------------------------------------- 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: 0.7200 moved from start: 1.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 13770 Z= 0.405 Angle : 1.200 15.916 18414 Z= 0.621 Chirality : 0.058 0.334 2070 Planarity : 0.013 0.179 2367 Dihedral : 6.936 22.030 1800 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 34.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.16 % Allowed : 4.65 % 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: -1.85 (0.19), residues: 1611 helix: -1.63 (0.13), residues: 1179 sheet: None (None), residues: 0 loop : 0.73 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE D 120 TYR 0.014 0.002 TYR A 8 ARG 0.013 0.001 ARG E 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 115 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ASP cc_start: 0.8306 (m-30) cc_final: 0.8009 (p0) REVERT: F 5 ARG cc_start: 0.8399 (mtt180) cc_final: 0.7839 (tpp-160) REVERT: F 24 PHE cc_start: 0.8558 (t80) cc_final: 0.8190 (t80) REVERT: F 44 LEU cc_start: 0.9764 (tp) cc_final: 0.9542 (tp) REVERT: F 48 LEU cc_start: 0.9542 (mt) cc_final: 0.9185 (mt) REVERT: F 54 LEU cc_start: 0.8378 (tt) cc_final: 0.8122 (tt) REVERT: F 64 GLU cc_start: 0.8400 (pt0) cc_final: 0.7880 (pt0) REVERT: F 65 LEU cc_start: 0.9143 (mm) cc_final: 0.8640 (mm) REVERT: F 67 PHE cc_start: 0.8685 (t80) cc_final: 0.8090 (t80) REVERT: F 68 ARG cc_start: 0.8898 (mmm160) cc_final: 0.7906 (mmm160) REVERT: F 86 MET cc_start: 0.7403 (mmp) cc_final: 0.6660 (mmt) REVERT: F 107 GLN cc_start: 0.8646 (mp10) cc_final: 0.8386 (mp10) REVERT: F 133 LEU cc_start: 0.6962 (mt) cc_final: 0.6689 (mt) REVERT: F 142 ILE cc_start: 0.8545 (mm) cc_final: 0.7871 (mm) REVERT: F 143 PHE cc_start: 0.9178 (m-10) cc_final: 0.8838 (m-10) REVERT: F 144 ILE cc_start: 0.9034 (mt) cc_final: 0.8834 (mt) REVERT: F 152 LEU cc_start: 0.7735 (tp) cc_final: 0.7245 (tp) REVERT: F 168 ASN cc_start: 0.5464 (t0) cc_final: 0.4660 (t0) outliers start: 2 outliers final: 0 residues processed: 114 average time/residue: 0.2039 time to fit residues: 25.0705 Evaluate side-chains 81 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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: 3.9990 chunk 45 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 40 optimal weight: 40.0000 chunk 147 optimal weight: 8.9990 chunk 159 optimal weight: 0.0050 chunk 131 optimal weight: 0.0050 chunk 146 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.9812 ------------------------------------------------------------------------------- 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: 0.7257 moved from start: 1.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 13770 Z= 0.378 Angle : 1.189 11.774 18414 Z= 0.610 Chirality : 0.056 0.167 2070 Planarity : 0.011 0.085 2367 Dihedral : 6.983 27.384 1800 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 39.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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: -2.39 (0.19), residues: 1611 helix: -1.74 (0.13), residues: 1152 sheet: None (None), residues: 0 loop : -0.53 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.051 0.004 PHE E 122 TYR 0.013 0.002 TYR B 78 ARG 0.005 0.001 ARG D 118 *********************** 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 103 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ASP cc_start: 0.7893 (m-30) cc_final: 0.7501 (m-30) REVERT: F 36 GLU cc_start: 0.8061 (pp20) cc_final: 0.7769 (pp20) REVERT: F 44 LEU cc_start: 0.9774 (tp) cc_final: 0.9558 (tp) REVERT: F 48 LEU cc_start: 0.9463 (mt) cc_final: 0.9040 (mt) REVERT: F 53 MET cc_start: 0.7737 (mpp) cc_final: 0.7325 (mpp) REVERT: F 54 LEU cc_start: 0.8177 (tt) cc_final: 0.7479 (tt) REVERT: F 64 GLU cc_start: 0.8452 (pt0) cc_final: 0.7581 (pt0) REVERT: F 67 PHE cc_start: 0.8629 (t80) cc_final: 0.7669 (t80) REVERT: F 86 MET cc_start: 0.7341 (mmp) cc_final: 0.6630 (mmt) REVERT: F 97 GLN cc_start: 0.8688 (tt0) cc_final: 0.7943 (tp40) REVERT: F 105 LEU cc_start: 0.9395 (mt) cc_final: 0.9000 (mt) REVERT: F 115 SER cc_start: 0.9108 (t) cc_final: 0.8844 (p) REVERT: F 121 LYS cc_start: 0.7612 (ttmm) cc_final: 0.7393 (ttmm) REVERT: F 137 MET cc_start: 0.6842 (mtt) cc_final: 0.6614 (mtt) REVERT: F 142 ILE cc_start: 0.8275 (mm) cc_final: 0.7747 (mm) REVERT: F 152 LEU cc_start: 0.7747 (tp) cc_final: 0.7330 (tp) REVERT: F 168 ASN cc_start: 0.6533 (t0) cc_final: 0.5385 (t0) REVERT: F 173 LYS cc_start: 0.8875 (ptmm) cc_final: 0.8362 (mptt) REVERT: F 178 TYR cc_start: 0.8508 (t80) cc_final: 0.8145 (t80) outliers start: 2 outliers final: 0 residues processed: 102 average time/residue: 0.2108 time to fit residues: 23.2699 Evaluate side-chains 84 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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: 20.0000 chunk 110 optimal weight: 0.9980 chunk 76 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 98 optimal weight: 30.0000 chunk 147 optimal weight: 0.7980 chunk 156 optimal weight: 0.0060 chunk 77 optimal weight: 0.0370 chunk 140 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 overall best weight: 1.1676 ------------------------------------------------------------------------------- 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 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 1.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 13770 Z= 0.425 Angle : 1.157 17.398 18414 Z= 0.584 Chirality : 0.057 0.231 2070 Planarity : 0.010 0.098 2367 Dihedral : 7.188 27.163 1800 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 46.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.58 % Allowed : 4.07 % Favored : 95.35 % 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: -1.87 (0.21), residues: 1611 helix: -1.60 (0.14), residues: 1089 sheet: None (None), residues: 0 loop : 0.10 (0.31), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.037 0.004 PHE I 122 TYR 0.058 0.004 TYR G 8 ARG 0.008 0.002 ARG D 33 *********************** 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 93 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ASP cc_start: 0.6790 (m-30) cc_final: 0.6029 (m-30) REVERT: F 40 ASP cc_start: 0.7502 (p0) cc_final: 0.7180 (p0) REVERT: F 43 MET cc_start: 0.9023 (mpp) cc_final: 0.8452 (mmt) REVERT: F 44 LEU cc_start: 0.9721 (tp) cc_final: 0.9509 (tp) REVERT: F 48 LEU cc_start: 0.9459 (mt) cc_final: 0.9125 (mt) REVERT: F 54 LEU cc_start: 0.8146 (tt) cc_final: 0.7623 (tt) REVERT: F 63 LYS cc_start: 0.8306 (mtpt) cc_final: 0.7977 (mtmt) REVERT: F 64 GLU cc_start: 0.8138 (pt0) cc_final: 0.7655 (pt0) REVERT: F 67 PHE cc_start: 0.8377 (t80) cc_final: 0.7944 (t80) REVERT: F 86 MET cc_start: 0.7512 (mmp) cc_final: 0.6968 (mmt) REVERT: F 97 GLN cc_start: 0.8689 (tt0) cc_final: 0.8198 (tp40) REVERT: F 98 ILE cc_start: 0.7970 (pt) cc_final: 0.7686 (pt) REVERT: F 105 LEU cc_start: 0.9389 (mt) cc_final: 0.8933 (mt) REVERT: F 142 ILE cc_start: 0.8102 (mm) cc_final: 0.7690 (mm) REVERT: F 143 PHE cc_start: 0.9099 (m-10) cc_final: 0.8848 (m-10) REVERT: F 159 ILE cc_start: 0.8441 (tp) cc_final: 0.8013 (tp) REVERT: F 161 LYS cc_start: 0.7600 (mtmt) cc_final: 0.7375 (mtmt) REVERT: F 168 ASN cc_start: 0.6572 (t0) cc_final: 0.5490 (t0) REVERT: F 173 LYS cc_start: 0.8893 (ptmm) cc_final: 0.8423 (mptt) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.1769 time to fit residues: 17.9315 Evaluate side-chains 74 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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: 10.0000 chunk 88 optimal weight: 0.0770 chunk 2 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 108 optimal weight: 40.0000 chunk 0 optimal weight: 30.0000 chunk 79 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 overall best weight: 5.6146 ------------------------------------------------------------------------------- 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 125 GLN F 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 1.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 13770 Z= 0.422 Angle : 1.164 16.744 18414 Z= 0.585 Chirality : 0.053 0.185 2070 Planarity : 0.017 0.248 2367 Dihedral : 7.439 31.908 1800 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 44.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % 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: -1.87 (0.21), residues: 1611 helix: -1.46 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : -0.26 (0.31), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.050 0.003 PHE I 122 TYR 0.014 0.003 TYR D 8 ARG 0.008 0.001 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 5 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 92 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 33 ARG cc_start: 0.3580 (ptt180) cc_final: 0.2729 (mtt180) REVERT: F 43 MET cc_start: 0.8993 (mpp) cc_final: 0.8551 (mmt) REVERT: F 48 LEU cc_start: 0.9584 (mt) cc_final: 0.9304 (mt) REVERT: F 53 MET cc_start: 0.8074 (mpp) cc_final: 0.7805 (mpp) REVERT: F 54 LEU cc_start: 0.8217 (tt) cc_final: 0.7665 (tt) REVERT: F 97 GLN cc_start: 0.8724 (tt0) cc_final: 0.8314 (tp40) REVERT: F 168 ASN cc_start: 0.6291 (t0) cc_final: 0.5252 (t0) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2160 time to fit residues: 21.3946 Evaluate side-chains 69 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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: 5.9990 chunk 141 optimal weight: 5.9990 chunk 30 optimal weight: 0.0040 chunk 91 optimal weight: 40.0000 chunk 38 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 51 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 overall best weight: 2.9398 ------------------------------------------------------------------------------- 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 125 GLN F 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 1.5500 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= 0.322 Angle : 1.117 12.511 18414 Z= 0.563 Chirality : 0.053 0.184 2070 Planarity : 0.010 0.095 2367 Dihedral : 7.088 29.558 1800 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 40.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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: -1.89 (0.21), residues: 1611 helix: -1.37 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -0.57 (0.30), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE B 122 TYR 0.015 0.002 TYR H 78 ARG 0.018 0.002 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 6 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 86 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 23 LYS cc_start: 0.8791 (ttmt) cc_final: 0.8049 (tppt) REVERT: F 43 MET cc_start: 0.8783 (mpp) cc_final: 0.8551 (mmt) REVERT: F 54 LEU cc_start: 0.8272 (tt) cc_final: 0.7898 (tt) REVERT: F 61 PHE cc_start: 0.8456 (t80) cc_final: 0.7278 (t80) REVERT: F 97 GLN cc_start: 0.8589 (tt0) cc_final: 0.8288 (tm-30) REVERT: F 98 ILE cc_start: 0.8171 (pt) cc_final: 0.7445 (pt) REVERT: F 116 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8784 (tp30) REVERT: F 119 SER cc_start: 0.7461 (p) cc_final: 0.6675 (t) REVERT: F 143 PHE cc_start: 0.9049 (m-10) cc_final: 0.8826 (m-10) REVERT: F 160 LEU cc_start: 0.8954 (mt) cc_final: 0.8634 (mt) REVERT: F 168 ASN cc_start: 0.6377 (t0) cc_final: 0.5217 (t0) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1970 time to fit residues: 18.4339 Evaluate side-chains 63 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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: 5.9990 chunk 17 optimal weight: 0.0470 chunk 89 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 72 optimal weight: 40.0000 overall best weight: 1.8082 ------------------------------------------------------------------------------- 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 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 1.5962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13770 Z= 0.357 Angle : 1.139 9.608 18414 Z= 0.597 Chirality : 0.054 0.185 2070 Planarity : 0.007 0.062 2367 Dihedral : 7.438 28.745 1800 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 39.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % 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: -2.27 (0.20), residues: 1611 helix: -1.76 (0.14), residues: 1125 sheet: None (None), residues: 0 loop : -0.26 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE B 122 TYR 0.020 0.003 TYR A 178 ARG 0.005 0.001 ARG E 33 *********************** REFINEMENT MACRO_CYCLE 7 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 87 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 24 PHE cc_start: 0.8564 (t80) cc_final: 0.8240 (t80) REVERT: F 44 LEU cc_start: 0.9622 (tp) cc_final: 0.9380 (tp) REVERT: F 48 LEU cc_start: 0.9572 (mt) cc_final: 0.9226 (mt) REVERT: F 53 MET cc_start: 0.8073 (mpp) cc_final: 0.7549 (mpp) REVERT: F 61 PHE cc_start: 0.8464 (t80) cc_final: 0.7526 (t80) REVERT: F 64 GLU cc_start: 0.7657 (pt0) cc_final: 0.6913 (pt0) REVERT: F 67 PHE cc_start: 0.8294 (t80) cc_final: 0.7797 (t80) REVERT: F 85 GLU cc_start: 0.8721 (mp0) cc_final: 0.8375 (mp0) REVERT: F 86 MET cc_start: 0.7921 (mmp) cc_final: 0.7131 (mmt) REVERT: F 97 GLN cc_start: 0.8576 (tt0) cc_final: 0.8045 (tt0) REVERT: F 106 TYR cc_start: 0.9016 (t80) cc_final: 0.8540 (t80) REVERT: F 116 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8682 (tp30) REVERT: F 119 SER cc_start: 0.7138 (p) cc_final: 0.5978 (t) REVERT: F 141 ASP cc_start: 0.8080 (m-30) cc_final: 0.7712 (m-30) REVERT: F 142 ILE cc_start: 0.7727 (mp) cc_final: 0.7046 (tp) REVERT: F 143 PHE cc_start: 0.9008 (m-10) cc_final: 0.8674 (m-10) REVERT: F 168 ASN cc_start: 0.5292 (t0) cc_final: 0.4351 (t0) REVERT: F 173 LYS cc_start: 0.9058 (pptt) cc_final: 0.7886 (mptt) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2096 time to fit residues: 19.6785 Evaluate side-chains 73 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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: 5.9990 chunk 62 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 99 optimal weight: 40.0000 chunk 106 optimal weight: 2.9990 chunk 77 optimal weight: 0.0010 chunk 14 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 1.6287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 13770 Z= 0.343 Angle : 1.138 12.308 18414 Z= 0.584 Chirality : 0.053 0.213 2070 Planarity : 0.008 0.060 2367 Dihedral : 7.330 28.258 1800 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 35.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % 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: -1.87 (0.20), residues: 1611 helix: -1.45 (0.14), residues: 1098 sheet: None (None), residues: 0 loop : -0.24 (0.31), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.002 PHE F 122 TYR 0.022 0.003 TYR H 78 ARG 0.015 0.002 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 8 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 82 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ASP cc_start: 0.6135 (m-30) cc_final: 0.5773 (m-30) REVERT: F 10 ILE cc_start: 0.9091 (mm) cc_final: 0.8784 (mm) REVERT: F 24 PHE cc_start: 0.8524 (t80) cc_final: 0.8302 (t80) REVERT: F 44 LEU cc_start: 0.9607 (tp) cc_final: 0.9395 (tp) REVERT: F 48 LEU cc_start: 0.9560 (mt) cc_final: 0.9278 (mt) REVERT: F 64 GLU cc_start: 0.7682 (pt0) cc_final: 0.6318 (tt0) REVERT: F 67 PHE cc_start: 0.8295 (t80) cc_final: 0.7729 (t80) REVERT: F 82 ARG cc_start: 0.7570 (mmp80) cc_final: 0.7138 (mmp-170) REVERT: F 86 MET cc_start: 0.8009 (mmp) cc_final: 0.6956 (mmt) REVERT: F 97 GLN cc_start: 0.8498 (tt0) cc_final: 0.8104 (pm20) REVERT: F 116 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8414 (mt-10) REVERT: F 141 ASP cc_start: 0.7981 (m-30) cc_final: 0.7683 (m-30) REVERT: F 142 ILE cc_start: 0.7769 (mp) cc_final: 0.7273 (tp) REVERT: F 143 PHE cc_start: 0.9010 (m-10) cc_final: 0.8718 (m-10) REVERT: F 168 ASN cc_start: 0.5266 (t0) cc_final: 0.4476 (t0) REVERT: F 173 LYS cc_start: 0.9024 (pptt) cc_final: 0.7841 (mptt) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2018 time to fit residues: 17.9097 Evaluate side-chains 66 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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: 0.0170 chunk 136 optimal weight: 8.9990 chunk 145 optimal weight: 30.0000 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 114 optimal weight: 0.0980 chunk 44 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 137 optimal weight: 8.9990 chunk 144 optimal weight: 40.0000 chunk 95 optimal weight: 0.0070 overall best weight: 1.4038 ------------------------------------------------------------------------------- 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: 0.7182 moved from start: 1.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 13770 Z= 0.333 Angle : 1.156 11.113 18414 Z= 0.602 Chirality : 0.058 0.223 2070 Planarity : 0.008 0.058 2367 Dihedral : 7.489 28.282 1800 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 37.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: -1.95 (0.20), residues: 1611 helix: -1.47 (0.14), residues: 1071 sheet: None (None), residues: 0 loop : -0.46 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE E 122 TYR 0.018 0.003 TYR D 78 ARG 0.016 0.002 ARG G 33 *********************** REFINEMENT MACRO_CYCLE 9 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 76 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 LYS cc_start: 0.8836 (tttt) cc_final: 0.8357 (tptm) REVERT: F 24 PHE cc_start: 0.8450 (t80) cc_final: 0.8243 (t80) REVERT: F 28 ASP cc_start: 0.8466 (p0) cc_final: 0.7848 (p0) REVERT: F 33 ARG cc_start: 0.4499 (mtt90) cc_final: 0.4230 (ptt180) REVERT: F 48 LEU cc_start: 0.9475 (mt) cc_final: 0.9267 (mt) REVERT: F 61 PHE cc_start: 0.8306 (t80) cc_final: 0.7881 (t80) REVERT: F 67 PHE cc_start: 0.8262 (t80) cc_final: 0.7631 (t80) REVERT: F 82 ARG cc_start: 0.7531 (mmp80) cc_final: 0.7065 (mmp-170) REVERT: F 86 MET cc_start: 0.7968 (mmp) cc_final: 0.6968 (mmt) REVERT: F 116 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8300 (mt-10) REVERT: F 141 ASP cc_start: 0.8099 (m-30) cc_final: 0.7894 (m-30) REVERT: F 143 PHE cc_start: 0.9089 (m-10) cc_final: 0.8671 (m-10) REVERT: F 162 ARG cc_start: 0.7904 (tpt90) cc_final: 0.7557 (tpt170) REVERT: F 168 ASN cc_start: 0.5612 (t0) cc_final: 0.4656 (t0) REVERT: F 173 LYS cc_start: 0.9051 (pptt) cc_final: 0.7917 (mptt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2186 time to fit residues: 17.9749 Evaluate side-chains 64 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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: 30.0000 chunk 93 optimal weight: 7.9990 chunk 72 optimal weight: 50.0000 chunk 106 optimal weight: 10.0000 chunk 161 optimal weight: 40.0000 chunk 148 optimal weight: 6.9990 chunk 128 optimal weight: 0.4980 chunk 13 optimal weight: 30.0000 chunk 99 optimal weight: 0.0980 chunk 78 optimal weight: 0.3980 chunk 102 optimal weight: 0.0980 overall best weight: 1.6182 ------------------------------------------------------------------------------- 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: 0.7148 moved from start: 1.6881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13770 Z= 0.325 Angle : 1.123 10.857 18414 Z= 0.587 Chirality : 0.056 0.198 2070 Planarity : 0.008 0.080 2367 Dihedral : 7.309 28.357 1800 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 38.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: -2.23 (0.19), residues: 1611 helix: -1.68 (0.13), residues: 1062 sheet: None (None), residues: 0 loop : -0.61 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHE C 122 TYR 0.018 0.003 TYR C 78 ARG 0.019 0.003 ARG C 33 ********************** REFINEMENT MACRO_CYCLE 10 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 75 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 48 LEU cc_start: 0.9502 (mt) cc_final: 0.9274 (mt) REVERT: F 68 ARG cc_start: 0.8609 (mmt-90) cc_final: 0.7978 (mmp80) REVERT: F 82 ARG cc_start: 0.7558 (mmp80) cc_final: 0.7124 (mmp-170) REVERT: F 86 MET cc_start: 0.7953 (mmp) cc_final: 0.6772 (mmt) REVERT: F 116 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8200 (mt-10) REVERT: F 121 LYS cc_start: 0.7721 (tptp) cc_final: 0.7361 (tptp) REVERT: F 139 LEU cc_start: 0.9008 (mm) cc_final: 0.8421 (mm) REVERT: F 141 ASP cc_start: 0.8054 (m-30) cc_final: 0.7834 (m-30) REVERT: F 143 PHE cc_start: 0.9052 (m-10) cc_final: 0.8663 (m-10) REVERT: F 173 LYS cc_start: 0.8979 (pptt) cc_final: 0.7807 (mptt) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2185 time to fit residues: 17.7228 Evaluate side-chains 62 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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: 7.9990 chunk 39 optimal weight: 30.0000 chunk 118 optimal weight: 6.9990 chunk 18 optimal weight: 40.0000 chunk 35 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 132 optimal weight: 0.0050 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 overall best weight: 3.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.122728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.105500 restraints weight = 5482.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.108266 restraints weight = 3895.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.110324 restraints weight = 2976.835| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 1.7101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 13770 Z= 0.335 Angle : 1.093 9.849 18414 Z= 0.581 Chirality : 0.054 0.194 2070 Planarity : 0.008 0.089 2367 Dihedral : 7.222 27.621 1800 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 38.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % 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: -2.22 (0.19), residues: 1611 helix: -1.67 (0.13), residues: 1080 sheet: None (None), residues: 0 loop : -0.56 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.031 0.003 PHE B 24 TYR 0.015 0.003 TYR G 178 ARG 0.021 0.002 ARG F 33 =============================================================================== Job complete usr+sys time: 2531.63 seconds wall clock time: 46 minutes 36.83 seconds (2796.83 seconds total)