Starting phenix.real_space_refine on Wed Feb 14 08:43:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cea_16602/02_2024/8cea_16602.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cea_16602/02_2024/8cea_16602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cea_16602/02_2024/8cea_16602.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cea_16602/02_2024/8cea_16602.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cea_16602/02_2024/8cea_16602.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cea_16602/02_2024/8cea_16602.pdb" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.025 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 43 5.16 5 C 5858 2.51 5 N 1550 2.21 5 O 1519 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "a GLU 5": "OE1" <-> "OE2" Residue "a GLU 15": "OE1" <-> "OE2" Residue "a GLU 59": "OE1" <-> "OE2" Residue "a GLU 111": "OE1" <-> "OE2" Residue "b GLU 10": "OE1" <-> "OE2" Residue "b GLU 20": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8970 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1595 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1656 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 202} Chain: "C" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1930 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 11, 'TRANS': 229} Chain: "D" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 538 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "a" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1595 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "b" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1656 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 202} Time building chain proxies: 5.18, per 1000 atoms: 0.58 Number of scatterers: 8970 At special positions: 0 Unit cell: (107.42, 83.64, 112.34, 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 43 16.00 O 1519 8.00 N 1550 7.00 C 5858 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: 3.23 Conformation dependent library (CDL) restraints added in 1.8 seconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 68.0% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 70 through 76 Processing helix chain 'A' and resid 92 through 100 removed outlier: 4.242A pdb=" N TYR A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.532A pdb=" N GLN A 128 " --> pdb=" O PRO A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.766A pdb=" N ALA A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 145 removed outlier: 3.713A pdb=" N THR A 145 " --> pdb=" O LEU A 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 160 through 176 removed outlier: 3.651A pdb=" N VAL A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 169 " --> pdb=" O ASP A 165 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 17 removed outlier: 4.233A pdb=" N HIS B 17 " --> pdb=" O VAL B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 4.171A pdb=" N LEU B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 42 through 66 removed outlier: 3.959A pdb=" N LEU B 46 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ARG B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) Proline residue: B 51 - end of helix removed outlier: 3.695A pdb=" N TRP B 55 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 71 through 76 removed outlier: 4.423A pdb=" N GLN B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 88 through 105 removed outlier: 3.590A pdb=" N VAL B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 104 " --> pdb=" O HIS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 119 removed outlier: 4.094A pdb=" N LEU B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Proline residue: B 113 - end of helix removed outlier: 3.735A pdb=" N MET B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 151 Proline residue: B 138 - end of helix Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 158 through 185 removed outlier: 4.115A pdb=" N SER B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Proline residue: B 167 - end of helix Proline residue: B 171 - end of helix removed outlier: 3.639A pdb=" N MET B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 220 Proline residue: B 208 - end of helix removed outlier: 3.600A pdb=" N ALA B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 8 Processing helix chain 'C' and resid 10 through 42 Proline residue: C 23 - end of helix Processing helix chain 'C' and resid 51 through 54 Processing helix chain 'C' and resid 55 through 84 removed outlier: 4.159A pdb=" N LEU C 59 " --> pdb=" O ARG C 55 " (cutoff:3.500A) Proline residue: C 62 - end of helix removed outlier: 3.973A pdb=" N ILE C 80 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 115 removed outlier: 4.180A pdb=" N LEU C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA C 92 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Proline residue: C 98 - end of helix removed outlier: 3.567A pdb=" N GLY C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 128 through 147 Processing helix chain 'C' and resid 152 through 177 Proline residue: C 171 - end of helix Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 199 through 229 removed outlier: 3.657A pdb=" N GLU C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 243 removed outlier: 3.837A pdb=" N SER C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 69 removed outlier: 3.574A pdb=" N VAL D 21 " --> pdb=" O TYR D 17 " (cutoff:3.500A) Proline residue: D 31 - end of helix Processing helix chain 'a' and resid 41 through 51 removed outlier: 3.545A pdb=" N THR a 50 " --> pdb=" O LEU a 46 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 75 Processing helix chain 'a' and resid 92 through 100 removed outlier: 4.310A pdb=" N TYR a 100 " --> pdb=" O ASN a 96 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 117 removed outlier: 3.679A pdb=" N ALA a 116 " --> pdb=" O ALA a 112 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY a 117 " --> pdb=" O LEU a 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 129 Processing helix chain 'a' and resid 130 through 140 removed outlier: 4.249A pdb=" N ALA a 138 " --> pdb=" O GLN a 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 141 through 144 Processing helix chain 'a' and resid 160 through 177 removed outlier: 3.774A pdb=" N GLN a 173 " --> pdb=" O GLN a 169 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS a 174 " --> pdb=" O ARG a 170 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 15 Processing helix chain 'b' and resid 21 through 39 removed outlier: 3.973A pdb=" N LEU b 25 " --> pdb=" O ILE b 21 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE b 28 " --> pdb=" O PRO b 24 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU b 29 " --> pdb=" O LEU b 25 " (cutoff:3.500A) Proline residue: b 36 - end of helix Processing helix chain 'b' and resid 44 through 66 Proline residue: b 51 - end of helix Processing helix chain 'b' and resid 67 through 70 Processing helix chain 'b' and resid 71 through 77 removed outlier: 4.126A pdb=" N GLN b 75 " --> pdb=" O ARG b 71 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP b 76 " --> pdb=" O ASP b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 84 removed outlier: 3.901A pdb=" N GLN b 81 " --> pdb=" O GLY b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 119 removed outlier: 3.717A pdb=" N MET b 102 " --> pdb=" O MET b 98 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL b 103 " --> pdb=" O ALA b 99 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR b 104 " --> pdb=" O HIS b 100 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU b 106 " --> pdb=" O MET b 102 " (cutoff:3.500A) Proline residue: b 107 - end of helix Proline residue: b 113 - end of helix Processing helix chain 'b' and resid 122 through 152 removed outlier: 4.017A pdb=" N LEU b 135 " --> pdb=" O LEU b 131 " (cutoff:3.500A) Proline residue: b 138 - end of helix Proline residue: b 146 - end of helix Processing helix chain 'b' and resid 159 through 165 removed outlier: 3.630A pdb=" N SER b 162 " --> pdb=" O VAL b 159 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 183 Processing helix chain 'b' and resid 189 through 219 removed outlier: 3.692A pdb=" N ILE b 195 " --> pdb=" O GLY b 191 " (cutoff:3.500A) Proline residue: b 208 - end of helix removed outlier: 3.643A pdb=" N ALA b 213 " --> pdb=" O PHE b 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 removed outlier: 5.453A pdb=" N ALA A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 61 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU A 8 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLU A 59 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 6.257A pdb=" N LEU A 79 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP A 153 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE A 81 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL A 32 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TRP A 31 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE A 199 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN A 33 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 16 through 26 removed outlier: 5.610A pdb=" N THR a 17 " --> pdb=" O ARG a 13 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARG a 13 " --> pdb=" O THR a 17 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE a 19 " --> pdb=" O CYS a 11 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU a 9 " --> pdb=" O GLY a 21 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER a 23 " --> pdb=" O ARG a 7 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG a 7 " --> pdb=" O SER a 23 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR a 25 " --> pdb=" O GLU a 5 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU a 5 " --> pdb=" O THR a 25 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU a 9 " --> pdb=" O ALA a 57 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA a 57 " --> pdb=" O LEU a 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 78 through 81 removed outlier: 6.202A pdb=" N LEU a 79 " --> pdb=" O ILE a 151 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ASP a 153 " --> pdb=" O LEU a 79 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE a 81 " --> pdb=" O ASP a 153 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR a 184 " --> pdb=" O LEU a 152 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU a 30 " --> pdb=" O VAL a 181 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N LEU a 183 " --> pdb=" O GLU a 30 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL a 32 " --> pdb=" O LEU a 183 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG a 197 " --> pdb=" O TRP a 31 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1449 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: 2.23 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2092 1.33 - 1.46: 1941 1.46 - 1.58: 5071 1.58 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 9185 Sorted by residual: bond pdb=" C ILE B 170 " pdb=" N PRO B 171 " ideal model delta sigma weight residual 1.335 1.392 -0.057 1.36e-02 5.41e+03 1.76e+01 bond pdb=" C THR B 137 " pdb=" N PRO B 138 " ideal model delta sigma weight residual 1.335 1.383 -0.048 1.36e-02 5.41e+03 1.25e+01 bond pdb=" CA ARG b 12 " pdb=" C ARG b 12 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.37e-02 5.33e+03 9.64e+00 bond pdb=" C ARG b 12 " pdb=" N VAL b 13 " ideal model delta sigma weight residual 1.335 1.303 0.031 1.15e-02 7.56e+03 7.28e+00 bond pdb=" CA ILE D 30 " pdb=" CB ILE D 30 " ideal model delta sigma weight residual 1.539 1.526 0.013 5.40e-03 3.43e+04 5.60e+00 ... (remaining 9180 not shown) Histogram of bond angle deviations from ideal: 96.98 - 104.43: 168 104.43 - 111.89: 4434 111.89 - 119.34: 3329 119.34 - 126.79: 4401 126.79 - 134.25: 199 Bond angle restraints: 12531 Sorted by residual: angle pdb=" N PHE C 209 " pdb=" CA PHE C 209 " pdb=" C PHE C 209 " ideal model delta sigma weight residual 111.14 104.49 6.65 1.08e+00 8.57e-01 3.79e+01 angle pdb=" CA GLU A 15 " pdb=" CB GLU A 15 " pdb=" CG GLU A 15 " ideal model delta sigma weight residual 114.10 124.93 -10.83 2.00e+00 2.50e-01 2.93e+01 angle pdb=" N GLU D 57 " pdb=" CA GLU D 57 " pdb=" CB GLU D 57 " ideal model delta sigma weight residual 110.41 118.70 -8.29 1.68e+00 3.54e-01 2.43e+01 angle pdb=" C ARG a 102 " pdb=" CA ARG a 102 " pdb=" CB ARG a 102 " ideal model delta sigma weight residual 117.23 110.56 6.67 1.36e+00 5.41e-01 2.40e+01 angle pdb=" CA MET b 129 " pdb=" CB MET b 129 " pdb=" CG MET b 129 " ideal model delta sigma weight residual 114.10 123.85 -9.75 2.00e+00 2.50e-01 2.38e+01 ... (remaining 12526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.42: 4868 18.42 - 36.85: 426 36.85 - 55.27: 86 55.27 - 73.69: 7 73.69 - 92.11: 6 Dihedral angle restraints: 5393 sinusoidal: 2102 harmonic: 3291 Sorted by residual: dihedral pdb=" CA HIS C 60 " pdb=" C HIS C 60 " pdb=" N VAL C 61 " pdb=" CA VAL C 61 " ideal model delta harmonic sigma weight residual -180.00 -157.68 -22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA GLN b 81 " pdb=" C GLN b 81 " pdb=" N LEU b 82 " pdb=" CA LEU b 82 " ideal model delta harmonic sigma weight residual 180.00 158.77 21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA LEU b 154 " pdb=" C LEU b 154 " pdb=" N LYS b 155 " pdb=" CA LYS b 155 " ideal model delta harmonic sigma weight residual -180.00 -159.04 -20.96 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 5390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1127 0.055 - 0.110: 267 0.110 - 0.165: 71 0.165 - 0.220: 13 0.220 - 0.275: 4 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA GLU A 15 " pdb=" N GLU A 15 " pdb=" C GLU A 15 " pdb=" CB GLU A 15 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE C 57 " pdb=" CA ILE C 57 " pdb=" CG1 ILE C 57 " pdb=" CG2 ILE C 57 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1479 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 128 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ARG C 128 " 0.059 2.00e-02 2.50e+03 pdb=" O ARG C 128 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU C 129 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 50 " -0.056 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO B 51 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 15 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.08e+00 pdb=" CD GLU A 15 " 0.052 2.00e-02 2.50e+03 pdb=" OE1 GLU A 15 " -0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU A 15 " -0.018 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1796 2.78 - 3.31: 8679 3.31 - 3.84: 14544 3.84 - 4.37: 16100 4.37 - 4.90: 27312 Nonbonded interactions: 68431 Sorted by model distance: nonbonded pdb=" ND2 ASN C 223 " pdb=" OE1 GLN D 42 " model vdw 2.254 2.520 nonbonded pdb=" O MET A 171 " pdb=" OG1 THR A 175 " model vdw 2.272 2.440 nonbonded pdb=" O PHE B 142 " pdb=" OG SER B 207 " model vdw 2.338 2.440 nonbonded pdb=" NH1 ARG a 135 " pdb=" OG1 THR a 157 " model vdw 2.362 2.520 nonbonded pdb=" N GLN C 50 " pdb=" OE1 GLN C 50 " model vdw 2.381 2.520 ... (remaining 68426 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 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.410 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 25.820 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.005 0.057 9185 Z= 0.329 Angle : 1.112 15.454 12531 Z= 0.570 Chirality : 0.054 0.275 1482 Planarity : 0.008 0.084 1557 Dihedral : 14.353 92.115 3265 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -1.36 (0.24), residues: 1141 helix: -0.52 (0.19), residues: 689 sheet: -0.60 (0.84), residues: 44 loop : -1.41 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP b 55 HIS 0.007 0.001 HIS A 174 PHE 0.036 0.002 PHE a 19 TYR 0.027 0.002 TYR C 58 ARG 0.008 0.001 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8515 (mt) cc_final: 0.8268 (mp) REVERT: D 50 VAL cc_start: 0.8388 (t) cc_final: 0.8183 (t) REVERT: a 5 GLU cc_start: 0.7378 (pp20) cc_final: 0.6929 (pp20) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.1950 time to fit residues: 79.9075 Evaluate side-chains 239 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 133 GLN A 154 GLN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 23 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9185 Z= 0.227 Angle : 0.718 9.793 12531 Z= 0.349 Chirality : 0.043 0.190 1482 Planarity : 0.006 0.062 1557 Dihedral : 5.041 17.716 1236 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.10 % Allowed : 13.28 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1141 helix: 0.42 (0.20), residues: 696 sheet: 0.28 (0.90), residues: 44 loop : -1.36 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 66 HIS 0.004 0.001 HIS A 174 PHE 0.025 0.001 PHE B 28 TYR 0.012 0.001 TYR A 100 ARG 0.003 0.000 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 262 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: B 83 MET cc_start: 0.7146 (mtp) cc_final: 0.6917 (mtm) REVERT: C 54 TYR cc_start: 0.7841 (t80) cc_final: 0.7596 (t80) outliers start: 29 outliers final: 22 residues processed: 270 average time/residue: 0.1937 time to fit residues: 73.1742 Evaluate side-chains 263 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 241 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 162 ASN Chi-restraints excluded: chain a residue 190 ASN Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 152 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 0.1980 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN C 90 ASN ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 75 HIS a 186 HIS ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9185 Z= 0.229 Angle : 0.691 9.072 12531 Z= 0.334 Chirality : 0.042 0.204 1482 Planarity : 0.005 0.054 1557 Dihedral : 4.769 19.809 1236 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.39 % Allowed : 17.67 % Favored : 77.94 % 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: 0.13 (0.25), residues: 1141 helix: 0.86 (0.20), residues: 705 sheet: 0.61 (0.94), residues: 44 loop : -1.36 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 66 HIS 0.005 0.001 HIS A 174 PHE 0.026 0.001 PHE B 28 TYR 0.019 0.002 TYR C 48 ARG 0.002 0.000 ARG C 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 253 time to evaluate : 0.966 Fit side-chains REVERT: C 33 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8376 (tt) REVERT: C 96 MET cc_start: 0.8069 (mtm) cc_final: 0.7848 (mtm) REVERT: a 111 GLU cc_start: 0.6962 (pm20) cc_final: 0.6683 (pm20) outliers start: 41 outliers final: 27 residues processed: 267 average time/residue: 0.1924 time to fit residues: 71.5861 Evaluate side-chains 272 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 244 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 162 ASN Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain a residue 190 ASN Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 85 LEU Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 152 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 HIS C 147 HIS D 53 GLN ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9185 Z= 0.218 Angle : 0.687 9.060 12531 Z= 0.331 Chirality : 0.042 0.216 1482 Planarity : 0.005 0.049 1557 Dihedral : 4.594 17.513 1236 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.35 % Allowed : 20.02 % Favored : 74.63 % 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: 0.51 (0.26), residues: 1141 helix: 1.19 (0.20), residues: 698 sheet: 0.53 (0.94), residues: 44 loop : -1.20 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP C 234 HIS 0.005 0.001 HIS A 174 PHE 0.025 0.001 PHE B 28 TYR 0.012 0.001 TYR A 74 ARG 0.005 0.000 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 254 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: C 118 MET cc_start: 0.8505 (mpp) cc_final: 0.8300 (mpp) REVERT: D 54 ARG cc_start: 0.8535 (tmt-80) cc_final: 0.8110 (tpp-160) REVERT: a 111 GLU cc_start: 0.6998 (pm20) cc_final: 0.6731 (pm20) REVERT: a 190 ASN cc_start: 0.7853 (OUTLIER) cc_final: 0.7455 (p0) outliers start: 50 outliers final: 33 residues processed: 269 average time/residue: 0.1991 time to fit residues: 74.2491 Evaluate side-chains 278 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 244 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 162 ASN Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain a residue 190 ASN Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 100 HIS Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 152 VAL Chi-restraints excluded: chain b residue 190 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 0.0020 chunk 74 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 overall best weight: 2.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9185 Z= 0.280 Angle : 0.718 8.392 12531 Z= 0.346 Chirality : 0.044 0.231 1482 Planarity : 0.005 0.053 1557 Dihedral : 4.602 17.267 1236 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.28 % Allowed : 22.59 % Favored : 73.13 % 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: 0.51 (0.26), residues: 1141 helix: 1.19 (0.20), residues: 705 sheet: 0.54 (0.95), residues: 44 loop : -1.25 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 66 HIS 0.007 0.001 HIS A 174 PHE 0.026 0.002 PHE B 28 TYR 0.016 0.002 TYR C 48 ARG 0.004 0.000 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 257 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 144 LEU cc_start: 0.9285 (pt) cc_final: 0.8893 (pp) REVERT: B 20 GLU cc_start: 0.8171 (tp30) cc_final: 0.7921 (mm-30) REVERT: C 226 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8501 (tt) REVERT: a 111 GLU cc_start: 0.7165 (pm20) cc_final: 0.6843 (pm20) REVERT: a 190 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7422 (p0) REVERT: b 72 ASP cc_start: 0.8579 (t0) cc_final: 0.8163 (t0) REVERT: b 129 MET cc_start: 0.7373 (tpt) cc_final: 0.7169 (tpt) outliers start: 40 outliers final: 31 residues processed: 272 average time/residue: 0.2014 time to fit residues: 75.5090 Evaluate side-chains 282 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 249 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain a residue 190 ASN Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 100 HIS Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 152 VAL Chi-restraints excluded: chain b residue 190 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 128 GLN ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9185 Z= 0.254 Angle : 0.698 8.091 12531 Z= 0.335 Chirality : 0.043 0.247 1482 Planarity : 0.005 0.053 1557 Dihedral : 4.523 20.202 1236 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.14 % Allowed : 22.91 % Favored : 71.95 % 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: 0.62 (0.26), residues: 1141 helix: 1.32 (0.20), residues: 703 sheet: 0.52 (0.95), residues: 44 loop : -1.26 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 66 HIS 0.006 0.001 HIS A 68 PHE 0.027 0.001 PHE B 28 TYR 0.010 0.001 TYR A 100 ARG 0.003 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 252 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 144 LEU cc_start: 0.9275 (pt) cc_final: 0.8896 (pp) REVERT: B 20 GLU cc_start: 0.8162 (tp30) cc_final: 0.7915 (mm-30) REVERT: C 226 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8542 (tt) REVERT: D 54 ARG cc_start: 0.8651 (tpt170) cc_final: 0.8303 (tpp-160) REVERT: a 111 GLU cc_start: 0.7133 (pm20) cc_final: 0.6849 (pm20) REVERT: a 190 ASN cc_start: 0.7828 (OUTLIER) cc_final: 0.7392 (p0) REVERT: b 72 ASP cc_start: 0.8822 (t0) cc_final: 0.8317 (t0) outliers start: 48 outliers final: 37 residues processed: 269 average time/residue: 0.1920 time to fit residues: 73.1089 Evaluate side-chains 277 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 238 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 145 THR Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain a residue 190 ASN Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 152 VAL Chi-restraints excluded: chain b residue 165 VAL Chi-restraints excluded: chain b residue 190 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 0.0060 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 107 optimal weight: 0.2980 chunk 67 optimal weight: 0.0670 chunk 65 optimal weight: 0.0060 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 43 optimal weight: 5.9990 overall best weight: 0.0948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9185 Z= 0.188 Angle : 0.700 10.144 12531 Z= 0.333 Chirality : 0.041 0.195 1482 Planarity : 0.005 0.052 1557 Dihedral : 4.443 21.411 1236 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.07 % Allowed : 25.16 % Favored : 70.77 % 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: 0.73 (0.26), residues: 1141 helix: 1.48 (0.20), residues: 699 sheet: -0.07 (0.81), residues: 54 loop : -1.29 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP b 26 HIS 0.023 0.001 HIS A 68 PHE 0.029 0.001 PHE B 28 TYR 0.008 0.001 TYR A 100 ARG 0.003 0.000 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 257 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 144 LEU cc_start: 0.9298 (pt) cc_final: 0.8926 (pp) REVERT: C 33 LEU cc_start: 0.8612 (tt) cc_final: 0.8273 (tt) REVERT: C 96 MET cc_start: 0.8037 (mtm) cc_final: 0.7758 (mtm) REVERT: C 226 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8512 (tt) REVERT: D 54 ARG cc_start: 0.8633 (tpt170) cc_final: 0.8269 (tpp-160) REVERT: a 111 GLU cc_start: 0.7006 (pm20) cc_final: 0.6805 (pm20) REVERT: a 190 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7384 (p0) REVERT: b 72 ASP cc_start: 0.8787 (t0) cc_final: 0.8339 (t0) outliers start: 38 outliers final: 26 residues processed: 270 average time/residue: 0.1815 time to fit residues: 69.2168 Evaluate side-chains 267 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 239 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 190 ASN Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 165 VAL Chi-restraints excluded: chain b residue 190 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 0.0670 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9185 Z= 0.290 Angle : 0.759 9.048 12531 Z= 0.360 Chirality : 0.045 0.283 1482 Planarity : 0.005 0.052 1557 Dihedral : 4.475 24.986 1236 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.18 % Allowed : 25.70 % Favored : 70.13 % 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: 0.59 (0.26), residues: 1141 helix: 1.35 (0.20), residues: 706 sheet: 0.37 (0.93), residues: 44 loop : -1.39 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 66 HIS 0.005 0.001 HIS A 174 PHE 0.027 0.002 PHE B 28 TYR 0.017 0.002 TYR A 100 ARG 0.005 0.000 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 246 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 144 LEU cc_start: 0.9296 (pt) cc_final: 0.8933 (pp) REVERT: C 96 MET cc_start: 0.8103 (mtm) cc_final: 0.7850 (mtm) REVERT: C 226 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8627 (tt) REVERT: b 72 ASP cc_start: 0.8833 (t0) cc_final: 0.8440 (t0) outliers start: 39 outliers final: 31 residues processed: 262 average time/residue: 0.1710 time to fit residues: 64.2118 Evaluate side-chains 272 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 240 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 165 VAL Chi-restraints excluded: chain b residue 190 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 103 optimal weight: 0.0870 chunk 60 optimal weight: 0.0570 chunk 43 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9185 Z= 0.207 Angle : 0.729 10.062 12531 Z= 0.345 Chirality : 0.043 0.296 1482 Planarity : 0.005 0.052 1557 Dihedral : 4.397 24.963 1236 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.43 % Allowed : 27.09 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1141 helix: 1.53 (0.20), residues: 701 sheet: 0.39 (0.93), residues: 44 loop : -1.32 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP b 26 HIS 0.003 0.000 HIS b 100 PHE 0.030 0.001 PHE B 28 TYR 0.013 0.001 TYR A 100 ARG 0.003 0.000 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 254 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 144 LEU cc_start: 0.9303 (pt) cc_final: 0.8948 (pp) REVERT: C 96 MET cc_start: 0.7977 (mtm) cc_final: 0.7729 (mtm) REVERT: C 226 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8603 (tt) REVERT: a 190 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7553 (p0) REVERT: a 193 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6681 (tm-30) REVERT: b 72 ASP cc_start: 0.8791 (t0) cc_final: 0.8454 (t0) outliers start: 32 outliers final: 25 residues processed: 266 average time/residue: 0.1821 time to fit residues: 68.7030 Evaluate side-chains 273 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 246 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 190 ASN Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 165 VAL Chi-restraints excluded: chain b residue 190 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 88 optimal weight: 20.0000 chunk 9 optimal weight: 0.0970 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 70 optimal weight: 30.0000 chunk 94 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9185 Z= 0.209 Angle : 0.727 10.129 12531 Z= 0.344 Chirality : 0.043 0.313 1482 Planarity : 0.005 0.053 1557 Dihedral : 4.323 25.099 1236 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.32 % Allowed : 27.30 % Favored : 69.38 % 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: 0.82 (0.26), residues: 1141 helix: 1.55 (0.20), residues: 699 sheet: 0.43 (0.91), residues: 44 loop : -1.27 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 234 HIS 0.003 0.000 HIS b 100 PHE 0.029 0.001 PHE B 28 TYR 0.017 0.001 TYR C 48 ARG 0.002 0.000 ARG D 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 247 time to evaluate : 1.459 Fit side-chains revert: symmetry clash REVERT: A 144 LEU cc_start: 0.9294 (pt) cc_final: 0.8943 (pp) REVERT: C 33 LEU cc_start: 0.8598 (tt) cc_final: 0.8265 (tt) REVERT: C 96 MET cc_start: 0.7990 (mtm) cc_final: 0.7750 (mtm) REVERT: C 226 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8564 (tt) REVERT: a 190 ASN cc_start: 0.7842 (OUTLIER) cc_final: 0.7544 (p0) REVERT: b 72 ASP cc_start: 0.8798 (t0) cc_final: 0.8490 (t0) outliers start: 31 outliers final: 27 residues processed: 258 average time/residue: 0.1821 time to fit residues: 66.6668 Evaluate side-chains 274 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 245 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 190 ASN Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 165 VAL Chi-restraints excluded: chain b residue 190 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.0030 chunk 88 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.124907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.095451 restraints weight = 16972.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.098479 restraints weight = 10333.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.100536 restraints weight = 7569.417| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9185 Z= 0.275 Angle : 0.757 9.315 12531 Z= 0.359 Chirality : 0.044 0.312 1482 Planarity : 0.005 0.053 1557 Dihedral : 4.350 25.424 1236 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.43 % Allowed : 27.84 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1141 helix: 1.48 (0.20), residues: 703 sheet: 0.65 (0.94), residues: 44 loop : -1.31 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP b 26 HIS 0.004 0.001 HIS A 174 PHE 0.029 0.001 PHE B 28 TYR 0.017 0.001 TYR A 100 ARG 0.004 0.000 ARG D 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2153.18 seconds wall clock time: 39 minutes 55.47 seconds (2395.47 seconds total)