Starting phenix.real_space_refine on Fri Nov 15 10:22:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cea_16602/11_2024/8cea_16602.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cea_16602/11_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_16602/11_2024/8cea_16602.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cea_16602/11_2024/8cea_16602.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cea_16602/11_2024/8cea_16602.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cea_16602/11_2024/8cea_16602.cif" } 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. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 5.61, per 1000 atoms: 0.63 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.2 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: 0.89 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: 2.29 Time building geometry restraints manager: 2.79 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: 0.00 - 3.09: 12200 3.09 - 6.18: 267 6.18 - 9.27: 59 9.27 - 12.36: 4 12.36 - 15.45: 1 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 3.120 nonbonded pdb=" O MET A 171 " pdb=" OG1 THR A 175 " model vdw 2.272 3.040 nonbonded pdb=" O PHE B 142 " pdb=" OG SER B 207 " model vdw 2.338 3.040 nonbonded pdb=" NH1 ARG a 135 " pdb=" OG1 THR a 157 " model vdw 2.362 3.120 nonbonded pdb=" N GLN C 50 " pdb=" OE1 GLN C 50 " model vdw 2.381 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.900 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.650 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.380 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.019 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: 0.2035 time to fit residues: 83.0039 Evaluate side-chains 239 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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: 1.9990 chunk 28 optimal weight: 0.0970 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 chunk 65 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 C 6 HIS ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 186 HIS ** 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: 0.7834 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9185 Z= 0.199 Angle : 0.725 9.954 12531 Z= 0.351 Chirality : 0.042 0.193 1482 Planarity : 0.006 0.061 1557 Dihedral : 5.054 17.952 1236 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.78 % Allowed : 12.96 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1141 helix: 0.47 (0.20), residues: 695 sheet: 0.23 (0.90), residues: 44 loop : -1.41 (0.30), residues: 402 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 0.027 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 296 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 270 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LEU cc_start: 0.8776 (mt) cc_final: 0.8465 (tt) REVERT: B 83 MET cc_start: 0.7037 (mtp) cc_final: 0.6691 (mtm) REVERT: C 54 TYR cc_start: 0.7820 (t80) cc_final: 0.7580 (t80) outliers start: 26 outliers final: 15 residues processed: 277 average time/residue: 0.1978 time to fit residues: 76.1271 Evaluate side-chains 259 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 244 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 4.9990 chunk 31 optimal weight: 0.0040 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN C 90 ASN ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 75 HIS a 186 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9185 Z= 0.316 Angle : 0.754 8.432 12531 Z= 0.372 Chirality : 0.045 0.213 1482 Planarity : 0.006 0.056 1557 Dihedral : 4.862 18.325 1236 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.03 % Allowed : 17.77 % Favored : 77.19 % 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: 0.07 (0.25), residues: 1141 helix: 0.83 (0.20), residues: 701 sheet: 0.32 (0.94), residues: 44 loop : -1.34 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 234 HIS 0.007 0.001 HIS A 174 PHE 0.023 0.001 PHE B 28 TYR 0.014 0.002 TYR A 100 ARG 0.008 0.001 ARG C 13 *********************** 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 304 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 257 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7815 (ttp80) REVERT: B 192 TYR cc_start: 0.6959 (m-10) cc_final: 0.6689 (m-10) REVERT: a 15 GLU cc_start: 0.7349 (pp20) cc_final: 0.6854 (pp20) REVERT: b 72 ASP cc_start: 0.8042 (t0) cc_final: 0.7799 (t0) outliers start: 47 outliers final: 32 residues processed: 280 average time/residue: 0.2216 time to fit residues: 86.8645 Evaluate side-chains 282 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 250 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 48 LEU Chi-restraints excluded: chain A residue 89 THR 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 109 LEU Chi-restraints excluded: chain B residue 170 ILE 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 91 LEU Chi-restraints excluded: chain C residue 109 VAL 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 224 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain a residue 145 THR Chi-restraints excluded: chain a residue 157 THR Chi-restraints excluded: chain a residue 181 VAL 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: 0.8980 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 HIS ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN a 101 HIS b 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9185 Z= 0.230 Angle : 0.713 8.501 12531 Z= 0.347 Chirality : 0.043 0.219 1482 Planarity : 0.005 0.053 1557 Dihedral : 4.726 16.923 1236 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.60 % Allowed : 21.20 % Favored : 74.20 % 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: 0.43 (0.25), residues: 1141 helix: 1.13 (0.20), residues: 700 sheet: 0.21 (0.94), residues: 44 loop : -1.20 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 234 HIS 0.005 0.001 HIS A 174 PHE 0.025 0.001 PHE B 28 TYR 0.011 0.001 TYR A 100 ARG 0.002 0.000 ARG B 48 *********************** 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 298 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 255 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 96 MET cc_start: 0.8146 (mtm) cc_final: 0.7843 (mtm) REVERT: C 226 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8441 (tt) REVERT: a 11 CYS cc_start: 0.7384 (t) cc_final: 0.7168 (p) REVERT: b 72 ASP cc_start: 0.8362 (t0) cc_final: 0.8118 (t0) outliers start: 43 outliers final: 29 residues processed: 271 average time/residue: 0.1977 time to fit residues: 74.4885 Evaluate side-chains 275 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 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 148 VAL 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 C residue 91 LEU 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 D residue 27 MET Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain a residue 181 VAL 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 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 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: 0.9980 chunk 80 optimal weight: 0.0770 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 36 optimal weight: 0.0670 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 HIS b 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2976 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= 0.200 Angle : 0.710 8.516 12531 Z= 0.343 Chirality : 0.042 0.229 1482 Planarity : 0.005 0.052 1557 Dihedral : 4.593 17.550 1236 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.28 % Allowed : 22.06 % Favored : 73.66 % 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: 0.56 (0.25), residues: 1141 helix: 1.28 (0.20), residues: 697 sheet: 0.18 (0.92), residues: 44 loop : -1.21 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 66 HIS 0.005 0.000 HIS A 174 PHE 0.027 0.001 PHE B 28 TYR 0.015 0.001 TYR C 48 ARG 0.003 0.000 ARG A 16 *********************** 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 312 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 272 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 GLU cc_start: 0.8084 (tp30) cc_final: 0.7840 (mm-30) REVERT: C 219 MET cc_start: 0.8939 (tmm) cc_final: 0.8673 (tmm) REVERT: C 226 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8469 (tt) REVERT: a 15 GLU cc_start: 0.7198 (pp20) cc_final: 0.6860 (pp20) REVERT: b 3 PHE cc_start: 0.9015 (t80) cc_final: 0.8637 (t80) REVERT: b 72 ASP cc_start: 0.8453 (t0) cc_final: 0.8235 (t0) outliers start: 40 outliers final: 32 residues processed: 284 average time/residue: 0.1989 time to fit residues: 78.8488 Evaluate side-chains 283 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 250 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 68 HIS Chi-restraints excluded: chain A residue 89 THR 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 207 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 112 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 226 LEU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain a residue 181 VAL 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 100 HIS Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 150 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 9185 Z= 0.379 Angle : 0.815 7.638 12531 Z= 0.396 Chirality : 0.046 0.249 1482 Planarity : 0.005 0.051 1557 Dihedral : 4.811 29.653 1236 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.78 % Allowed : 22.38 % Favored : 71.84 % 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: 0.26 (0.25), residues: 1141 helix: 1.04 (0.20), residues: 711 sheet: -0.01 (0.91), residues: 44 loop : -1.41 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 66 HIS 0.008 0.001 HIS A 174 PHE 0.027 0.002 PHE B 28 TYR 0.012 0.002 TYR A 100 ARG 0.005 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 310 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 256 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.9278 (pt) cc_final: 0.8866 (pp) REVERT: B 20 GLU cc_start: 0.8193 (tp30) cc_final: 0.7927 (mm-30) REVERT: C 199 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6708 (ptt90) REVERT: C 210 LEU cc_start: 0.9052 (tt) cc_final: 0.8822 (tt) REVERT: C 226 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8712 (tt) REVERT: a 15 GLU cc_start: 0.7066 (pp20) cc_final: 0.6817 (pp20) outliers start: 54 outliers final: 44 residues processed: 279 average time/residue: 0.2046 time to fit residues: 79.2743 Evaluate side-chains 288 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 48 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 196 ILE 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 207 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 199 ARG 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 D residue 27 MET Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 157 THR Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 83 MET Chi-restraints excluded: chain b residue 100 HIS Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 150 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.0010 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 107 optimal weight: 0.0570 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.7708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS C 52 ASN b 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9185 Z= 0.254 Angle : 0.756 9.447 12531 Z= 0.366 Chirality : 0.044 0.272 1482 Planarity : 0.005 0.050 1557 Dihedral : 4.645 20.393 1236 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.25 % Allowed : 24.41 % Favored : 70.34 % 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 (0.25), residues: 1141 helix: 1.18 (0.20), residues: 710 sheet: -0.07 (0.91), residues: 44 loop : -1.38 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 66 HIS 0.006 0.001 HIS A 68 PHE 0.028 0.001 PHE B 28 TYR 0.011 0.001 TYR B 192 ARG 0.004 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 307 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 258 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.9266 (pt) cc_final: 0.8867 (pp) REVERT: B 20 GLU cc_start: 0.8141 (tp30) cc_final: 0.7912 (mm-30) REVERT: B 122 ASP cc_start: 0.7780 (p0) cc_final: 0.6718 (p0) REVERT: C 199 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6593 (ptt90) REVERT: C 210 LEU cc_start: 0.8965 (tt) cc_final: 0.8757 (tt) REVERT: C 226 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8614 (tt) REVERT: a 15 GLU cc_start: 0.7187 (pp20) cc_final: 0.6983 (pp20) REVERT: a 193 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6582 (tm-30) outliers start: 49 outliers final: 39 residues processed: 280 average time/residue: 0.2026 time to fit residues: 78.9852 Evaluate side-chains 291 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 250 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 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 37 LEU Chi-restraints excluded: chain B residue 63 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 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 25 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 199 ARG 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 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 181 VAL 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 139 THR Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 152 VAL Chi-restraints excluded: chain b residue 165 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 0.0000 chunk 21 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 133 GLN ** C 52 ASN ** 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: 0.8109 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9185 Z= 0.324 Angle : 0.795 7.768 12531 Z= 0.386 Chirality : 0.045 0.254 1482 Planarity : 0.005 0.049 1557 Dihedral : 4.727 30.649 1236 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.03 % Allowed : 25.27 % Favored : 69.70 % 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: 1.15 (0.20), residues: 710 sheet: -0.11 (0.90), residues: 44 loop : -1.44 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 66 HIS 0.009 0.001 HIS A 68 PHE 0.028 0.002 PHE B 28 TYR 0.011 0.002 TYR A 100 ARG 0.005 0.000 ARG B 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 297 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 250 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.9278 (pt) cc_final: 0.8886 (pp) REVERT: B 20 GLU cc_start: 0.8186 (tp30) cc_final: 0.7936 (mm-30) REVERT: B 122 ASP cc_start: 0.7848 (p0) cc_final: 0.6795 (p0) REVERT: C 199 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6549 (ptt90) REVERT: C 210 LEU cc_start: 0.9039 (tt) cc_final: 0.8790 (tt) REVERT: C 226 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8743 (tt) REVERT: a 193 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6548 (tm-30) outliers start: 47 outliers final: 41 residues processed: 271 average time/residue: 0.2035 time to fit residues: 78.4757 Evaluate side-chains 282 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 239 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 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 37 LEU Chi-restraints excluded: chain B residue 63 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 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 25 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 199 ARG 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 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 49 LEU Chi-restraints excluded: chain a residue 145 THR Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 83 MET Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 152 VAL Chi-restraints excluded: chain b residue 165 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 103 optimal weight: 0.0970 chunk 60 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN b 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9185 Z= 0.213 Angle : 0.767 8.820 12531 Z= 0.370 Chirality : 0.044 0.264 1482 Planarity : 0.005 0.050 1557 Dihedral : 4.684 43.037 1236 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.28 % Allowed : 26.66 % Favored : 69.06 % 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: 0.45 (0.25), residues: 1141 helix: 1.31 (0.20), residues: 709 sheet: -0.64 (0.76), residues: 54 loop : -1.51 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 234 HIS 0.016 0.001 HIS A 68 PHE 0.030 0.001 PHE B 28 TYR 0.010 0.001 TYR B 192 ARG 0.004 0.000 ARG a 16 *********************** 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 293 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 253 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 144 LEU cc_start: 0.9271 (pt) cc_final: 0.8875 (pp) REVERT: B 20 GLU cc_start: 0.8102 (tp30) cc_final: 0.7871 (mm-30) REVERT: B 122 ASP cc_start: 0.7616 (p0) cc_final: 0.6625 (p0) REVERT: C 199 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6507 (ptt90) REVERT: C 226 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8759 (tt) REVERT: D 50 VAL cc_start: 0.8670 (t) cc_final: 0.8451 (t) REVERT: a 193 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6586 (tm-30) outliers start: 40 outliers final: 28 residues processed: 269 average time/residue: 0.1894 time to fit residues: 72.1403 Evaluate side-chains 278 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 248 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 89 THR 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 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 195 ILE 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 83 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 199 ARG Chi-restraints excluded: chain C residue 211 LEU 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 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 139 THR Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 152 VAL Chi-restraints excluded: chain b residue 165 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 111 optimal weight: 0.0470 chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 68 optimal weight: 0.1980 chunk 54 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 overall best weight: 0.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 133 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9185 Z= 0.213 Angle : 0.773 10.872 12531 Z= 0.368 Chirality : 0.044 0.319 1482 Planarity : 0.005 0.051 1557 Dihedral : 4.652 47.320 1236 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.89 % Allowed : 28.27 % Favored : 68.84 % 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: 0.52 (0.26), residues: 1141 helix: 1.36 (0.20), residues: 707 sheet: -0.59 (0.77), residues: 54 loop : -1.47 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP b 26 HIS 0.003 0.001 HIS b 100 PHE 0.029 0.001 PHE B 28 TYR 0.020 0.001 TYR C 48 ARG 0.004 0.000 ARG D 56 ********************** 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 291 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 264 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: A 144 LEU cc_start: 0.9276 (pt) cc_final: 0.8888 (pp) REVERT: B 122 ASP cc_start: 0.7586 (p0) cc_final: 0.6960 (p0) REVERT: C 226 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8649 (tt) REVERT: a 193 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6487 (tm-30) REVERT: b 3 PHE cc_start: 0.8974 (t80) cc_final: 0.8679 (t80) outliers start: 27 outliers final: 25 residues processed: 274 average time/residue: 0.1892 time to fit residues: 73.5224 Evaluate side-chains 279 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 253 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 83 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 226 LEU 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 b residue 35 PHE Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 152 VAL Chi-restraints excluded: chain b residue 165 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.0770 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS a 63 GLN b 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.128157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.098390 restraints weight = 16779.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101512 restraints weight = 10151.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103638 restraints weight = 7406.395| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9185 Z= 0.219 Angle : 0.779 8.904 12531 Z= 0.371 Chirality : 0.044 0.382 1482 Planarity : 0.005 0.052 1557 Dihedral : 4.609 50.487 1236 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.85 % Allowed : 28.05 % Favored : 68.09 % 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: 0.55 (0.26), residues: 1141 helix: 1.41 (0.20), residues: 704 sheet: -0.56 (0.77), residues: 54 loop : -1.49 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP b 26 HIS 0.004 0.001 HIS A 68 PHE 0.029 0.001 PHE B 28 TYR 0.009 0.001 TYR B 192 ARG 0.006 0.000 ARG A 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2206.40 seconds wall clock time: 40 minutes 42.82 seconds (2442.82 seconds total)