Starting phenix.real_space_refine on Fri Jan 19 10:55:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j80_36055/01_2024/8j80_36055.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j80_36055/01_2024/8j80_36055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j80_36055/01_2024/8j80_36055.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j80_36055/01_2024/8j80_36055.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j80_36055/01_2024/8j80_36055.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j80_36055/01_2024/8j80_36055.pdb" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.082 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 48 5.16 5 C 7149 2.51 5 N 1862 2.21 5 O 2112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 372": "OD1" <-> "OD2" Residue "F PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 11172 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2281 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Chain: "C" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "E" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1642 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "B" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2262 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 8, 'TRANS': 279} Chain breaks: 1 Chain: "F" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1642 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "D" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.26, per 1000 atoms: 0.56 Number of scatterers: 11172 At special positions: 0 Unit cell: (89.832, 112.684, 159.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 48 16.00 O 2112 8.00 N 1862 7.00 C 7149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 200 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 198 " distance=2.03 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: 4.52 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 70 " pdb="ZN ZN B 401 " - pdb=" ND1 HIS B 164 " 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2698 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 26 sheets defined 33.2% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 removed outlier: 3.842A pdb=" N PHE A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 28 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 58 Processing helix chain 'A' and resid 60 through 89 removed outlier: 3.599A pdb=" N LEU A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N SER A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 129 removed outlier: 3.967A pdb=" N VAL A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 159 Processing helix chain 'A' and resid 160 through 163 removed outlier: 3.684A pdb=" N GLY A 163 " --> pdb=" O LYS A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 230 through 260 removed outlier: 3.774A pdb=" N LEU A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 294 removed outlier: 3.668A pdb=" N ILE A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.419A pdb=" N ASN A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 347 through 363 Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.831A pdb=" N ALA C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 186 through 193 removed outlier: 3.829A pdb=" N HIS C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.638A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'B' and resid 24 through 32 removed outlier: 3.755A pdb=" N SER B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 31 " --> pdb=" O ARG B 27 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 59 removed outlier: 3.534A pdb=" N LEU B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 47 " --> pdb=" O CYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 89 removed outlier: 3.655A pdb=" N ILE B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 132 removed outlier: 3.525A pdb=" N THR B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 124 " --> pdb=" O PHE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 158 Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 241 through 260 removed outlier: 5.095A pdb=" N GLY B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 294 removed outlier: 3.910A pdb=" N ILE B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 298 through 303 removed outlier: 4.558A pdb=" N ASN B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 314 Processing helix chain 'B' and resid 347 through 362 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.555A pdb=" N THR F 90 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 193 No H-bonds generated for 'chain 'F' and resid 191 through 193' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.518A pdb=" N ASP D 86 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 83 through 87' Processing helix chain 'D' and resid 125 through 132 Processing helix chain 'D' and resid 187 through 193 removed outlier: 3.920A pdb=" N HIS D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 330 removed outlier: 5.698A pdb=" N LEU A 321 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE A 341 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLU A 323 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS A 339 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.559A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.559A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR C 101 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'C' and resid 118 through 122 removed outlier: 5.841A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 157 through 159 removed outlier: 4.458A pdb=" N TRP C 152 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.612A pdb=" N VAL E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'E' and resid 125 through 129 removed outlier: 5.880A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 125 through 129 removed outlier: 5.880A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 156 through 159 Processing sheet with id=AB5, first strand: chain 'B' and resid 318 through 330 removed outlier: 5.669A pdb=" N LEU B 321 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 341 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU B 323 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS B 339 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.530A pdb=" N VAL F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.929A pdb=" N TYR F 107 " --> pdb=" O ARG F 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 125 through 129 removed outlier: 6.219A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 125 through 129 removed outlier: 6.219A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 156 through 159 Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.530A pdb=" N MET D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N TYR D 53 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 14 removed outlier: 3.712A pdb=" N THR D 101 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AC7, first strand: chain 'D' and resid 118 through 122 removed outlier: 5.790A pdb=" N TYR D 177 " --> pdb=" O ASN D 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 157 through 159 removed outlier: 4.577A pdb=" N TRP D 152 " --> pdb=" O ARG D 159 " (cutoff:3.500A) 663 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3523 1.34 - 1.46: 2537 1.46 - 1.58: 5313 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 11443 Sorted by residual: bond pdb=" N HIS B 138 " pdb=" CA HIS B 138 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.19e-02 7.06e+03 7.56e+00 bond pdb=" CA PRO A 133 " pdb=" C PRO A 133 " ideal model delta sigma weight residual 1.517 1.541 -0.024 9.30e-03 1.16e+04 6.80e+00 bond pdb=" N ASP A 135 " pdb=" CA ASP A 135 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.19e-02 7.06e+03 6.34e+00 bond pdb=" N MET E 140 " pdb=" CA MET E 140 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.23e-02 6.61e+03 6.17e+00 bond pdb=" N VAL A 136 " pdb=" CA VAL A 136 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.25e-02 6.40e+03 6.17e+00 ... (remaining 11438 not shown) Histogram of bond angle deviations from ideal: 99.12 - 106.13: 295 106.13 - 113.13: 6228 113.13 - 120.14: 3849 120.14 - 127.14: 5055 127.14 - 134.15: 152 Bond angle restraints: 15579 Sorted by residual: angle pdb=" N PRO A 133 " pdb=" CA PRO A 133 " pdb=" C PRO A 133 " ideal model delta sigma weight residual 110.70 115.54 -4.84 1.22e+00 6.72e-01 1.57e+01 angle pdb=" CA PRO A 133 " pdb=" C PRO A 133 " pdb=" N PRO A 134 " ideal model delta sigma weight residual 117.93 122.38 -4.45 1.20e+00 6.94e-01 1.38e+01 angle pdb=" CA ASP B 267 " pdb=" CB ASP B 267 " pdb=" CG ASP B 267 " ideal model delta sigma weight residual 112.60 116.03 -3.43 1.00e+00 1.00e+00 1.18e+01 angle pdb=" CA MET C 179 " pdb=" CB MET C 179 " pdb=" CG MET C 179 " ideal model delta sigma weight residual 114.10 120.44 -6.34 2.00e+00 2.50e-01 1.00e+01 angle pdb=" CA LEU C 129 " pdb=" CB LEU C 129 " pdb=" CG LEU C 129 " ideal model delta sigma weight residual 116.30 127.31 -11.01 3.50e+00 8.16e-02 9.89e+00 ... (remaining 15574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5869 17.99 - 35.99: 659 35.99 - 53.98: 167 53.98 - 71.98: 48 71.98 - 89.97: 13 Dihedral angle restraints: 6756 sinusoidal: 2570 harmonic: 4186 Sorted by residual: dihedral pdb=" CB CYS E 145 " pdb=" SG CYS E 145 " pdb=" SG CYS E 200 " pdb=" CB CYS E 200 " ideal model delta sinusoidal sigma weight residual 93.00 49.18 43.82 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CB CYS D 138 " pdb=" SG CYS D 138 " pdb=" SG CYS D 198 " pdb=" CB CYS D 198 " ideal model delta sinusoidal sigma weight residual -86.00 -124.02 38.02 1 1.00e+01 1.00e-02 2.04e+01 dihedral pdb=" CA TYR E 94 " pdb=" C TYR E 94 " pdb=" N CYS E 95 " pdb=" CA CYS E 95 " ideal model delta harmonic sigma weight residual 180.00 160.90 19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 6753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1328 0.049 - 0.099: 345 0.099 - 0.148: 97 0.148 - 0.197: 9 0.197 - 0.246: 4 Chirality restraints: 1783 Sorted by residual: chirality pdb=" CA ASP B 267 " pdb=" N ASP B 267 " pdb=" C ASP B 267 " pdb=" CB ASP B 267 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB VAL F 188 " pdb=" CA VAL F 188 " pdb=" CG1 VAL F 188 " pdb=" CG2 VAL F 188 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA VAL A 136 " pdb=" N VAL A 136 " pdb=" C VAL A 136 " pdb=" CB VAL A 136 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1780 not shown) Planarity restraints: 1973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 140 " 0.435 9.50e-02 1.11e+02 1.95e-01 2.34e+01 pdb=" NE ARG B 140 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG B 140 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 140 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 140 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 287 " -0.264 9.50e-02 1.11e+02 1.18e-01 8.61e+00 pdb=" NE ARG A 287 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 287 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 287 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 287 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 188 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO F 189 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO F 189 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 189 " -0.032 5.00e-02 4.00e+02 ... (remaining 1970 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 76 2.57 - 3.15: 8703 3.15 - 3.74: 18060 3.74 - 4.32: 25536 4.32 - 4.90: 41560 Nonbonded interactions: 93935 Sorted by model distance: nonbonded pdb=" OD2 ASP B 74 " pdb="ZN ZN B 401 " model vdw 1.989 2.230 nonbonded pdb=" OD2 ASP B 244 " pdb="ZN ZN B 401 " model vdw 2.027 2.230 nonbonded pdb=" OD1 ASP B 74 " pdb="ZN ZN B 401 " model vdw 2.074 2.230 nonbonded pdb=" OD1 ASP A 74 " pdb=" NE2 HIS A 240 " model vdw 2.256 2.520 nonbonded pdb=" O VAL A 318 " pdb=" NH1 ARG E 56 " model vdw 2.257 2.520 ... (remaining 93930 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' and (resid 22 through 163 or resid 233 through 376)) selection = (chain 'B' and (resid 22 through 163 or resid 233 through 376)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 2.760 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 35.510 Find NCS groups from input model: 0.680 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:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 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 0.045 11443 Z= 0.312 Angle : 0.728 11.009 15579 Z= 0.387 Chirality : 0.048 0.246 1783 Planarity : 0.007 0.195 1973 Dihedral : 17.007 89.971 4034 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.05 % Allowed : 25.06 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 0.48 (0.22), residues: 1428 helix: 0.84 (0.26), residues: 417 sheet: 0.68 (0.23), residues: 479 loop : -0.32 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 159 HIS 0.007 0.001 HIS A 240 PHE 0.024 0.002 PHE D 36 TYR 0.024 0.002 TYR C 91 ARG 0.018 0.001 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ARG cc_start: 0.7207 (mmm-85) cc_final: 0.6983 (tmm-80) REVERT: A 287 ARG cc_start: 0.7360 (ttp-170) cc_final: 0.6152 (mmp-170) REVERT: A 322 GLN cc_start: 0.7785 (pt0) cc_final: 0.7083 (pm20) REVERT: C 10 SER cc_start: 0.8380 (t) cc_final: 0.8078 (m) REVERT: C 11 LEU cc_start: 0.7358 (tt) cc_final: 0.6943 (pt) REVERT: C 58 LEU cc_start: 0.8537 (mt) cc_final: 0.8270 (mm) REVERT: C 72 ARG cc_start: 0.6186 (ttm-80) cc_final: 0.5133 (mtp85) REVERT: C 97 GLU cc_start: 0.7623 (tt0) cc_final: 0.6391 (tm-30) REVERT: E 5 GLN cc_start: 0.7150 (mt0) cc_final: 0.6491 (mp10) REVERT: E 94 TYR cc_start: 0.7492 (m-80) cc_final: 0.7281 (m-80) REVERT: B 48 PHE cc_start: 0.7940 (t80) cc_final: 0.7740 (t80) REVERT: B 89 LYS cc_start: 0.7483 (mttp) cc_final: 0.7268 (mttp) REVERT: B 287 ARG cc_start: 0.6777 (ttm110) cc_final: 0.5405 (mmt180) REVERT: B 288 GLU cc_start: 0.7031 (tt0) cc_final: 0.6595 (tm-30) REVERT: B 303 ASN cc_start: 0.7708 (m-40) cc_final: 0.7470 (m110) REVERT: B 307 GLN cc_start: 0.6282 (tm-30) cc_final: 0.6013 (tp-100) REVERT: B 310 GLN cc_start: 0.7587 (tt0) cc_final: 0.6559 (mm110) REVERT: F 3 GLN cc_start: 0.7321 (tt0) cc_final: 0.6322 (tm-30) REVERT: F 46 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6213 (mt-10) REVERT: D 72 ARG cc_start: 0.6486 (mtm-85) cc_final: 0.5911 (mtp85) REVERT: D 203 LYS cc_start: 0.8815 (tmmm) cc_final: 0.8348 (tmmt) outliers start: 38 outliers final: 14 residues processed: 189 average time/residue: 1.1124 time to fit residues: 229.2534 Evaluate side-chains 143 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 201 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 110 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 0.0570 chunk 82 optimal weight: 40.0000 chunk 128 optimal weight: 20.0000 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 161 HIS A 232 GLN A 303 ASN A 310 GLN A 325 HIS A 356 HIS C 57 ASN C 141 ASN E 73 ASN E 83 ASN E 160 ASN E 204 HIS B 111 ASN B 137 HIS B 260 ASN B 356 HIS F 73 ASN F 204 HIS ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11443 Z= 0.158 Angle : 0.553 8.880 15579 Z= 0.284 Chirality : 0.043 0.278 1783 Planarity : 0.004 0.050 1973 Dihedral : 5.899 101.198 1566 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.53 % Allowed : 24.50 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 1.20 (0.22), residues: 1428 helix: 1.85 (0.26), residues: 419 sheet: 1.00 (0.23), residues: 477 loop : -0.19 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 327 HIS 0.007 0.001 HIS F 169 PHE 0.017 0.001 PHE E 80 TYR 0.012 0.001 TYR F 94 ARG 0.007 0.001 ARG C 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 143 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.6962 (ttp80) cc_final: 0.6703 (ttp80) REVERT: A 231 ARG cc_start: 0.7171 (mmm-85) cc_final: 0.6885 (ttt-90) REVERT: A 287 ARG cc_start: 0.7372 (ttp-170) cc_final: 0.6119 (mmt-90) REVERT: A 322 GLN cc_start: 0.7791 (pt0) cc_final: 0.7141 (pm20) REVERT: C 10 SER cc_start: 0.8426 (t) cc_final: 0.8087 (m) REVERT: C 11 LEU cc_start: 0.7271 (tt) cc_final: 0.6874 (pt) REVERT: C 72 ARG cc_start: 0.6178 (ttm-80) cc_final: 0.5220 (mtp-110) REVERT: C 97 GLU cc_start: 0.7628 (tt0) cc_final: 0.6373 (tm-30) REVERT: E 5 GLN cc_start: 0.7120 (mt0) cc_final: 0.6504 (mp10) REVERT: E 70 SER cc_start: 0.7652 (t) cc_final: 0.7094 (p) REVERT: B 89 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7265 (mttp) REVERT: B 104 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6811 (mt-10) REVERT: B 287 ARG cc_start: 0.6721 (ttm110) cc_final: 0.5272 (mmp-170) REVERT: B 288 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6629 (tm-30) REVERT: B 303 ASN cc_start: 0.7742 (m-40) cc_final: 0.7444 (m110) REVERT: B 307 GLN cc_start: 0.6274 (tm-30) cc_final: 0.5918 (mm-40) REVERT: B 310 GLN cc_start: 0.7484 (tt0) cc_final: 0.6511 (mm-40) REVERT: F 3 GLN cc_start: 0.7250 (tt0) cc_final: 0.6244 (tm-30) REVERT: F 46 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6258 (mt-10) REVERT: F 218 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7339 (ttt180) REVERT: D 49 LYS cc_start: 0.7522 (tttt) cc_final: 0.7310 (tttp) REVERT: D 72 ARG cc_start: 0.6448 (mtm-85) cc_final: 0.5926 (mtp85) REVERT: D 146 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8214 (mmtm) outliers start: 44 outliers final: 11 residues processed: 173 average time/residue: 1.3176 time to fit residues: 245.6404 Evaluate side-chains 152 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain F residue 218 ARG Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 60.0000 chunk 39 optimal weight: 8.9990 chunk 106 optimal weight: 0.0570 chunk 87 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 138 optimal weight: 30.0000 chunk 114 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN E 83 ASN E 110 GLN B 164 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 HIS ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11443 Z= 0.393 Angle : 0.638 7.281 15579 Z= 0.335 Chirality : 0.047 0.270 1783 Planarity : 0.005 0.076 1973 Dihedral : 5.363 59.535 1555 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.50 % Allowed : 23.61 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 1.06 (0.22), residues: 1428 helix: 1.63 (0.25), residues: 421 sheet: 0.88 (0.23), residues: 479 loop : -0.13 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 52 HIS 0.010 0.001 HIS B 137 PHE 0.022 0.002 PHE A 359 TYR 0.018 0.002 TYR F 94 ARG 0.006 0.001 ARG F 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 136 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7005 (ttp80) cc_final: 0.6684 (ttp80) REVERT: A 231 ARG cc_start: 0.7013 (mmm-85) cc_final: 0.6720 (tmm-80) REVERT: A 287 ARG cc_start: 0.7397 (ttp-170) cc_final: 0.6111 (mmt-90) REVERT: C 10 SER cc_start: 0.8418 (t) cc_final: 0.8070 (m) REVERT: C 72 ARG cc_start: 0.6270 (ttm-80) cc_final: 0.5260 (mtp-110) REVERT: C 97 GLU cc_start: 0.7763 (tt0) cc_final: 0.6512 (tm-30) REVERT: E 5 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6610 (mp10) REVERT: E 18 LEU cc_start: 0.7415 (tp) cc_final: 0.7032 (tp) REVERT: E 57 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7487 (m) REVERT: E 94 TYR cc_start: 0.7941 (m-80) cc_final: 0.7660 (m-80) REVERT: B 89 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7345 (mttp) REVERT: B 287 ARG cc_start: 0.6852 (ttm110) cc_final: 0.5506 (mmt180) REVERT: B 288 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6791 (tm-30) REVERT: B 303 ASN cc_start: 0.7927 (m-40) cc_final: 0.7562 (m110) REVERT: B 307 GLN cc_start: 0.6386 (tm-30) cc_final: 0.5968 (tp-100) REVERT: B 310 GLN cc_start: 0.7484 (tt0) cc_final: 0.6606 (mm-40) REVERT: B 322 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7242 (mt0) REVERT: B 376 MET cc_start: 0.6556 (OUTLIER) cc_final: 0.5517 (tpt) REVERT: F 46 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6487 (mt-10) REVERT: D 32 TYR cc_start: 0.6956 (OUTLIER) cc_final: 0.6376 (m-10) REVERT: D 49 LYS cc_start: 0.7416 (tttt) cc_final: 0.7169 (tttp) REVERT: D 72 ARG cc_start: 0.6348 (mtm-85) cc_final: 0.5768 (mtp85) REVERT: D 109 GLU cc_start: 0.6084 (OUTLIER) cc_final: 0.5701 (tt0) outliers start: 56 outliers final: 26 residues processed: 171 average time/residue: 1.2272 time to fit residues: 226.7253 Evaluate side-chains 169 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 218 ARG Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 203 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 66 optimal weight: 30.0000 chunk 14 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 128 optimal weight: 0.3980 chunk 136 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN E 83 ASN ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11443 Z= 0.347 Angle : 0.613 7.475 15579 Z= 0.320 Chirality : 0.045 0.244 1783 Planarity : 0.005 0.071 1973 Dihedral : 5.370 59.938 1555 Min Nonbonded Distance : 1.449 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.87 % Favored : 97.06 % Rotamer: Outliers : 4.90 % Allowed : 23.53 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 1.11 (0.22), residues: 1428 helix: 1.62 (0.25), residues: 421 sheet: 0.98 (0.23), residues: 479 loop : -0.13 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 52 HIS 0.018 0.002 HIS B 70 PHE 0.021 0.002 PHE C 36 TYR 0.017 0.002 TYR F 94 ARG 0.006 0.000 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 138 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.6984 (ttp80) cc_final: 0.6611 (ttp80) REVERT: A 55 TYR cc_start: 0.3587 (OUTLIER) cc_final: 0.3344 (t80) REVERT: A 231 ARG cc_start: 0.7003 (mmm-85) cc_final: 0.6727 (tmm-80) REVERT: A 287 ARG cc_start: 0.7309 (ttp-170) cc_final: 0.6059 (mmt-90) REVERT: C 10 SER cc_start: 0.8398 (t) cc_final: 0.8048 (m) REVERT: C 72 ARG cc_start: 0.6367 (ttm-80) cc_final: 0.5357 (mtp-110) REVERT: C 97 GLU cc_start: 0.7811 (tt0) cc_final: 0.6538 (tm-30) REVERT: E 5 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6579 (mp10) REVERT: E 18 LEU cc_start: 0.7458 (tp) cc_final: 0.7128 (tp) REVERT: E 57 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7442 (m) REVERT: E 70 SER cc_start: 0.7862 (OUTLIER) cc_final: 0.7297 (p) REVERT: E 94 TYR cc_start: 0.7944 (m-80) cc_final: 0.7632 (m-80) REVERT: B 89 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7351 (mttp) REVERT: B 287 ARG cc_start: 0.6826 (ttm110) cc_final: 0.5495 (mmt180) REVERT: B 288 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6801 (tm-30) REVERT: B 303 ASN cc_start: 0.7896 (m-40) cc_final: 0.7470 (m110) REVERT: B 307 GLN cc_start: 0.6361 (tm-30) cc_final: 0.5947 (tp-100) REVERT: B 310 GLN cc_start: 0.7484 (tt0) cc_final: 0.6598 (mm-40) REVERT: B 376 MET cc_start: 0.6578 (OUTLIER) cc_final: 0.5542 (tpt) REVERT: F 5 GLN cc_start: 0.6417 (OUTLIER) cc_final: 0.5787 (pm20) REVERT: F 46 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6483 (mt-10) REVERT: F 82 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7237 (ttm) REVERT: F 218 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7243 (ttt180) REVERT: D 32 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.6304 (m-10) REVERT: D 49 LYS cc_start: 0.7416 (tttt) cc_final: 0.7160 (tttp) REVERT: D 72 ARG cc_start: 0.6359 (mtm-85) cc_final: 0.5759 (mtp85) REVERT: D 109 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5715 (tt0) REVERT: D 203 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8609 (tmmt) outliers start: 61 outliers final: 29 residues processed: 174 average time/residue: 1.1817 time to fit residues: 222.5702 Evaluate side-chains 178 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 136 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 218 ARG Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 203 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 30.0000 chunk 77 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 122 optimal weight: 40.0000 chunk 34 optimal weight: 8.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN E 83 ASN ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11443 Z= 0.230 Angle : 0.568 9.335 15579 Z= 0.294 Chirality : 0.043 0.219 1783 Planarity : 0.004 0.052 1973 Dihedral : 5.228 58.824 1555 Min Nonbonded Distance : 1.503 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.37 % Allowed : 24.82 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 1.31 (0.22), residues: 1428 helix: 1.89 (0.25), residues: 418 sheet: 1.10 (0.23), residues: 479 loop : -0.11 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 52 HIS 0.012 0.001 HIS B 70 PHE 0.018 0.002 PHE C 36 TYR 0.014 0.001 TYR F 94 ARG 0.006 0.000 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 139 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.6993 (ttp80) cc_final: 0.6583 (ttp80) REVERT: A 55 TYR cc_start: 0.3655 (OUTLIER) cc_final: 0.3383 (t80) REVERT: A 287 ARG cc_start: 0.7281 (ttp-170) cc_final: 0.6038 (mmt-90) REVERT: A 322 GLN cc_start: 0.7857 (pt0) cc_final: 0.7169 (pm20) REVERT: C 10 SER cc_start: 0.8402 (t) cc_final: 0.8037 (m) REVERT: C 72 ARG cc_start: 0.6361 (ttm-80) cc_final: 0.5364 (mtp-110) REVERT: C 97 GLU cc_start: 0.7785 (tt0) cc_final: 0.6510 (tm-30) REVERT: E 5 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6545 (mp10) REVERT: E 18 LEU cc_start: 0.7447 (tp) cc_final: 0.7146 (tp) REVERT: E 94 TYR cc_start: 0.7968 (m-80) cc_final: 0.7581 (m-80) REVERT: B 89 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7312 (mttp) REVERT: B 287 ARG cc_start: 0.6810 (ttm110) cc_final: 0.5444 (mmt180) REVERT: B 288 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6731 (tm-30) REVERT: B 303 ASN cc_start: 0.7893 (m-40) cc_final: 0.7437 (m110) REVERT: B 307 GLN cc_start: 0.6412 (tm-30) cc_final: 0.6031 (tp-100) REVERT: B 310 GLN cc_start: 0.7462 (tt0) cc_final: 0.6566 (mm-40) REVERT: B 376 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.5257 (tpt) REVERT: F 3 GLN cc_start: 0.7093 (tt0) cc_final: 0.6049 (tm-30) REVERT: F 5 GLN cc_start: 0.6478 (OUTLIER) cc_final: 0.5445 (pm20) REVERT: F 46 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6438 (mt-10) REVERT: F 218 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7191 (ttt180) REVERT: D 32 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.6172 (m-10) REVERT: D 49 LYS cc_start: 0.7414 (tttt) cc_final: 0.7175 (tttp) REVERT: D 72 ARG cc_start: 0.6395 (mtm-85) cc_final: 0.5786 (mtp85) REVERT: D 109 GLU cc_start: 0.6050 (OUTLIER) cc_final: 0.5625 (tt0) REVERT: D 203 LYS cc_start: 0.8972 (tmmm) cc_final: 0.8525 (tmmt) outliers start: 42 outliers final: 23 residues processed: 167 average time/residue: 1.2826 time to fit residues: 230.9724 Evaluate side-chains 166 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 218 ARG Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 174 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 chunk 63 optimal weight: 40.0000 chunk 11 optimal weight: 1.9990 chunk 71 optimal weight: 70.0000 chunk 131 optimal weight: 40.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN E 83 ASN E 110 GLN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11443 Z= 0.185 Angle : 0.546 8.121 15579 Z= 0.280 Chirality : 0.042 0.203 1783 Planarity : 0.004 0.054 1973 Dihedral : 5.026 57.472 1554 Min Nonbonded Distance : 1.571 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.69 % Allowed : 25.46 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 1.48 (0.22), residues: 1428 helix: 2.12 (0.25), residues: 418 sheet: 1.14 (0.23), residues: 477 loop : -0.03 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 52 HIS 0.008 0.001 HIS B 70 PHE 0.016 0.001 PHE E 80 TYR 0.012 0.001 TYR F 94 ARG 0.011 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 137 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.6983 (ttp80) cc_final: 0.6541 (ttp80) REVERT: A 55 TYR cc_start: 0.3623 (OUTLIER) cc_final: 0.3349 (t80) REVERT: A 231 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.5303 (tmm-80) REVERT: A 287 ARG cc_start: 0.7283 (ttp-170) cc_final: 0.6016 (mmt-90) REVERT: A 322 GLN cc_start: 0.7834 (pt0) cc_final: 0.7155 (pm20) REVERT: C 10 SER cc_start: 0.8397 (t) cc_final: 0.8021 (m) REVERT: C 72 ARG cc_start: 0.6354 (ttm-80) cc_final: 0.5359 (mtp-110) REVERT: C 97 GLU cc_start: 0.7770 (tt0) cc_final: 0.6496 (tm-30) REVERT: E 5 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6580 (mp10) REVERT: E 57 THR cc_start: 0.7732 (OUTLIER) cc_final: 0.7491 (m) REVERT: E 70 SER cc_start: 0.7863 (OUTLIER) cc_final: 0.7383 (p) REVERT: E 94 TYR cc_start: 0.7904 (m-80) cc_final: 0.7531 (m-80) REVERT: B 89 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7323 (mttp) REVERT: B 287 ARG cc_start: 0.6785 (ttm110) cc_final: 0.5349 (mmt180) REVERT: B 288 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6679 (tm-30) REVERT: B 303 ASN cc_start: 0.7894 (m-40) cc_final: 0.7456 (m110) REVERT: B 307 GLN cc_start: 0.6401 (tm-30) cc_final: 0.6030 (tp-100) REVERT: B 310 GLN cc_start: 0.7485 (tt0) cc_final: 0.6598 (mm-40) REVERT: B 376 MET cc_start: 0.6606 (OUTLIER) cc_final: 0.6327 (tpp) REVERT: F 3 GLN cc_start: 0.7133 (tt0) cc_final: 0.6103 (tm-30) REVERT: F 5 GLN cc_start: 0.6425 (OUTLIER) cc_final: 0.5375 (pm20) REVERT: F 46 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6423 (mt-10) REVERT: F 218 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7197 (ttt180) REVERT: D 32 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.5992 (m-10) REVERT: D 49 LYS cc_start: 0.7414 (tttt) cc_final: 0.7177 (tttp) REVERT: D 72 ARG cc_start: 0.6387 (mtm-85) cc_final: 0.5784 (mtp85) REVERT: D 109 GLU cc_start: 0.6041 (OUTLIER) cc_final: 0.5623 (tt0) REVERT: D 203 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8592 (tmmt) outliers start: 46 outliers final: 19 residues processed: 165 average time/residue: 1.2618 time to fit residues: 224.8448 Evaluate side-chains 162 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 218 ARG Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 203 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 135 optimal weight: 50.0000 chunk 85 optimal weight: 0.0870 chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 84 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 overall best weight: 1.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN E 83 ASN F 83 ASN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11443 Z= 0.211 Angle : 0.568 9.862 15579 Z= 0.289 Chirality : 0.043 0.186 1783 Planarity : 0.004 0.053 1973 Dihedral : 4.760 56.219 1552 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.37 % Allowed : 25.86 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 1.49 (0.22), residues: 1428 helix: 2.08 (0.25), residues: 419 sheet: 1.20 (0.23), residues: 477 loop : -0.03 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 52 HIS 0.004 0.001 HIS B 164 PHE 0.019 0.002 PHE C 213 TYR 0.014 0.001 TYR F 94 ARG 0.008 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 136 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.6982 (ttp80) cc_final: 0.6520 (ttp80) REVERT: A 55 TYR cc_start: 0.3697 (OUTLIER) cc_final: 0.3418 (t80) REVERT: A 264 MET cc_start: 0.8828 (tpp) cc_final: 0.8434 (tpp) REVERT: A 287 ARG cc_start: 0.7291 (ttp-170) cc_final: 0.6011 (mmt-90) REVERT: A 322 GLN cc_start: 0.7845 (pt0) cc_final: 0.7169 (pm20) REVERT: C 72 ARG cc_start: 0.6354 (ttm-80) cc_final: 0.5839 (ttm-80) REVERT: C 97 GLU cc_start: 0.7745 (tt0) cc_final: 0.6498 (tm-30) REVERT: E 5 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6577 (mp10) REVERT: E 18 LEU cc_start: 0.7510 (tp) cc_final: 0.7169 (tp) REVERT: E 57 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7482 (m) REVERT: E 70 SER cc_start: 0.7867 (OUTLIER) cc_final: 0.7376 (p) REVERT: E 94 TYR cc_start: 0.7924 (m-80) cc_final: 0.7585 (m-80) REVERT: E 156 THR cc_start: 0.8684 (m) cc_final: 0.8296 (p) REVERT: B 89 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7333 (mttp) REVERT: B 287 ARG cc_start: 0.6790 (ttm110) cc_final: 0.5325 (mmt180) REVERT: B 288 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6696 (tm-30) REVERT: B 303 ASN cc_start: 0.7889 (m-40) cc_final: 0.7433 (m110) REVERT: B 307 GLN cc_start: 0.6408 (tm-30) cc_final: 0.6030 (tp-100) REVERT: B 310 GLN cc_start: 0.7485 (tt0) cc_final: 0.6595 (mm-40) REVERT: B 322 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7358 (mt0) REVERT: B 376 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.6367 (tpp) REVERT: F 3 GLN cc_start: 0.7174 (tt0) cc_final: 0.6125 (tm-30) REVERT: F 5 GLN cc_start: 0.6439 (OUTLIER) cc_final: 0.5376 (pm20) REVERT: F 46 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6421 (mt-10) REVERT: F 218 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7213 (ttt180) REVERT: D 32 TYR cc_start: 0.6762 (OUTLIER) cc_final: 0.6068 (m-10) REVERT: D 49 LYS cc_start: 0.7426 (tttt) cc_final: 0.7191 (tttp) REVERT: D 72 ARG cc_start: 0.6401 (mtm-85) cc_final: 0.5789 (mtp85) REVERT: D 109 GLU cc_start: 0.6024 (OUTLIER) cc_final: 0.5594 (tt0) REVERT: D 203 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8614 (tmmt) outliers start: 42 outliers final: 22 residues processed: 164 average time/residue: 1.2718 time to fit residues: 224.8144 Evaluate side-chains 162 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 218 ARG Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 203 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 26 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 50.0000 chunk 12 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 118 optimal weight: 40.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN E 83 ASN E 110 GLN B 161 HIS F 83 ASN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11443 Z= 0.322 Angle : 0.617 10.226 15579 Z= 0.315 Chirality : 0.045 0.179 1783 Planarity : 0.005 0.064 1973 Dihedral : 4.861 54.681 1552 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.45 % Allowed : 26.18 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 1.37 (0.22), residues: 1428 helix: 1.85 (0.25), residues: 419 sheet: 1.21 (0.23), residues: 479 loop : -0.09 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 52 HIS 0.005 0.001 HIS C 38 PHE 0.020 0.002 PHE A 359 TYR 0.018 0.002 TYR F 94 ARG 0.008 0.001 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 137 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7000 (ttp80) cc_final: 0.6531 (ttp80) REVERT: A 55 TYR cc_start: 0.3763 (OUTLIER) cc_final: 0.3455 (t80) REVERT: A 287 ARG cc_start: 0.7343 (ttp-170) cc_final: 0.6054 (mmt-90) REVERT: C 72 ARG cc_start: 0.6358 (ttm-80) cc_final: 0.5345 (mtp-110) REVERT: C 97 GLU cc_start: 0.7800 (tt0) cc_final: 0.6530 (tm-30) REVERT: E 5 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6583 (mp10) REVERT: E 18 LEU cc_start: 0.7536 (tp) cc_final: 0.7166 (tp) REVERT: E 57 THR cc_start: 0.7732 (OUTLIER) cc_final: 0.7458 (m) REVERT: E 70 SER cc_start: 0.7878 (OUTLIER) cc_final: 0.7307 (p) REVERT: E 94 TYR cc_start: 0.7952 (m-80) cc_final: 0.7691 (m-80) REVERT: B 89 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7366 (mttp) REVERT: B 287 ARG cc_start: 0.6837 (ttm110) cc_final: 0.5456 (mmt180) REVERT: B 288 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6737 (tm-30) REVERT: B 303 ASN cc_start: 0.7880 (m-40) cc_final: 0.7408 (m110) REVERT: B 307 GLN cc_start: 0.6381 (tm-30) cc_final: 0.5954 (tp-100) REVERT: B 310 GLN cc_start: 0.7487 (tt0) cc_final: 0.6597 (mm-40) REVERT: B 322 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7199 (mt0) REVERT: B 376 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.5547 (tpt) REVERT: F 3 GLN cc_start: 0.7129 (tt0) cc_final: 0.6102 (tm-30) REVERT: F 5 GLN cc_start: 0.6448 (OUTLIER) cc_final: 0.5383 (pm20) REVERT: F 46 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6381 (mt-10) REVERT: F 218 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7254 (ttt180) REVERT: D 32 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.6282 (m-10) REVERT: D 72 ARG cc_start: 0.6413 (mtm-85) cc_final: 0.5783 (mtp85) REVERT: D 109 GLU cc_start: 0.5993 (OUTLIER) cc_final: 0.5567 (tt0) REVERT: D 187 LYS cc_start: 0.7834 (tppp) cc_final: 0.7421 (mptt) REVERT: D 203 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8627 (tmmt) outliers start: 43 outliers final: 26 residues processed: 162 average time/residue: 1.2222 time to fit residues: 214.3068 Evaluate side-chains 174 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 135 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 218 ARG Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 203 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.0270 chunk 130 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 99 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 114 optimal weight: 30.0000 chunk 119 optimal weight: 40.0000 chunk 83 optimal weight: 5.9990 chunk 133 optimal weight: 50.0000 chunk 81 optimal weight: 3.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN E 83 ASN F 83 ASN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11443 Z= 0.156 Angle : 0.567 12.815 15579 Z= 0.281 Chirality : 0.042 0.174 1783 Planarity : 0.004 0.052 1973 Dihedral : 4.618 53.454 1552 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.25 % Allowed : 27.63 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 1.59 (0.22), residues: 1428 helix: 2.19 (0.25), residues: 419 sheet: 1.27 (0.23), residues: 482 loop : -0.02 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 52 HIS 0.004 0.001 HIS B 70 PHE 0.016 0.001 PHE E 80 TYR 0.010 0.001 TYR F 94 ARG 0.009 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.6962 (ttp80) cc_final: 0.6497 (ttp80) REVERT: A 55 TYR cc_start: 0.3729 (OUTLIER) cc_final: 0.3472 (t80) REVERT: A 287 ARG cc_start: 0.7276 (ttp-170) cc_final: 0.6017 (mmt-90) REVERT: A 322 GLN cc_start: 0.7825 (pt0) cc_final: 0.7166 (pm20) REVERT: C 24 ARG cc_start: 0.6630 (ttm-80) cc_final: 0.5891 (ttp-170) REVERT: C 72 ARG cc_start: 0.6382 (ttm-80) cc_final: 0.5860 (ttm-80) REVERT: C 97 GLU cc_start: 0.7736 (tt0) cc_final: 0.6475 (tm-30) REVERT: E 5 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6521 (pm20) REVERT: E 18 LEU cc_start: 0.7581 (tp) cc_final: 0.7217 (tp) REVERT: E 70 SER cc_start: 0.7866 (OUTLIER) cc_final: 0.7383 (p) REVERT: E 94 TYR cc_start: 0.7896 (m-80) cc_final: 0.7487 (m-80) REVERT: E 156 THR cc_start: 0.8682 (m) cc_final: 0.8298 (p) REVERT: B 89 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7329 (mmtp) REVERT: B 287 ARG cc_start: 0.6754 (ttm110) cc_final: 0.5301 (mmt180) REVERT: B 288 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6631 (tm-30) REVERT: B 303 ASN cc_start: 0.7875 (m-40) cc_final: 0.7397 (m110) REVERT: B 307 GLN cc_start: 0.6381 (tm-30) cc_final: 0.6023 (tp-100) REVERT: B 310 GLN cc_start: 0.7450 (tt0) cc_final: 0.6602 (mm-40) REVERT: B 322 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7198 (mt0) REVERT: B 376 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.6340 (tpp) REVERT: F 3 GLN cc_start: 0.7205 (tt0) cc_final: 0.6176 (tm-30) REVERT: F 5 GLN cc_start: 0.6456 (OUTLIER) cc_final: 0.5401 (pm20) REVERT: F 46 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6476 (mt-10) REVERT: F 218 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7399 (mtt90) REVERT: D 32 TYR cc_start: 0.6698 (OUTLIER) cc_final: 0.5923 (m-10) REVERT: D 72 ARG cc_start: 0.6411 (mtm-85) cc_final: 0.5771 (mtp85) REVERT: D 109 GLU cc_start: 0.6009 (OUTLIER) cc_final: 0.5602 (tt0) REVERT: D 203 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8636 (tmmt) outliers start: 28 outliers final: 13 residues processed: 151 average time/residue: 1.3273 time to fit residues: 215.7727 Evaluate side-chains 158 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 218 ARG Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 203 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.0470 chunk 93 optimal weight: 3.9990 chunk 140 optimal weight: 0.2980 chunk 129 optimal weight: 0.7980 chunk 111 optimal weight: 0.5980 chunk 11 optimal weight: 30.0000 chunk 86 optimal weight: 20.0000 chunk 68 optimal weight: 40.0000 chunk 88 optimal weight: 0.0030 chunk 119 optimal weight: 40.0000 chunk 34 optimal weight: 0.8980 overall best weight: 0.3488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN E 83 ASN F 83 ASN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11443 Z= 0.136 Angle : 0.544 10.618 15579 Z= 0.268 Chirality : 0.042 0.204 1783 Planarity : 0.004 0.050 1973 Dihedral : 4.173 48.669 1548 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.77 % Allowed : 28.27 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 1.76 (0.23), residues: 1428 helix: 2.37 (0.25), residues: 419 sheet: 1.36 (0.23), residues: 482 loop : 0.03 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 52 HIS 0.004 0.001 HIS B 70 PHE 0.016 0.001 PHE E 80 TYR 0.012 0.001 TYR D 53 ARG 0.009 0.000 ARG D 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.6940 (ttp80) cc_final: 0.6514 (ttp80) REVERT: A 55 TYR cc_start: 0.3770 (OUTLIER) cc_final: 0.3535 (t80) REVERT: A 287 ARG cc_start: 0.7231 (ttp-170) cc_final: 0.5969 (mmp80) REVERT: A 322 GLN cc_start: 0.7820 (pt0) cc_final: 0.7160 (pm20) REVERT: C 72 ARG cc_start: 0.6424 (ttm-80) cc_final: 0.5909 (ttm-80) REVERT: C 97 GLU cc_start: 0.7666 (tt0) cc_final: 0.6419 (tm-30) REVERT: E 5 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6554 (pm20) REVERT: E 18 LEU cc_start: 0.7567 (tp) cc_final: 0.7202 (tp) REVERT: E 70 SER cc_start: 0.7865 (OUTLIER) cc_final: 0.7376 (p) REVERT: E 94 TYR cc_start: 0.7743 (m-80) cc_final: 0.7416 (m-80) REVERT: E 156 THR cc_start: 0.8683 (m) cc_final: 0.8309 (p) REVERT: B 48 PHE cc_start: 0.7776 (t80) cc_final: 0.7425 (t80) REVERT: B 287 ARG cc_start: 0.6709 (ttm110) cc_final: 0.5246 (mmp-170) REVERT: B 288 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6479 (tm-30) REVERT: B 303 ASN cc_start: 0.7824 (m-40) cc_final: 0.7331 (m110) REVERT: B 307 GLN cc_start: 0.6320 (tm-30) cc_final: 0.5966 (tp-100) REVERT: B 310 GLN cc_start: 0.7495 (tt0) cc_final: 0.6617 (mm-40) REVERT: B 376 MET cc_start: 0.6396 (OUTLIER) cc_final: 0.6026 (tpt) REVERT: F 5 GLN cc_start: 0.6467 (OUTLIER) cc_final: 0.5851 (pm20) REVERT: F 46 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6474 (mt-10) REVERT: F 218 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7195 (mtt90) REVERT: D 32 TYR cc_start: 0.6642 (OUTLIER) cc_final: 0.5820 (m-10) REVERT: D 72 ARG cc_start: 0.6447 (mtm-85) cc_final: 0.5797 (mtp85) REVERT: D 203 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8735 (tmmt) outliers start: 22 outliers final: 10 residues processed: 153 average time/residue: 1.3294 time to fit residues: 219.4041 Evaluate side-chains 156 residues out of total 1245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 218 ARG Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 203 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 46 optimal weight: 30.0000 chunk 115 optimal weight: 0.0010 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 80 optimal weight: 0.0370 overall best weight: 1.4070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN E 83 ASN E 110 GLN F 83 ASN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.255023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.219920 restraints weight = 11428.167| |-----------------------------------------------------------------------------| r_work (start): 0.4425 rms_B_bonded: 1.39 r_work: 0.4257 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4219 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11443 Z= 0.179 Angle : 0.565 12.126 15579 Z= 0.281 Chirality : 0.042 0.171 1783 Planarity : 0.004 0.052 1973 Dihedral : 4.233 49.596 1548 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.85 % Allowed : 28.19 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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: 1.75 (0.22), residues: 1428 helix: 2.28 (0.25), residues: 419 sheet: 1.43 (0.23), residues: 477 loop : 0.03 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 52 HIS 0.003 0.001 HIS B 70 PHE 0.016 0.001 PHE E 80 TYR 0.012 0.001 TYR E 94 ARG 0.009 0.000 ARG D 18 =============================================================================== Job complete usr+sys time: 4318.58 seconds wall clock time: 77 minutes 30.93 seconds (4650.93 seconds total)