Starting phenix.real_space_refine on Mon May 12 20:03:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ije_60629/05_2025/9ije_60629.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ije_60629/05_2025/9ije_60629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ije_60629/05_2025/9ije_60629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ije_60629/05_2025/9ije_60629.map" model { file = "/net/cci-nas-00/data/ceres_data/9ije_60629/05_2025/9ije_60629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ije_60629/05_2025/9ije_60629.cif" } resolution = 2.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.113 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 5931 2.51 5 N 1617 2.21 5 O 1731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9340 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2539 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 67 Chain: "N" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 950 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1754 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1886 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 237} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1804 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 393 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Unusual residues: {'ALE': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 5.38, per 1000 atoms: 0.58 Number of scatterers: 9340 At special positions: 0 Unit cell: (89.8475, 123.405, 126.652, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 1731 8.00 N 1617 7.00 C 5931 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2278 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 16 sheets defined 36.1% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'B' and resid 1 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 87 through 91 removed outlier: 4.110A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 65 Processing helix chain 'R' and resid 71 through 90 removed outlier: 4.179A pdb=" N PHE R 75 " --> pdb=" O MET R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 101 Processing helix chain 'R' and resid 106 through 141 removed outlier: 3.508A pdb=" N GLU R 111 " --> pdb=" O ALA R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 149 Processing helix chain 'R' and resid 150 through 175 Proline residue: R 172 - end of helix Processing helix chain 'R' and resid 203 through 213 Processing helix chain 'R' and resid 213 through 243 Processing helix chain 'R' and resid 290 through 317 removed outlier: 3.754A pdb=" N PHE R 301 " --> pdb=" O ILE R 297 " (cutoff:3.500A) Proline residue: R 307 - end of helix Processing helix chain 'R' and resid 319 through 323 Processing helix chain 'R' and resid 324 through 337 Processing helix chain 'R' and resid 337 through 347 Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 349 through 362 Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.703A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.756A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.285A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.508A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 340 removed outlier: 3.653A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 Processing helix chain 'C' and resid 11 through 23 Processing helix chain 'C' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.581A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.801A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.803A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.600A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.640A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.676A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.755A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.675A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.861A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.338A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'D' and resid 147 through 148 removed outlier: 6.483A pdb=" N VAL D 147 " --> pdb=" O GLU D 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 194 through 195 removed outlier: 6.544A pdb=" N TRP D 176 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TYR D 190 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU D 174 " --> pdb=" O TYR D 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 210 through 212 removed outlier: 9.436A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1496 1.30 - 1.43: 2563 1.43 - 1.56: 5387 1.56 - 1.69: 2 1.69 - 1.82: 87 Bond restraints: 9535 Sorted by residual: bond pdb=" C3 ALE R 401 " pdb=" O1 ALE R 401 " ideal model delta sigma weight residual 1.353 1.505 -0.152 2.00e-02 2.50e+03 5.81e+01 bond pdb=" C ASP R 117 " pdb=" O ASP R 117 " ideal model delta sigma weight residual 1.236 1.172 0.065 1.15e-02 7.56e+03 3.17e+01 bond pdb=" CA SER B 227 " pdb=" CB SER B 227 " ideal model delta sigma weight residual 1.535 1.480 0.055 1.32e-02 5.74e+03 1.71e+01 bond pdb=" CA SER B 245 " pdb=" CB SER B 245 " ideal model delta sigma weight residual 1.534 1.479 0.056 1.45e-02 4.76e+03 1.48e+01 bond pdb=" C4 ALE R 401 " pdb=" O2 ALE R 401 " ideal model delta sigma weight residual 1.351 1.416 -0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 9530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 12590 1.93 - 3.85: 316 3.85 - 5.78: 40 5.78 - 7.70: 12 7.70 - 9.63: 2 Bond angle restraints: 12960 Sorted by residual: angle pdb=" CA ASP R 117 " pdb=" CB ASP R 117 " pdb=" CG ASP R 117 " ideal model delta sigma weight residual 112.60 119.24 -6.64 1.00e+00 1.00e+00 4.41e+01 angle pdb=" CA GLY R 318 " pdb=" C GLY R 318 " pdb=" O GLY R 318 " ideal model delta sigma weight residual 122.23 118.03 4.20 6.90e-01 2.10e+00 3.71e+01 angle pdb=" CA GLY A 345 " pdb=" C GLY A 345 " pdb=" N ARG A 346 " ideal model delta sigma weight residual 118.46 124.96 -6.50 1.15e+00 7.56e-01 3.19e+01 angle pdb=" C THR C 52 " pdb=" CA THR C 52 " pdb=" CB THR C 52 " ideal model delta sigma weight residual 110.17 104.68 5.49 9.90e-01 1.02e+00 3.07e+01 angle pdb=" CA ASP B 247 " pdb=" CB ASP B 247 " pdb=" CG ASP B 247 " ideal model delta sigma weight residual 112.60 117.90 -5.30 1.00e+00 1.00e+00 2.81e+01 ... (remaining 12955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4962 17.71 - 35.42: 496 35.42 - 53.13: 135 53.13 - 70.83: 34 70.83 - 88.54: 8 Dihedral angle restraints: 5635 sinusoidal: 2095 harmonic: 3540 Sorted by residual: dihedral pdb=" CA GLU D 234 " pdb=" C GLU D 234 " pdb=" N TYR D 235 " pdb=" CA TYR D 235 " ideal model delta harmonic sigma weight residual 180.00 -156.56 -23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA LEU A 281 " pdb=" C LEU A 281 " pdb=" N ASN A 282 " pdb=" CA ASN A 282 " ideal model delta harmonic sigma weight residual 180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -118.58 32.58 1 1.00e+01 1.00e-02 1.51e+01 ... (remaining 5632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1443 0.114 - 0.228: 41 0.228 - 0.342: 3 0.342 - 0.456: 0 0.456 - 0.570: 1 Chirality restraints: 1488 Sorted by residual: chirality pdb=" C7 ALE R 401 " pdb=" C1 ALE R 401 " pdb=" C8 ALE R 401 " pdb=" O3 ALE R 401 " both_signs ideal model delta sigma weight residual False 2.28 2.85 -0.57 2.00e-01 2.50e+01 8.13e+00 chirality pdb=" CA THR C 52 " pdb=" N THR C 52 " pdb=" C THR C 52 " pdb=" CB THR C 52 " both_signs ideal model delta sigma weight residual False 2.53 2.79 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA VAL R 323 " pdb=" N VAL R 323 " pdb=" C VAL R 323 " pdb=" CB VAL R 323 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1485 not shown) Planarity restraints: 1648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 74 " -0.064 5.00e-02 4.00e+02 9.47e-02 1.44e+01 pdb=" N PRO D 75 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 92 " 0.056 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO R 93 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO R 93 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 93 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 244 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C GLY B 244 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY B 244 " 0.018 2.00e-02 2.50e+03 pdb=" N SER B 245 " 0.016 2.00e-02 2.50e+03 ... (remaining 1645 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1729 2.77 - 3.30: 8515 3.30 - 3.84: 15752 3.84 - 4.37: 18931 4.37 - 4.90: 33135 Nonbonded interactions: 78062 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.240 3.040 nonbonded pdb=" N GLU A 304 " pdb=" OE1 GLU A 304 " model vdw 2.248 3.120 nonbonded pdb=" O TYR R 204 " pdb=" OG SER R 208 " model vdw 2.272 3.040 nonbonded pdb=" NZ LYS D 163 " pdb=" OE2 GLU D 234 " model vdw 2.274 3.120 nonbonded pdb=" OG SER D 52 " pdb=" OE2 GLU A 21 " model vdw 2.305 3.040 ... (remaining 78057 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.860 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 0.152 9539 Z= 0.300 Angle : 0.695 9.626 12968 Z= 0.447 Chirality : 0.050 0.570 1488 Planarity : 0.006 0.105 1648 Dihedral : 15.986 88.544 3345 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.15 % Allowed : 19.61 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.24), residues: 1207 helix: 1.79 (0.25), residues: 393 sheet: 0.85 (0.28), residues: 301 loop : -0.12 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 113 HIS 0.005 0.001 HIS A 347 PHE 0.012 0.001 PHE R 309 TYR 0.025 0.002 TYR D 235 ARG 0.015 0.001 ARG D 160 Details of bonding type rmsd hydrogen bonds : bond 0.17047 ( 481) hydrogen bonds : angle 6.49754 ( 1344) SS BOND : bond 0.00164 ( 4) SS BOND : angle 1.03436 ( 8) covalent geometry : bond 0.00480 ( 9535) covalent geometry : angle 0.69508 (12960) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.102 Fit side-chains REVERT: B 189 SER cc_start: 0.9143 (t) cc_final: 0.8916 (p) REVERT: N 83 MET cc_start: 0.8606 (mtp) cc_final: 0.8304 (mtm) REVERT: D 63 THR cc_start: 0.8665 (p) cc_final: 0.8401 (t) REVERT: D 160 ARG cc_start: 0.7182 (ttm-80) cc_final: 0.6949 (ttp80) REVERT: D 186 GLN cc_start: 0.8194 (pt0) cc_final: 0.7839 (pt0) REVERT: D 234 GLU cc_start: 0.8051 (mp0) cc_final: 0.7661 (mp0) REVERT: R 155 ARG cc_start: 0.7091 (ttp-110) cc_final: 0.6157 (mmm160) REVERT: R 333 TRP cc_start: 0.8128 (m100) cc_final: 0.7204 (m-10) REVERT: R 358 ARG cc_start: 0.6732 (mtm110) cc_final: 0.6412 (ttp-110) REVERT: A 254 ASN cc_start: 0.8682 (t0) cc_final: 0.8429 (m-40) REVERT: C 42 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.5931 (mp0) outliers start: 21 outliers final: 12 residues processed: 165 average time/residue: 1.4109 time to fit residues: 247.2977 Evaluate side-chains 147 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 0.0010 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 109 optimal weight: 20.0000 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN N 120 GLN D 3 GLN D 77 ASN D 142 GLN D 179 GLN D 183 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 239 ASN A 380 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.126828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.097709 restraints weight = 11774.547| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.27 r_work: 0.3097 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9539 Z= 0.118 Angle : 0.513 6.798 12968 Z= 0.276 Chirality : 0.042 0.198 1488 Planarity : 0.005 0.067 1648 Dihedral : 5.786 54.283 1360 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.17 % Allowed : 20.22 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.24), residues: 1207 helix: 2.45 (0.25), residues: 392 sheet: 0.89 (0.28), residues: 300 loop : 0.02 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS A 347 PHE 0.013 0.001 PHE A 212 TYR 0.017 0.001 TYR D 235 ARG 0.005 0.000 ARG R 358 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 481) hydrogen bonds : angle 4.58603 ( 1344) SS BOND : bond 0.00254 ( 4) SS BOND : angle 0.67639 ( 8) covalent geometry : bond 0.00262 ( 9535) covalent geometry : angle 0.51330 (12960) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: B 10 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.5996 (tp30) REVERT: B 189 SER cc_start: 0.9081 (t) cc_final: 0.8631 (p) REVERT: B 217 MET cc_start: 0.8063 (pp-130) cc_final: 0.7774 (pp-130) REVERT: B 314 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8183 (ttt180) REVERT: N 1 GLN cc_start: 0.7444 (pm20) cc_final: 0.7231 (pm20) REVERT: N 83 MET cc_start: 0.8794 (mtp) cc_final: 0.8373 (mtm) REVERT: D 18 ARG cc_start: 0.7088 (tpp-160) cc_final: 0.6692 (tpp-160) REVERT: D 180 ARG cc_start: 0.7724 (mtt180) cc_final: 0.7448 (mtt180) REVERT: D 186 GLN cc_start: 0.8386 (pt0) cc_final: 0.8168 (pt0) REVERT: D 234 GLU cc_start: 0.8187 (mp0) cc_final: 0.7865 (mp0) REVERT: D 235 TYR cc_start: 0.6825 (OUTLIER) cc_final: 0.6579 (m-80) REVERT: R 148 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7971 (mp) REVERT: R 333 TRP cc_start: 0.8154 (m100) cc_final: 0.7009 (m-10) REVERT: C 21 MET cc_start: 0.7124 (tpp) cc_final: 0.6766 (tpt) REVERT: C 42 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: C 58 GLU cc_start: 0.8118 (pt0) cc_final: 0.7594 (pm20) outliers start: 31 outliers final: 11 residues processed: 163 average time/residue: 1.3885 time to fit residues: 240.4921 Evaluate side-chains 150 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 42 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 90 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 293 ASN N 120 GLN D 3 GLN D 77 ASN D 183 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.126839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098268 restraints weight = 11930.224| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.19 r_work: 0.3096 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9539 Z= 0.115 Angle : 0.501 6.406 12968 Z= 0.267 Chirality : 0.041 0.198 1488 Planarity : 0.005 0.060 1648 Dihedral : 5.451 54.797 1345 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.27 % Allowed : 21.35 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.24), residues: 1207 helix: 2.59 (0.25), residues: 388 sheet: 0.83 (0.28), residues: 300 loop : -0.01 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 347 PHE 0.013 0.001 PHE A 212 TYR 0.018 0.001 TYR D 235 ARG 0.007 0.000 ARG R 358 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 481) hydrogen bonds : angle 4.37351 ( 1344) SS BOND : bond 0.00294 ( 4) SS BOND : angle 0.65968 ( 8) covalent geometry : bond 0.00257 ( 9535) covalent geometry : angle 0.50046 (12960) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: B 189 SER cc_start: 0.8957 (t) cc_final: 0.8400 (p) REVERT: B 217 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7529 (pp-130) REVERT: N 1 GLN cc_start: 0.7441 (pm20) cc_final: 0.7056 (pm20) REVERT: N 83 MET cc_start: 0.8577 (mtp) cc_final: 0.8233 (mtm) REVERT: D 160 ARG cc_start: 0.7438 (mtp-110) cc_final: 0.6917 (ttp-110) REVERT: D 234 GLU cc_start: 0.8195 (mp0) cc_final: 0.7784 (mp0) REVERT: D 235 TYR cc_start: 0.6615 (OUTLIER) cc_final: 0.6212 (t80) REVERT: R 298 MET cc_start: 0.7230 (mmm) cc_final: 0.7004 (mmp) REVERT: R 333 TRP cc_start: 0.7996 (m100) cc_final: 0.6785 (m-10) REVERT: C 21 MET cc_start: 0.7007 (tpp) cc_final: 0.6600 (tpt) REVERT: C 42 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6753 (mp0) outliers start: 32 outliers final: 16 residues processed: 155 average time/residue: 1.3285 time to fit residues: 218.7118 Evaluate side-chains 149 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 42 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 117 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN N 120 GLN D 3 GLN D 77 ASN D 183 GLN D 186 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.096362 restraints weight = 11842.824| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.16 r_work: 0.3069 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9539 Z= 0.144 Angle : 0.532 6.646 12968 Z= 0.284 Chirality : 0.042 0.207 1488 Planarity : 0.005 0.058 1648 Dihedral : 5.551 52.465 1345 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.58 % Allowed : 20.33 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.24), residues: 1207 helix: 2.47 (0.26), residues: 387 sheet: 0.75 (0.28), residues: 300 loop : -0.05 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.005 0.001 HIS A 347 PHE 0.014 0.001 PHE A 212 TYR 0.017 0.002 TYR D 235 ARG 0.007 0.000 ARG R 358 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 481) hydrogen bonds : angle 4.45696 ( 1344) SS BOND : bond 0.00328 ( 4) SS BOND : angle 0.83850 ( 8) covalent geometry : bond 0.00334 ( 9535) covalent geometry : angle 0.53221 (12960) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.8485 (pp-130) cc_final: 0.8161 (pp-130) REVERT: B 189 SER cc_start: 0.8977 (t) cc_final: 0.8410 (p) REVERT: B 217 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7515 (pp-130) REVERT: B 234 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.6742 (t80) REVERT: N 1 GLN cc_start: 0.7525 (pm20) cc_final: 0.7156 (pm20) REVERT: N 83 MET cc_start: 0.8543 (mtp) cc_final: 0.8200 (mtm) REVERT: D 160 ARG cc_start: 0.7377 (mtp-110) cc_final: 0.6919 (ttp-110) REVERT: D 235 TYR cc_start: 0.6595 (OUTLIER) cc_final: 0.6100 (t80) REVERT: R 291 LEU cc_start: 0.8314 (tp) cc_final: 0.8095 (tp) REVERT: R 298 MET cc_start: 0.7329 (mmm) cc_final: 0.7117 (mmp) REVERT: R 333 TRP cc_start: 0.8062 (m100) cc_final: 0.6884 (m-10) REVERT: C 21 MET cc_start: 0.7042 (tpp) cc_final: 0.6613 (tpt) REVERT: C 42 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6775 (mp0) outliers start: 35 outliers final: 20 residues processed: 155 average time/residue: 1.2747 time to fit residues: 210.6011 Evaluate side-chains 154 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 42 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 92 optimal weight: 0.4980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 293 ASN N 120 GLN D 3 GLN D 77 ASN D 183 GLN D 186 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.127636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099197 restraints weight = 12008.616| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.16 r_work: 0.3119 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9539 Z= 0.098 Angle : 0.478 6.006 12968 Z= 0.255 Chirality : 0.040 0.179 1488 Planarity : 0.005 0.055 1648 Dihedral : 4.998 51.906 1345 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.78 % Allowed : 20.12 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1207 helix: 2.77 (0.26), residues: 388 sheet: 0.79 (0.28), residues: 301 loop : -0.03 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 PHE 0.013 0.001 PHE A 212 TYR 0.016 0.001 TYR D 235 ARG 0.008 0.000 ARG R 358 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 481) hydrogen bonds : angle 4.14920 ( 1344) SS BOND : bond 0.00249 ( 4) SS BOND : angle 0.55686 ( 8) covalent geometry : bond 0.00213 ( 9535) covalent geometry : angle 0.47835 (12960) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.8392 (pp-130) cc_final: 0.8088 (pp-130) REVERT: B 234 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.6796 (t80) REVERT: N 1 GLN cc_start: 0.7521 (pm20) cc_final: 0.7165 (pm20) REVERT: N 5 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7814 (tp40) REVERT: N 80 TYR cc_start: 0.8535 (m-80) cc_final: 0.8206 (m-80) REVERT: N 83 MET cc_start: 0.8583 (mtp) cc_final: 0.8246 (mtm) REVERT: D 160 ARG cc_start: 0.7345 (mtp-110) cc_final: 0.6898 (ttp-110) REVERT: D 235 TYR cc_start: 0.6410 (OUTLIER) cc_final: 0.5962 (t80) REVERT: R 117 ASP cc_start: 0.8917 (t0) cc_final: 0.8714 (t0) REVERT: R 148 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7901 (mp) REVERT: R 333 TRP cc_start: 0.7998 (m100) cc_final: 0.6817 (m-10) REVERT: A 25 MET cc_start: 0.7312 (mmm) cc_final: 0.6908 (mtp) REVERT: C 21 MET cc_start: 0.7002 (tpp) cc_final: 0.6579 (tpt) REVERT: C 42 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6680 (mp0) outliers start: 37 outliers final: 22 residues processed: 161 average time/residue: 1.3123 time to fit residues: 224.6586 Evaluate side-chains 158 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 12 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN N 77 ASN N 120 GLN D 3 GLN D 183 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.126078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.097570 restraints weight = 11893.742| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.15 r_work: 0.3095 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9539 Z= 0.118 Angle : 0.501 6.332 12968 Z= 0.266 Chirality : 0.041 0.184 1488 Planarity : 0.005 0.059 1648 Dihedral : 4.969 47.345 1343 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.29 % Allowed : 20.43 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1207 helix: 2.71 (0.26), residues: 388 sheet: 0.74 (0.28), residues: 302 loop : -0.01 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 PHE 0.013 0.001 PHE A 212 TYR 0.015 0.001 TYR D 235 ARG 0.009 0.000 ARG R 358 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 481) hydrogen bonds : angle 4.23622 ( 1344) SS BOND : bond 0.00277 ( 4) SS BOND : angle 0.88431 ( 8) covalent geometry : bond 0.00269 ( 9535) covalent geometry : angle 0.50032 (12960) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8204 (pp-130) REVERT: B 234 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.6738 (t80) REVERT: N 1 GLN cc_start: 0.7481 (pm20) cc_final: 0.7138 (pm20) REVERT: N 83 MET cc_start: 0.8571 (mtp) cc_final: 0.8262 (mtm) REVERT: D 160 ARG cc_start: 0.7302 (mtp-110) cc_final: 0.6880 (ttp-110) REVERT: D 235 TYR cc_start: 0.6500 (OUTLIER) cc_final: 0.5994 (t80) REVERT: R 151 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7125 (ttmm) REVERT: R 333 TRP cc_start: 0.8064 (m100) cc_final: 0.6869 (m-10) REVERT: A 25 MET cc_start: 0.7379 (mmm) cc_final: 0.7003 (mtp) REVERT: A 346 ARG cc_start: 0.7025 (ptp-110) cc_final: 0.6148 (ptp-110) REVERT: C 21 MET cc_start: 0.7057 (tpp) cc_final: 0.6626 (tpt) REVERT: C 42 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6696 (mp0) outliers start: 42 outliers final: 24 residues processed: 163 average time/residue: 1.3960 time to fit residues: 241.8668 Evaluate side-chains 158 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 120 optimal weight: 0.2980 chunk 68 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 293 ASN N 77 ASN N 120 GLN D 3 GLN D 77 ASN D 183 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.127116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098672 restraints weight = 11976.058| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.16 r_work: 0.3112 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9539 Z= 0.105 Angle : 0.492 6.579 12968 Z= 0.260 Chirality : 0.041 0.181 1488 Planarity : 0.005 0.056 1648 Dihedral : 4.799 47.565 1343 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.68 % Allowed : 20.94 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.24), residues: 1207 helix: 2.80 (0.26), residues: 388 sheet: 0.68 (0.28), residues: 304 loop : 0.06 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 PHE 0.013 0.001 PHE A 212 TYR 0.016 0.001 TYR D 235 ARG 0.011 0.000 ARG R 358 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 481) hydrogen bonds : angle 4.17110 ( 1344) SS BOND : bond 0.00250 ( 4) SS BOND : angle 0.75453 ( 8) covalent geometry : bond 0.00236 ( 9535) covalent geometry : angle 0.49170 (12960) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8131 (pp-130) REVERT: B 234 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.6815 (t80) REVERT: N 1 GLN cc_start: 0.7496 (pm20) cc_final: 0.7141 (pm20) REVERT: N 83 MET cc_start: 0.8570 (mtp) cc_final: 0.8239 (mtm) REVERT: D 160 ARG cc_start: 0.7283 (mtp-110) cc_final: 0.6858 (ttp-110) REVERT: D 235 TYR cc_start: 0.6368 (OUTLIER) cc_final: 0.5859 (t80) REVERT: D 245 LEU cc_start: 0.7018 (tp) cc_final: 0.6812 (tt) REVERT: R 151 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7106 (ttmm) REVERT: R 333 TRP cc_start: 0.8006 (m100) cc_final: 0.6814 (m-10) REVERT: A 25 MET cc_start: 0.7363 (mmm) cc_final: 0.6999 (mtp) REVERT: C 21 MET cc_start: 0.7130 (tpp) cc_final: 0.6693 (tpt) REVERT: C 42 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6698 (mp0) outliers start: 36 outliers final: 25 residues processed: 158 average time/residue: 1.2973 time to fit residues: 218.2153 Evaluate side-chains 164 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 45 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 11 optimal weight: 0.3980 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN N 77 ASN N 120 GLN D 3 GLN D 183 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.097491 restraints weight = 12159.420| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.17 r_work: 0.3094 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9539 Z= 0.117 Angle : 0.509 6.975 12968 Z= 0.269 Chirality : 0.041 0.183 1488 Planarity : 0.005 0.059 1648 Dihedral : 4.963 48.150 1343 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.78 % Allowed : 20.63 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.24), residues: 1207 helix: 2.72 (0.26), residues: 388 sheet: 0.72 (0.28), residues: 302 loop : 0.04 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 PHE 0.013 0.001 PHE A 212 TYR 0.015 0.001 TYR D 235 ARG 0.012 0.000 ARG R 358 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 481) hydrogen bonds : angle 4.23770 ( 1344) SS BOND : bond 0.00252 ( 4) SS BOND : angle 0.81807 ( 8) covalent geometry : bond 0.00268 ( 9535) covalent geometry : angle 0.50873 (12960) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8202 (pp-130) REVERT: B 234 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.6744 (t80) REVERT: N 1 GLN cc_start: 0.7476 (pm20) cc_final: 0.7088 (pm20) REVERT: N 83 MET cc_start: 0.8541 (mtp) cc_final: 0.8231 (mtm) REVERT: D 160 ARG cc_start: 0.7254 (mtp-110) cc_final: 0.6857 (ttp-110) REVERT: D 235 TYR cc_start: 0.6475 (OUTLIER) cc_final: 0.5939 (t80) REVERT: R 151 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7037 (ttmm) REVERT: R 333 TRP cc_start: 0.8042 (m100) cc_final: 0.6839 (m-10) REVERT: A 25 MET cc_start: 0.7380 (mmm) cc_final: 0.6945 (mtp) REVERT: C 21 MET cc_start: 0.7121 (tpp) cc_final: 0.6646 (tpt) REVERT: C 42 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: C 46 LYS cc_start: 0.8129 (tppp) cc_final: 0.7301 (ptpp) outliers start: 37 outliers final: 26 residues processed: 161 average time/residue: 1.2847 time to fit residues: 220.2553 Evaluate side-chains 161 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 80 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN N 77 ASN N 120 GLN D 3 GLN D 77 ASN D 183 GLN A 236 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.096355 restraints weight = 11836.421| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.17 r_work: 0.3071 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9539 Z= 0.145 Angle : 0.538 7.337 12968 Z= 0.285 Chirality : 0.042 0.205 1488 Planarity : 0.005 0.060 1648 Dihedral : 5.224 48.506 1343 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.98 % Allowed : 20.43 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1207 helix: 2.56 (0.26), residues: 388 sheet: 0.75 (0.28), residues: 298 loop : 0.01 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.004 0.001 HIS A 347 PHE 0.013 0.001 PHE A 212 TYR 0.016 0.002 TYR D 235 ARG 0.013 0.000 ARG R 358 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 481) hydrogen bonds : angle 4.38137 ( 1344) SS BOND : bond 0.00296 ( 4) SS BOND : angle 0.93479 ( 8) covalent geometry : bond 0.00341 ( 9535) covalent geometry : angle 0.53810 (12960) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.6731 (t80) REVERT: N 1 GLN cc_start: 0.7460 (pm20) cc_final: 0.7171 (pm20) REVERT: N 76 LYS cc_start: 0.8253 (mtpt) cc_final: 0.7907 (mtmt) REVERT: N 83 MET cc_start: 0.8490 (mtp) cc_final: 0.8196 (mtm) REVERT: D 160 ARG cc_start: 0.7276 (mtp-110) cc_final: 0.6857 (ttp-110) REVERT: D 235 TYR cc_start: 0.6559 (OUTLIER) cc_final: 0.6033 (t80) REVERT: R 151 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7042 (ttmm) REVERT: R 333 TRP cc_start: 0.8064 (m100) cc_final: 0.6865 (m-10) REVERT: C 21 MET cc_start: 0.7131 (tpp) cc_final: 0.6646 (tpt) REVERT: C 42 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: C 46 LYS cc_start: 0.8225 (tppp) cc_final: 0.7459 (ptpt) outliers start: 39 outliers final: 29 residues processed: 164 average time/residue: 1.2262 time to fit residues: 214.6021 Evaluate side-chains 170 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 89 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN N 77 ASN N 120 GLN D 3 GLN D 183 GLN A 236 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.122505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.094100 restraints weight = 12010.010| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.16 r_work: 0.3039 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9539 Z= 0.207 Angle : 0.600 7.439 12968 Z= 0.320 Chirality : 0.045 0.239 1488 Planarity : 0.005 0.062 1648 Dihedral : 5.662 51.390 1343 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.17 % Allowed : 21.35 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.24), residues: 1207 helix: 2.26 (0.26), residues: 383 sheet: 0.68 (0.28), residues: 300 loop : -0.12 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 63 HIS 0.006 0.001 HIS A 347 PHE 0.014 0.002 PHE A 212 TYR 0.017 0.002 TYR D 235 ARG 0.014 0.001 ARG R 358 Details of bonding type rmsd hydrogen bonds : bond 0.04908 ( 481) hydrogen bonds : angle 4.66674 ( 1344) SS BOND : bond 0.00384 ( 4) SS BOND : angle 1.19945 ( 8) covalent geometry : bond 0.00494 ( 9535) covalent geometry : angle 0.59977 (12960) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.6608 (t80) REVERT: N 1 GLN cc_start: 0.7403 (pm20) cc_final: 0.6999 (pm20) REVERT: N 83 MET cc_start: 0.8501 (mtp) cc_final: 0.8291 (mtm) REVERT: D 160 ARG cc_start: 0.7330 (mtp-110) cc_final: 0.6894 (ttp-110) REVERT: D 234 GLU cc_start: 0.8169 (mp0) cc_final: 0.7859 (mp0) REVERT: D 235 TYR cc_start: 0.6633 (OUTLIER) cc_final: 0.6032 (t80) REVERT: R 151 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7085 (ttmm) REVERT: R 291 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7751 (tt) REVERT: R 333 TRP cc_start: 0.8117 (m100) cc_final: 0.6836 (m-10) REVERT: C 21 MET cc_start: 0.7157 (tpp) cc_final: 0.6678 (tpt) REVERT: C 46 LYS cc_start: 0.8279 (tppp) cc_final: 0.7470 (ptpt) outliers start: 31 outliers final: 26 residues processed: 157 average time/residue: 1.2650 time to fit residues: 211.5399 Evaluate side-chains 161 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 113 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 117 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 92 optimal weight: 0.0170 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 293 ASN N 77 ASN N 120 GLN D 3 GLN D 77 ASN D 183 GLN A 236 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.125489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.096934 restraints weight = 11882.002| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.22 r_work: 0.3083 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9539 Z= 0.119 Angle : 0.523 7.099 12968 Z= 0.278 Chirality : 0.041 0.200 1488 Planarity : 0.005 0.059 1648 Dihedral : 5.127 47.324 1343 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.27 % Allowed : 21.25 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.24), residues: 1207 helix: 2.52 (0.26), residues: 388 sheet: 0.74 (0.28), residues: 297 loop : -0.09 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 PHE 0.013 0.001 PHE A 212 TYR 0.016 0.001 TYR D 235 ARG 0.013 0.000 ARG R 358 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 481) hydrogen bonds : angle 4.31887 ( 1344) SS BOND : bond 0.00271 ( 4) SS BOND : angle 0.76472 ( 8) covalent geometry : bond 0.00272 ( 9535) covalent geometry : angle 0.52256 (12960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8741.85 seconds wall clock time: 150 minutes 39.63 seconds (9039.63 seconds total)