Starting phenix.real_space_refine on Sat Apr 6 02:27:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg6_29996/04_2024/8gg6_29996_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg6_29996/04_2024/8gg6_29996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg6_29996/04_2024/8gg6_29996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg6_29996/04_2024/8gg6_29996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg6_29996/04_2024/8gg6_29996_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg6_29996/04_2024/8gg6_29996_updated.pdb" } resolution = 3.3 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= -0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 45 5.16 5 C 4305 2.51 5 N 1156 2.21 5 O 1216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "R GLU 237": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6725 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1796 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 2 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 12, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 130 Chain: "B" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2437 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 332 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2109 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 98 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 19 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} Time building chain proxies: 4.20, per 1000 atoms: 0.62 Number of scatterers: 6725 At special positions: 0 Unit cell: (85.9023, 133.626, 99.7855, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 3 15.00 O 1216 8.00 N 1156 7.00 C 4305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.31 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.3 seconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1710 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 8 sheets defined 41.9% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 13 through 37 removed outlier: 3.692A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.600A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.763A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.546A pdb=" N ILE A 383 " --> pdb=" O CYS A 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.958A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 14 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'R' and resid 35 through 60 removed outlier: 3.872A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 64 No H-bonds generated for 'chain 'R' and resid 62 through 64' Processing helix chain 'R' and resid 68 through 85 removed outlier: 3.932A pdb=" N THR R 73 " --> pdb=" O TYR R 70 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA R 85 " --> pdb=" O MET R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 96 Processing helix chain 'R' and resid 103 through 136 removed outlier: 3.587A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 170 removed outlier: 3.884A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 179 through 185 Processing helix chain 'R' and resid 197 through 207 Processing helix chain 'R' and resid 209 through 237 removed outlier: 3.730A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE R 233 " --> pdb=" O GLN R 229 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 298 removed outlier: 3.808A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.502A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 321 removed outlier: 4.161A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 323 through 326 No H-bonds generated for 'chain 'R' and resid 323 through 326' Processing helix chain 'R' and resid 330 through 338 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.060A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.733A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.041A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.893A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.898A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.733A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.637A pdb=" N VAL B 296 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.682A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 885 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: 2.00 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1268 1.33 - 1.45: 1765 1.45 - 1.57: 3766 1.57 - 1.69: 6 1.69 - 1.82: 62 Bond restraints: 6867 Sorted by residual: bond pdb=" CA ALA B 106 " pdb=" C ALA B 106 " ideal model delta sigma weight residual 1.528 1.488 0.040 1.18e-02 7.18e+03 1.18e+01 bond pdb=" CA PHE B 235 " pdb=" C PHE B 235 " ideal model delta sigma weight residual 1.527 1.495 0.032 1.02e-02 9.61e+03 9.81e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 7.09e+00 bond pdb=" CA ALA B 231 " pdb=" CB ALA B 231 " ideal model delta sigma weight residual 1.533 1.488 0.045 1.72e-02 3.38e+03 6.98e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.573 -0.050 2.00e-02 2.50e+03 6.27e+00 ... (remaining 6862 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.04: 145 107.04 - 113.78: 3882 113.78 - 120.52: 2666 120.52 - 127.26: 2611 127.26 - 134.01: 76 Bond angle restraints: 9380 Sorted by residual: angle pdb=" N THR B 102 " pdb=" CA THR B 102 " pdb=" C THR B 102 " ideal model delta sigma weight residual 108.99 116.87 -7.88 1.57e+00 4.06e-01 2.52e+01 angle pdb=" N GLY A 355 " pdb=" CA GLY A 355 " pdb=" C GLY A 355 " ideal model delta sigma weight residual 115.36 108.83 6.53 1.33e+00 5.65e-01 2.41e+01 angle pdb=" N LEU R 115 " pdb=" CA LEU R 115 " pdb=" C LEU R 115 " ideal model delta sigma weight residual 111.28 115.81 -4.53 1.09e+00 8.42e-01 1.73e+01 angle pdb=" N ALA A 351 " pdb=" CA ALA A 351 " pdb=" C ALA A 351 " ideal model delta sigma weight residual 111.28 115.02 -3.74 1.09e+00 8.42e-01 1.18e+01 angle pdb=" N ALA B 231 " pdb=" CA ALA B 231 " pdb=" C ALA B 231 " ideal model delta sigma weight residual 108.75 114.28 -5.53 1.71e+00 3.42e-01 1.05e+01 ... (remaining 9375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 3916 34.93 - 69.87: 73 69.87 - 104.80: 7 104.80 - 139.74: 0 139.74 - 174.67: 1 Dihedral angle restraints: 3997 sinusoidal: 1362 harmonic: 2635 Sorted by residual: dihedral pdb=" C4' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 260.87 86.20 174.67 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 7.67 96.92 1 2.00e+01 2.50e-03 2.69e+01 dihedral pdb=" CG ARG B 219 " pdb=" CD ARG B 219 " pdb=" NE ARG B 219 " pdb=" CZ ARG B 219 " ideal model delta sinusoidal sigma weight residual -90.00 -46.92 -43.08 2 1.50e+01 4.44e-03 9.95e+00 ... (remaining 3994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 695 0.031 - 0.062: 264 0.062 - 0.093: 103 0.093 - 0.125: 46 0.125 - 0.156: 3 Chirality restraints: 1111 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CB THR R 56 " pdb=" CA THR R 56 " pdb=" OG1 THR R 56 " pdb=" CG2 THR R 56 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE B 157 " pdb=" N ILE B 157 " pdb=" C ILE B 157 " pdb=" CB ILE B 157 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 1108 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " -0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO G 53 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 113 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C ASP R 113 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP R 113 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL R 114 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 349 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C SER A 349 " -0.042 2.00e-02 2.50e+03 pdb=" O SER A 349 " 0.016 2.00e-02 2.50e+03 pdb=" N THR A 350 " 0.014 2.00e-02 2.50e+03 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 809 2.75 - 3.29: 6243 3.29 - 3.83: 10513 3.83 - 4.36: 11792 4.36 - 4.90: 22101 Nonbonded interactions: 51458 Sorted by model distance: nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.213 2.440 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.245 2.440 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.277 2.440 nonbonded pdb=" NE2 GLN G 18 " pdb=" OE2 GLU G 22 " model vdw 2.340 2.520 nonbonded pdb=" OE2 GLU R 187 " pdb=" OG1 THR R 189 " model vdw 2.344 2.440 ... (remaining 51453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 3.200 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: 0.000 Extract box with map and model: 7.590 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.770 Find NCS groups from input model: 0.170 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 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 : 0.004 0.053 6867 Z= 0.244 Angle : 0.548 7.885 9380 Z= 0.317 Chirality : 0.041 0.156 1111 Planarity : 0.004 0.083 1178 Dihedral : 15.251 174.672 2281 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.31 % Allowed : 11.98 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.28), residues: 890 helix: 1.84 (0.28), residues: 366 sheet: 0.13 (0.39), residues: 170 loop : -0.87 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 109 HIS 0.004 0.001 HIS B 142 PHE 0.017 0.001 PHE A 238 TYR 0.012 0.001 TYR B 59 ARG 0.008 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.742 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 95 average time/residue: 0.1992 time to fit residues: 25.1767 Evaluate side-chains 88 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 0.0170 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6867 Z= 0.186 Angle : 0.489 7.352 9380 Z= 0.267 Chirality : 0.042 0.136 1111 Planarity : 0.004 0.063 1178 Dihedral : 8.149 175.012 994 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.87 % Allowed : 12.60 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.28), residues: 890 helix: 2.11 (0.27), residues: 367 sheet: 0.47 (0.40), residues: 168 loop : -0.87 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.004 0.001 HIS R 296 PHE 0.015 0.001 PHE A 212 TYR 0.009 0.001 TYR A 253 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.770 Fit side-chains REVERT: A 211 LYS cc_start: 0.8216 (mptt) cc_final: 0.7564 (mptt) REVERT: A 220 HIS cc_start: 0.8024 (t70) cc_final: 0.7586 (t-170) REVERT: B 234 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8595 (t80) outliers start: 12 outliers final: 10 residues processed: 97 average time/residue: 0.1971 time to fit residues: 25.4584 Evaluate side-chains 101 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 328 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 0.0170 chunk 64 optimal weight: 0.0270 chunk 79 optimal weight: 0.6980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6867 Z= 0.135 Angle : 0.453 7.254 9380 Z= 0.245 Chirality : 0.040 0.132 1111 Planarity : 0.004 0.055 1178 Dihedral : 7.879 174.941 994 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.71 % Allowed : 14.31 % Favored : 83.98 % 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: 1.08 (0.28), residues: 890 helix: 2.21 (0.27), residues: 365 sheet: 0.58 (0.39), residues: 166 loop : -0.80 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS R 296 PHE 0.015 0.001 PHE A 212 TYR 0.007 0.001 TYR R 199 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.751 Fit side-chains REVERT: A 211 LYS cc_start: 0.8199 (mptt) cc_final: 0.7560 (mptt) REVERT: A 220 HIS cc_start: 0.8034 (t70) cc_final: 0.7634 (t-90) REVERT: B 234 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8586 (t80) REVERT: R 234 ASP cc_start: 0.8743 (t0) cc_final: 0.8439 (t0) outliers start: 11 outliers final: 7 residues processed: 101 average time/residue: 0.1947 time to fit residues: 26.4060 Evaluate side-chains 96 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.3980 chunk 42 optimal weight: 0.1980 chunk 8 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 0.0470 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 48 optimal weight: 0.0030 overall best weight: 0.2288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6867 Z= 0.111 Angle : 0.430 7.137 9380 Z= 0.231 Chirality : 0.040 0.130 1111 Planarity : 0.004 0.049 1178 Dihedral : 7.707 174.279 994 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.87 % Allowed : 15.24 % Favored : 82.89 % 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: 1.20 (0.28), residues: 890 helix: 2.35 (0.28), residues: 365 sheet: 0.65 (0.40), residues: 166 loop : -0.80 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS R 296 PHE 0.018 0.001 PHE A 222 TYR 0.007 0.001 TYR A 253 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.719 Fit side-chains REVERT: A 211 LYS cc_start: 0.8233 (mptt) cc_final: 0.7288 (mptt) REVERT: A 220 HIS cc_start: 0.7850 (t70) cc_final: 0.6902 (t70) REVERT: B 234 PHE cc_start: 0.9246 (OUTLIER) cc_final: 0.8659 (t80) REVERT: R 234 ASP cc_start: 0.8705 (t0) cc_final: 0.8387 (t0) REVERT: R 279 MET cc_start: 0.8392 (mmm) cc_final: 0.8111 (mmp) outliers start: 12 outliers final: 6 residues processed: 100 average time/residue: 0.1927 time to fit residues: 25.6175 Evaluate side-chains 97 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 328 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 0.1980 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 172 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6867 Z= 0.215 Angle : 0.482 7.389 9380 Z= 0.258 Chirality : 0.042 0.132 1111 Planarity : 0.004 0.050 1178 Dihedral : 7.857 174.625 994 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.64 % Allowed : 15.09 % Favored : 82.27 % 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: 1.08 (0.28), residues: 890 helix: 2.21 (0.27), residues: 366 sheet: 0.50 (0.39), residues: 174 loop : -0.80 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.003 0.001 HIS R 296 PHE 0.015 0.001 PHE B 241 TYR 0.009 0.001 TYR A 253 ARG 0.009 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 220 HIS cc_start: 0.8076 (t70) cc_final: 0.7708 (t-90) REVERT: B 59 TYR cc_start: 0.8339 (m-80) cc_final: 0.8002 (m-10) REVERT: B 217 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7726 (ppp) REVERT: B 234 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8593 (t80) REVERT: R 234 ASP cc_start: 0.8644 (t0) cc_final: 0.8320 (t0) outliers start: 17 outliers final: 14 residues processed: 99 average time/residue: 0.1994 time to fit residues: 26.2956 Evaluate side-chains 103 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 328 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 0.0370 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 172 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6867 Z= 0.156 Angle : 0.455 7.319 9380 Z= 0.244 Chirality : 0.041 0.129 1111 Planarity : 0.004 0.048 1178 Dihedral : 7.804 174.974 994 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.80 % Allowed : 15.40 % Favored : 81.80 % 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: 1.07 (0.28), residues: 890 helix: 2.21 (0.27), residues: 366 sheet: 0.59 (0.40), residues: 168 loop : -0.84 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.003 0.001 HIS R 296 PHE 0.013 0.001 PHE B 241 TYR 0.008 0.001 TYR A 253 ARG 0.008 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8234 (mptt) cc_final: 0.7897 (mmtm) REVERT: B 59 TYR cc_start: 0.8365 (m-80) cc_final: 0.8036 (m-10) REVERT: B 217 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7742 (ppp) REVERT: B 234 PHE cc_start: 0.9270 (OUTLIER) cc_final: 0.8663 (t80) outliers start: 18 outliers final: 14 residues processed: 100 average time/residue: 0.1872 time to fit residues: 24.9414 Evaluate side-chains 105 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 328 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 72 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 39 optimal weight: 0.0570 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 16 optimal weight: 0.0170 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6867 Z= 0.114 Angle : 0.430 7.114 9380 Z= 0.231 Chirality : 0.040 0.131 1111 Planarity : 0.004 0.046 1178 Dihedral : 7.654 174.018 994 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.33 % Allowed : 16.17 % Favored : 81.49 % 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: 1.19 (0.28), residues: 890 helix: 2.35 (0.28), residues: 365 sheet: 0.54 (0.40), residues: 173 loop : -0.78 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.003 0.001 HIS R 296 PHE 0.012 0.001 PHE A 212 TYR 0.006 0.001 TYR R 199 ARG 0.008 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.781 Fit side-chains REVERT: A 211 LYS cc_start: 0.8215 (mptt) cc_final: 0.7084 (mmtt) REVERT: A 220 HIS cc_start: 0.7890 (t70) cc_final: 0.7350 (t-90) REVERT: B 59 TYR cc_start: 0.8341 (m-80) cc_final: 0.8004 (m-10) REVERT: B 217 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7771 (ppp) REVERT: B 234 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8659 (t80) REVERT: R 279 MET cc_start: 0.8395 (mmm) cc_final: 0.8096 (mmp) outliers start: 15 outliers final: 11 residues processed: 104 average time/residue: 0.1944 time to fit residues: 26.7800 Evaluate side-chains 104 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 328 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 67 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 82 optimal weight: 0.0000 chunk 74 optimal weight: 0.3980 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.0000 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN R 172 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6867 Z= 0.123 Angle : 0.436 7.116 9380 Z= 0.234 Chirality : 0.040 0.134 1111 Planarity : 0.004 0.047 1178 Dihedral : 7.623 173.528 994 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.33 % Allowed : 16.64 % Favored : 81.03 % 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: 1.21 (0.28), residues: 890 helix: 2.39 (0.27), residues: 365 sheet: 0.57 (0.40), residues: 170 loop : -0.79 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 277 HIS 0.003 0.001 HIS R 296 PHE 0.014 0.001 PHE A 222 TYR 0.012 0.001 TYR B 111 ARG 0.008 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.713 Fit side-chains REVERT: A 211 LYS cc_start: 0.8266 (mptt) cc_final: 0.7076 (mmtt) REVERT: A 220 HIS cc_start: 0.7882 (t70) cc_final: 0.7311 (t-90) REVERT: B 59 TYR cc_start: 0.8368 (m-80) cc_final: 0.8049 (m-10) REVERT: B 217 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7755 (ppp) REVERT: B 234 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8707 (t80) REVERT: R 279 MET cc_start: 0.8431 (mmm) cc_final: 0.8097 (mmp) outliers start: 15 outliers final: 12 residues processed: 100 average time/residue: 0.1911 time to fit residues: 25.4390 Evaluate side-chains 105 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 328 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 72 optimal weight: 0.0470 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 0.0030 chunk 58 optimal weight: 0.6980 overall best weight: 0.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN R 172 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6867 Z= 0.125 Angle : 0.439 7.103 9380 Z= 0.235 Chirality : 0.040 0.138 1111 Planarity : 0.004 0.046 1178 Dihedral : 7.609 173.562 994 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.49 % Allowed : 16.80 % Favored : 80.72 % 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 (0.28), residues: 890 helix: 2.38 (0.28), residues: 366 sheet: 0.54 (0.40), residues: 176 loop : -0.73 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 277 HIS 0.003 0.001 HIS R 296 PHE 0.013 0.001 PHE A 222 TYR 0.006 0.001 TYR R 199 ARG 0.009 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8394 (m-80) cc_final: 0.8029 (m-10) REVERT: B 217 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7738 (ppp) REVERT: B 234 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8697 (t80) REVERT: R 279 MET cc_start: 0.8440 (mmm) cc_final: 0.8085 (mmp) outliers start: 16 outliers final: 13 residues processed: 101 average time/residue: 0.1886 time to fit residues: 25.5096 Evaluate side-chains 105 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 328 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.0000 chunk 81 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 7 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 0.0020 chunk 75 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 overall best weight: 0.2550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6867 Z= 0.114 Angle : 0.430 7.005 9380 Z= 0.231 Chirality : 0.040 0.134 1111 Planarity : 0.004 0.046 1178 Dihedral : 7.536 173.118 994 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.87 % Allowed : 16.95 % Favored : 81.18 % 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: 1.25 (0.28), residues: 890 helix: 2.40 (0.27), residues: 368 sheet: 0.57 (0.40), residues: 169 loop : -0.76 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.003 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.005 0.001 TYR R 199 ARG 0.009 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.781 Fit side-chains REVERT: B 59 TYR cc_start: 0.8382 (m-80) cc_final: 0.8015 (m-10) REVERT: B 234 PHE cc_start: 0.9270 (OUTLIER) cc_final: 0.8597 (t80) REVERT: R 82 MET cc_start: 0.8695 (tpp) cc_final: 0.8480 (mmm) REVERT: R 279 MET cc_start: 0.8415 (mmm) cc_final: 0.8015 (mmp) outliers start: 12 outliers final: 9 residues processed: 100 average time/residue: 0.1822 time to fit residues: 24.6621 Evaluate side-chains 99 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 328 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 72 optimal weight: 0.0270 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.102282 restraints weight = 9155.048| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.07 r_work: 0.3074 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6867 Z= 0.144 Angle : 0.452 7.083 9380 Z= 0.242 Chirality : 0.041 0.136 1111 Planarity : 0.004 0.046 1178 Dihedral : 7.584 173.201 994 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.87 % Allowed : 17.57 % Favored : 80.56 % 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: 1.21 (0.28), residues: 890 helix: 2.35 (0.27), residues: 369 sheet: 0.51 (0.39), residues: 176 loop : -0.76 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 277 HIS 0.003 0.001 HIS A 220 PHE 0.014 0.001 PHE A 212 TYR 0.007 0.001 TYR A 253 ARG 0.009 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1840.58 seconds wall clock time: 35 minutes 6.79 seconds (2106.79 seconds total)