Starting phenix.real_space_refine on Sat Apr 6 01:04:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unl_42408/04_2024/8unl_42408_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unl_42408/04_2024/8unl_42408.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/8unl_42408/04_2024/8unl_42408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unl_42408/04_2024/8unl_42408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unl_42408/04_2024/8unl_42408_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unl_42408/04_2024/8unl_42408_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= 0.027 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 40 5.16 5 C 4219 2.51 5 N 1122 2.21 5 O 1166 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 138": "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: 6550 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1692 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain breaks: 4 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 161 Chain: "B" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2400 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 118 Chain: "G" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 320 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2090 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 7, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 107 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 4.27, per 1000 atoms: 0.65 Number of scatterers: 6550 At special positions: 0 Unit cell: (83.2992, 134.493, 97.1824, 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 40 16.00 P 3 15.00 O 1166 8.00 N 1122 7.00 C 4219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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: 2.47 Conformation dependent library (CDL) restraints added in 1.8 seconds 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 8 sheets defined 42.8% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.984A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 296 through 301 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 Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.504A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.815A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 15 " --> pdb=" O ALA B 11 " (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 13 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'R' and resid 37 through 60 removed outlier: 3.538A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 96 removed outlier: 4.365A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 136 removed outlier: 3.926A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (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 165 removed outlier: 3.608A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU R 155 " --> pdb=" O ARG R 151 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 170 No H-bonds generated for 'chain 'R' and resid 167 through 170' Processing helix chain 'R' and resid 172 through 174 No H-bonds generated for 'chain 'R' and resid 172 through 174' Processing helix chain 'R' and resid 179 through 186 Processing helix chain 'R' and resid 197 through 207 Processing helix chain 'R' and resid 210 through 237 removed outlier: 4.058A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 298 removed outlier: 3.821A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.489A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 320 removed outlier: 3.538A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 326 Processing helix chain 'R' and resid 330 through 338 Processing sheet with id= A, first strand: chain 'A' and resid 286 through 292 removed outlier: 4.076A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.084A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.912A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.510A 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 150 removed outlier: 6.878A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.713A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.405A 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: 6.888A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 306 through 309 removed outlier: 3.770A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.656A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 939 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: 1.84 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1033 1.32 - 1.44: 1900 1.44 - 1.56: 3696 1.56 - 1.69: 7 1.69 - 1.81: 54 Bond restraints: 6690 Sorted by residual: bond pdb=" CA THR A 320 " pdb=" C THR A 320 " ideal model delta sigma weight residual 1.528 1.468 0.060 1.18e-02 7.18e+03 2.60e+01 bond pdb=" CA ASN R 148 " pdb=" C ASN R 148 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.30e-02 5.92e+03 2.50e+01 bond pdb=" CA LEU R 145 " pdb=" C LEU R 145 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.23e-02 6.61e+03 2.34e+01 bond pdb=" C5 GTP A 401 " pdb=" C6 GTP A 401 " ideal model delta sigma weight residual 1.390 1.476 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" CA GLN A 59 " pdb=" C GLN A 59 " ideal model delta sigma weight residual 1.524 1.475 0.048 1.27e-02 6.20e+03 1.45e+01 ... (remaining 6685 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.50: 217 107.50 - 114.60: 3941 114.60 - 121.69: 3496 121.69 - 128.79: 1439 128.79 - 135.88: 61 Bond angle restraints: 9154 Sorted by residual: angle pdb=" N SER A 352 " pdb=" CA SER A 352 " pdb=" C SER A 352 " ideal model delta sigma weight residual 111.28 123.06 -11.78 1.09e+00 8.42e-01 1.17e+02 angle pdb=" N ALA A 351 " pdb=" CA ALA A 351 " pdb=" C ALA A 351 " ideal model delta sigma weight residual 111.28 118.61 -7.33 1.09e+00 8.42e-01 4.53e+01 angle pdb=" N THR A 320 " pdb=" CA THR A 320 " pdb=" C THR A 320 " ideal model delta sigma weight residual 110.08 101.63 8.45 1.38e+00 5.25e-01 3.75e+01 angle pdb=" N SER R 143 " pdb=" CA SER R 143 " pdb=" C SER R 143 " ideal model delta sigma weight residual 111.28 117.78 -6.50 1.09e+00 8.42e-01 3.56e+01 angle pdb=" N THR R 146 " pdb=" CA THR R 146 " pdb=" C THR R 146 " ideal model delta sigma weight residual 109.50 100.99 8.51 1.58e+00 4.01e-01 2.90e+01 ... (remaining 9149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.00: 3780 31.00 - 62.01: 71 62.01 - 93.01: 2 93.01 - 124.02: 0 124.02 - 155.02: 5 Dihedral angle restraints: 3858 sinusoidal: 1250 harmonic: 2608 Sorted by residual: 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 -50.43 155.02 1 2.00e+01 2.50e-03 4.58e+01 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 260.87 124.05 136.82 1 2.00e+01 2.50e-03 4.15e+01 dihedral pdb=" O5' GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PA GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual -85.88 44.74 -130.62 1 2.00e+01 2.50e-03 3.96e+01 ... (remaining 3855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 838 0.046 - 0.091: 205 0.091 - 0.137: 57 0.137 - 0.182: 4 0.182 - 0.228: 1 Chirality restraints: 1105 Sorted by residual: chirality pdb=" CA SER A 352 " pdb=" N SER A 352 " pdb=" C SER A 352 " pdb=" CB SER A 352 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA HIS A 357 " pdb=" N HIS A 357 " pdb=" C HIS A 357 " pdb=" CB HIS A 357 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA ILE A 62 " pdb=" N ILE A 62 " pdb=" C ILE A 62 " pdb=" CB ILE A 62 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.66e-01 ... (remaining 1102 not shown) Planarity restraints: 1138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 360 " -0.070 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO A 361 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 360 " 0.022 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C TYR A 360 " -0.075 2.00e-02 2.50e+03 pdb=" O TYR A 360 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO A 361 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 320 " 0.035 5.00e-02 4.00e+02 5.22e-02 4.37e+00 pdb=" N PRO A 321 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.030 5.00e-02 4.00e+02 ... (remaining 1135 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1072 2.76 - 3.30: 6034 3.30 - 3.83: 10338 3.83 - 4.37: 11140 4.37 - 4.90: 21107 Nonbonded interactions: 49691 Sorted by model distance: nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.228 2.440 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.254 2.440 nonbonded pdb=" OD1 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.324 2.440 nonbonded pdb=" OH TYR R 209 " pdb=" O PHE R 290 " model vdw 2.339 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.344 2.440 ... (remaining 49686 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: 1.690 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: 22.810 Find NCS groups from input model: 0.180 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 0.086 6690 Z= 0.313 Angle : 0.679 11.780 9154 Z= 0.419 Chirality : 0.043 0.228 1105 Planarity : 0.005 0.110 1138 Dihedral : 14.030 155.022 2159 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.29), residues: 874 helix: 2.56 (0.27), residues: 380 sheet: 0.66 (0.43), residues: 160 loop : -0.74 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.011 0.001 HIS R 296 PHE 0.010 0.001 PHE R 49 TYR 0.011 0.001 TYR R 141 ARG 0.005 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.728 Fit side-chains REVERT: A 350 THR cc_start: 0.8696 (m) cc_final: 0.8468 (p) REVERT: A 369 THR cc_start: 0.8647 (p) cc_final: 0.8419 (p) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1513 time to fit residues: 18.0801 Evaluate side-chains 74 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6690 Z= 0.167 Angle : 0.453 5.941 9154 Z= 0.242 Chirality : 0.040 0.147 1105 Planarity : 0.003 0.037 1138 Dihedral : 9.271 144.781 975 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.49 % Allowed : 7.62 % Favored : 90.89 % 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: 1.53 (0.29), residues: 874 helix: 2.51 (0.27), residues: 393 sheet: 0.83 (0.43), residues: 156 loop : -0.81 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.007 0.001 HIS A 357 PHE 0.012 0.001 PHE B 199 TYR 0.019 0.001 TYR B 59 ARG 0.004 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.742 Fit side-chains REVERT: A 369 THR cc_start: 0.8657 (p) cc_final: 0.8450 (p) REVERT: R 82 MET cc_start: 0.8361 (ttm) cc_final: 0.8056 (ttp) outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 0.1445 time to fit residues: 15.8073 Evaluate side-chains 74 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6690 Z= 0.153 Angle : 0.427 5.466 9154 Z= 0.231 Chirality : 0.040 0.144 1105 Planarity : 0.003 0.037 1138 Dihedral : 7.995 141.246 975 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.32 % Allowed : 9.11 % Favored : 89.57 % 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: 1.57 (0.29), residues: 874 helix: 2.60 (0.27), residues: 392 sheet: 0.74 (0.42), residues: 162 loop : -0.84 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 297 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE B 241 TYR 0.014 0.001 TYR A 358 ARG 0.003 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.739 Fit side-chains REVERT: A 53 LYS cc_start: 0.8194 (mtmm) cc_final: 0.7961 (mtmm) REVERT: A 369 THR cc_start: 0.8691 (p) cc_final: 0.8485 (p) REVERT: B 258 ASP cc_start: 0.8731 (t0) cc_final: 0.8281 (t0) REVERT: R 82 MET cc_start: 0.8370 (ttm) cc_final: 0.8038 (ttp) outliers start: 8 outliers final: 7 residues processed: 74 average time/residue: 0.1459 time to fit residues: 15.8447 Evaluate side-chains 73 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 30.0000 chunk 71 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6690 Z= 0.195 Angle : 0.438 5.454 9154 Z= 0.236 Chirality : 0.040 0.144 1105 Planarity : 0.003 0.037 1138 Dihedral : 7.565 137.474 975 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.66 % Allowed : 10.43 % Favored : 87.91 % 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 (0.29), residues: 874 helix: 2.56 (0.27), residues: 392 sheet: 0.60 (0.41), residues: 168 loop : -0.83 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE B 241 TYR 0.013 0.001 TYR B 59 ARG 0.002 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.779 Fit side-chains REVERT: A 53 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7856 (mtmm) REVERT: A 369 THR cc_start: 0.8712 (p) cc_final: 0.8504 (p) REVERT: B 258 ASP cc_start: 0.8761 (t0) cc_final: 0.8293 (t0) REVERT: R 82 MET cc_start: 0.8388 (ttm) cc_final: 0.8066 (ttp) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.1442 time to fit residues: 16.3866 Evaluate side-chains 77 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE 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: 0.7980 chunk 35 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.0670 chunk 17 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6690 Z= 0.141 Angle : 0.409 5.435 9154 Z= 0.220 Chirality : 0.039 0.141 1105 Planarity : 0.003 0.037 1138 Dihedral : 7.154 133.288 975 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.49 % Allowed : 11.42 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.29), residues: 874 helix: 2.60 (0.27), residues: 392 sheet: 0.67 (0.40), residues: 168 loop : -0.77 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE B 241 TYR 0.010 0.001 TYR A 358 ARG 0.002 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.773 Fit side-chains REVERT: A 53 LYS cc_start: 0.8097 (mtmm) cc_final: 0.7795 (mtmm) REVERT: A 369 THR cc_start: 0.8676 (p) cc_final: 0.8465 (p) REVERT: B 258 ASP cc_start: 0.8777 (t0) cc_final: 0.8303 (t0) REVERT: R 82 MET cc_start: 0.8338 (ttm) cc_final: 0.7979 (ttp) outliers start: 9 outliers final: 9 residues processed: 80 average time/residue: 0.1703 time to fit residues: 19.3420 Evaluate side-chains 80 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.0020 chunk 21 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 83 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6690 Z= 0.126 Angle : 0.407 7.495 9154 Z= 0.216 Chirality : 0.039 0.143 1105 Planarity : 0.002 0.036 1138 Dihedral : 6.700 127.401 975 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.66 % Allowed : 12.09 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.29), residues: 874 helix: 2.65 (0.27), residues: 392 sheet: 0.70 (0.41), residues: 162 loop : -0.77 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 211 HIS 0.003 0.001 HIS A 357 PHE 0.010 0.001 PHE B 241 TYR 0.008 0.001 TYR B 59 ARG 0.007 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.794 Fit side-chains REVERT: A 53 LYS cc_start: 0.8012 (mtmm) cc_final: 0.7743 (mtmm) REVERT: A 271 ASN cc_start: 0.9188 (m-40) cc_final: 0.8971 (m-40) REVERT: A 369 THR cc_start: 0.8673 (p) cc_final: 0.8461 (p) REVERT: B 258 ASP cc_start: 0.8784 (t0) cc_final: 0.8306 (t0) REVERT: R 82 MET cc_start: 0.8405 (ttm) cc_final: 0.7987 (ttp) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 0.1398 time to fit residues: 16.9348 Evaluate side-chains 80 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 72 optimal weight: 0.0980 chunk 85 optimal weight: 0.0070 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6690 Z= 0.117 Angle : 0.399 6.083 9154 Z= 0.212 Chirality : 0.039 0.140 1105 Planarity : 0.002 0.036 1138 Dihedral : 6.277 121.359 975 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.32 % Allowed : 12.91 % Favored : 85.76 % 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: 1.68 (0.29), residues: 874 helix: 2.68 (0.27), residues: 392 sheet: 0.76 (0.42), residues: 162 loop : -0.74 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 211 HIS 0.003 0.001 HIS A 357 PHE 0.010 0.001 PHE B 199 TYR 0.008 0.001 TYR R 219 ARG 0.005 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.687 Fit side-chains REVERT: A 271 ASN cc_start: 0.9183 (m-40) cc_final: 0.8957 (m-40) REVERT: A 369 THR cc_start: 0.8655 (p) cc_final: 0.8438 (p) REVERT: B 258 ASP cc_start: 0.8802 (t0) cc_final: 0.8311 (t0) REVERT: R 82 MET cc_start: 0.8494 (ttm) cc_final: 0.8062 (ttp) outliers start: 8 outliers final: 7 residues processed: 83 average time/residue: 0.1349 time to fit residues: 16.7225 Evaluate side-chains 83 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6690 Z= 0.132 Angle : 0.412 5.967 9154 Z= 0.217 Chirality : 0.039 0.142 1105 Planarity : 0.002 0.036 1138 Dihedral : 6.171 119.441 975 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.49 % Allowed : 13.25 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.29), residues: 874 helix: 2.69 (0.27), residues: 392 sheet: 0.80 (0.42), residues: 162 loop : -0.74 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 211 HIS 0.003 0.001 HIS A 357 PHE 0.010 0.001 PHE B 199 TYR 0.008 0.001 TYR R 308 ARG 0.005 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.758 Fit side-chains REVERT: A 369 THR cc_start: 0.8666 (p) cc_final: 0.8452 (p) REVERT: B 258 ASP cc_start: 0.8799 (t0) cc_final: 0.8314 (t0) REVERT: R 82 MET cc_start: 0.8512 (ttm) cc_final: 0.8071 (ttp) outliers start: 9 outliers final: 8 residues processed: 79 average time/residue: 0.1547 time to fit residues: 18.1736 Evaluate side-chains 79 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6690 Z= 0.357 Angle : 0.537 6.176 9154 Z= 0.285 Chirality : 0.043 0.151 1105 Planarity : 0.003 0.037 1138 Dihedral : 6.575 122.851 975 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.82 % Allowed : 12.75 % Favored : 85.43 % 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 (0.29), residues: 874 helix: 2.28 (0.27), residues: 393 sheet: 0.47 (0.41), residues: 163 loop : -0.86 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.002 PHE B 241 TYR 0.014 0.002 TYR R 308 ARG 0.005 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.767 Fit side-chains REVERT: A 53 LYS cc_start: 0.8109 (mtmm) cc_final: 0.7752 (mtmm) REVERT: B 258 ASP cc_start: 0.8833 (t0) cc_final: 0.8382 (t0) REVERT: R 82 MET cc_start: 0.8557 (ttm) cc_final: 0.8231 (ttp) REVERT: R 187 GLU cc_start: 0.8255 (tp30) cc_final: 0.7974 (mm-30) outliers start: 11 outliers final: 10 residues processed: 79 average time/residue: 0.1436 time to fit residues: 16.5153 Evaluate side-chains 78 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 75 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6690 Z= 0.150 Angle : 0.439 5.873 9154 Z= 0.234 Chirality : 0.040 0.141 1105 Planarity : 0.003 0.038 1138 Dihedral : 6.200 117.452 975 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.32 % Allowed : 13.25 % Favored : 85.43 % 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: 1.41 (0.29), residues: 874 helix: 2.43 (0.27), residues: 392 sheet: 0.52 (0.41), residues: 168 loop : -0.79 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.001 PHE B 199 TYR 0.009 0.001 TYR R 308 ARG 0.004 0.000 ARG R 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 1.334 Fit side-chains REVERT: B 170 ASP cc_start: 0.8493 (t0) cc_final: 0.8222 (t0) REVERT: B 258 ASP cc_start: 0.8837 (t0) cc_final: 0.8394 (t0) REVERT: R 82 MET cc_start: 0.8481 (ttm) cc_final: 0.8075 (ttp) REVERT: R 187 GLU cc_start: 0.8148 (tp30) cc_final: 0.7843 (mm-30) outliers start: 8 outliers final: 7 residues processed: 79 average time/residue: 0.1893 time to fit residues: 22.6448 Evaluate side-chains 81 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.102270 restraints weight = 9718.947| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.84 r_work: 0.3050 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6690 Z= 0.170 Angle : 0.440 5.744 9154 Z= 0.233 Chirality : 0.040 0.142 1105 Planarity : 0.003 0.037 1138 Dihedral : 5.962 113.672 975 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.66 % Allowed : 13.08 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.29), residues: 874 helix: 2.47 (0.27), residues: 392 sheet: 0.55 (0.41), residues: 168 loop : -0.83 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.001 PHE B 241 TYR 0.009 0.001 TYR R 308 ARG 0.004 0.000 ARG R 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1642.62 seconds wall clock time: 30 minutes 57.37 seconds (1857.37 seconds total)