Starting phenix.real_space_refine on Fri Nov 15 06:37:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id8_35359/11_2024/8id8_35359.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id8_35359/11_2024/8id8_35359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id8_35359/11_2024/8id8_35359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id8_35359/11_2024/8id8_35359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id8_35359/11_2024/8id8_35359.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id8_35359/11_2024/8id8_35359.cif" } resolution = 3.0 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= 0.011 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 S 60 5.16 5 C 5518 2.51 5 N 1468 2.21 5 O 1588 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8635 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1752 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2554 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2170 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 102 Chain: "S" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1715 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "Y" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 417 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'YN9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.33, per 1000 atoms: 0.62 Number of scatterers: 8635 At special positions: 0 Unit cell: (105.456, 125.736, 116.61, 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 60 16.00 F 1 9.00 O 1588 8.00 N 1468 7.00 C 5518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 194 " distance=2.03 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 230 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.1 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 35.9% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.463A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.740A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.640A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.617A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.213A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.665A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'R' and resid 37 through 68 Processing helix chain 'R' and resid 68 through 73 Processing helix chain 'R' and resid 78 through 101 removed outlier: 3.710A pdb=" N LEU R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU R 87 " --> pdb=" O CYS R 83 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE R 88 " --> pdb=" O ALA R 84 " (cutoff:3.500A) Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 107 through 142 removed outlier: 3.885A pdb=" N CYS R 111 " --> pdb=" O GLY R 107 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS R 112 " --> pdb=" O PRO R 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU R 113 " --> pdb=" O VAL R 109 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR R 116 " --> pdb=" O HIS R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 176 removed outlier: 3.768A pdb=" N ALA R 156 " --> pdb=" O ARG R 152 " (cutoff:3.500A) Proline residue: R 172 - end of helix removed outlier: 3.723A pdb=" N VAL R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 217 removed outlier: 3.820A pdb=" N SER R 210 " --> pdb=" O SER R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 242 removed outlier: 3.661A pdb=" N THR R 242 " --> pdb=" O ARG R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 277 removed outlier: 3.587A pdb=" N ARG R 261 " --> pdb=" O GLN R 257 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE R 263 " --> pdb=" O ASP R 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR R 265 " --> pdb=" O ARG R 261 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE R 273 " --> pdb=" O LEU R 269 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE R 274 " --> pdb=" O MET R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 294 removed outlier: 3.617A pdb=" N ILE R 281 " --> pdb=" O TRP R 277 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN R 291 " --> pdb=" O ILE R 287 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE R 292 " --> pdb=" O LEU R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 321 removed outlier: 3.502A pdb=" N ASN R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'Y' and resid 8 through 23 Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'Y' and resid 45 through 48 removed outlier: 3.618A pdb=" N ASP Y 48 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.684A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.528A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.940A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.613A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.508A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.625A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.521A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 177 through 181 Processing sheet with id=AB1, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 5.351A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 141 through 143 Processing sheet with id=AB4, first strand: chain 'S' and resid 195 through 196 removed outlier: 5.829A pdb=" N LEU S 188 " --> pdb=" O LEU S 179 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU S 179 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 227 through 228 419 hydrogen bonds defined for protein. 1170 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: 2.59 Time building geometry restraints manager: 2.81 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: 2126 1.33 - 1.45: 1761 1.45 - 1.57: 4829 1.57 - 1.69: 4 1.69 - 1.82: 86 Bond restraints: 8806 Sorted by residual: bond pdb=" C1 YN9 R 401 " pdb=" C3 YN9 R 401 " ideal model delta sigma weight residual 1.481 1.595 -0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C2 YN9 R 401 " pdb=" C4 YN9 R 401 " ideal model delta sigma weight residual 1.501 1.606 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C1 YN9 R 401 " pdb=" C2 YN9 R 401 " ideal model delta sigma weight residual 1.400 1.486 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C9 YN9 R 401 " pdb=" O1 YN9 R 401 " ideal model delta sigma weight residual 1.353 1.432 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C5 YN9 R 401 " pdb=" C6 YN9 R 401 " ideal model delta sigma weight residual 1.503 1.580 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 8801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 11708 1.90 - 3.81: 218 3.81 - 5.71: 23 5.71 - 7.61: 5 7.61 - 9.52: 4 Bond angle restraints: 11958 Sorted by residual: angle pdb=" N TYR S 229 " pdb=" CA TYR S 229 " pdb=" C TYR S 229 " ideal model delta sigma weight residual 109.40 116.29 -6.89 1.63e+00 3.76e-01 1.79e+01 angle pdb=" N LEU R 173 " pdb=" CA LEU R 173 " pdb=" C LEU R 173 " ideal model delta sigma weight residual 111.82 116.17 -4.35 1.16e+00 7.43e-01 1.41e+01 angle pdb=" N ASP R 30 " pdb=" CA ASP R 30 " pdb=" C ASP R 30 " ideal model delta sigma weight residual 109.24 115.20 -5.96 1.67e+00 3.59e-01 1.27e+01 angle pdb=" C2 YN9 R 401 " pdb=" C4 YN9 R 401 " pdb=" O1 YN9 R 401 " ideal model delta sigma weight residual 107.97 117.49 -9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" N GLU Y 58 " pdb=" CA GLU Y 58 " pdb=" C GLU Y 58 " ideal model delta sigma weight residual 111.36 114.57 -3.21 1.09e+00 8.42e-01 8.69e+00 ... (remaining 11953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.31: 4811 20.31 - 40.62: 337 40.62 - 60.93: 41 60.93 - 81.24: 6 81.24 - 101.55: 1 Dihedral angle restraints: 5196 sinusoidal: 1904 harmonic: 3292 Sorted by residual: dihedral pdb=" CB CYS R 111 " pdb=" SG CYS R 111 " pdb=" SG CYS R 194 " pdb=" CB CYS R 194 " ideal model delta sinusoidal sigma weight residual 93.00 54.40 38.60 1 1.00e+01 1.00e-02 2.10e+01 dihedral pdb=" CA GLN S 143 " pdb=" C GLN S 143 " pdb=" N ALA S 144 " pdb=" CA ALA S 144 " ideal model delta harmonic sigma weight residual 180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP B 291 " pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta harmonic sigma weight residual 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 959 0.040 - 0.080: 323 0.080 - 0.119: 103 0.119 - 0.159: 17 0.159 - 0.199: 1 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA THR Y 52 " pdb=" N THR Y 52 " pdb=" C THR Y 52 " pdb=" CB THR Y 52 " both_signs ideal model delta sigma weight residual False 2.53 2.72 -0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA VAL S 37 " pdb=" N VAL S 37 " pdb=" C VAL S 37 " pdb=" CB VAL S 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1400 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 281 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO A 282 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO S 107 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL Y 54 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C VAL Y 54 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL Y 54 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO Y 55 " 0.012 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 3 2.09 - 2.80: 2119 2.80 - 3.50: 11287 3.50 - 4.20: 19674 4.20 - 4.90: 36008 Nonbonded interactions: 69091 Sorted by model distance: nonbonded pdb=" OH TYR A 230 " pdb=" CE1 PHE A 274 " model vdw 1.393 3.340 nonbonded pdb=" OD1 ASP A 341 " pdb=" NH1 ARG R 238 " model vdw 1.998 3.120 nonbonded pdb=" OH TYR A 230 " pdb=" CD1 PHE A 274 " model vdw 2.063 3.340 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.104 3.040 nonbonded pdb=" OH TYR R 165 " pdb=" OD1 ASN R 215 " model vdw 2.155 3.040 ... (remaining 69086 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.300 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 0.114 8806 Z= 0.293 Angle : 0.638 9.517 11958 Z= 0.358 Chirality : 0.044 0.199 1403 Planarity : 0.004 0.067 1500 Dihedral : 13.406 101.546 3058 Min Nonbonded Distance : 1.393 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.33 % Allowed : 0.78 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1115 helix: 1.13 (0.29), residues: 353 sheet: -0.82 (0.29), residues: 284 loop : -0.94 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 104 HIS 0.005 0.001 HIS S 35 PHE 0.016 0.001 PHE B 234 TYR 0.015 0.002 TYR B 59 ARG 0.007 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8191 (mttm) cc_final: 0.7982 (mttp) REVERT: A 208 ARG cc_start: 0.7998 (ttm-80) cc_final: 0.7764 (ttm110) REVERT: A 309 ASP cc_start: 0.7671 (m-30) cc_final: 0.7431 (m-30) REVERT: B 325 MET cc_start: 0.7529 (mmt) cc_final: 0.7132 (mmm) REVERT: R 47 LEU cc_start: 0.7519 (mt) cc_final: 0.7213 (mt) outliers start: 3 outliers final: 1 residues processed: 154 average time/residue: 1.2693 time to fit residues: 208.4706 Evaluate side-chains 120 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 204 GLN B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8806 Z= 0.227 Angle : 0.573 7.931 11958 Z= 0.302 Chirality : 0.043 0.150 1403 Planarity : 0.005 0.061 1500 Dihedral : 5.333 56.420 1231 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.33 % Allowed : 9.97 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.21 (0.25), residues: 1115 helix: 1.46 (0.29), residues: 358 sheet: -0.74 (0.30), residues: 279 loop : -0.93 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.005 0.001 HIS S 35 PHE 0.020 0.001 PHE R 177 TYR 0.014 0.001 TYR S 191 ARG 0.005 0.000 ARG R 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.954 Fit side-chains REVERT: A 308 GLU cc_start: 0.7874 (tt0) cc_final: 0.7639 (mt-10) REVERT: A 309 ASP cc_start: 0.7633 (m-30) cc_final: 0.7400 (m-30) REVERT: R 47 LEU cc_start: 0.7572 (mt) cc_final: 0.7310 (mt) outliers start: 21 outliers final: 8 residues processed: 136 average time/residue: 1.2026 time to fit residues: 174.7893 Evaluate side-chains 121 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 207 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 83 optimal weight: 0.0040 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8806 Z= 0.143 Angle : 0.501 7.503 11958 Z= 0.265 Chirality : 0.041 0.128 1403 Planarity : 0.004 0.054 1500 Dihedral : 4.915 52.259 1229 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.99 % Allowed : 13.73 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.13 (0.25), residues: 1115 helix: 1.84 (0.29), residues: 353 sheet: -0.50 (0.30), residues: 278 loop : -0.82 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE B 199 TYR 0.012 0.001 TYR S 191 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 308 GLU cc_start: 0.7833 (tt0) cc_final: 0.7591 (mt-10) REVERT: A 309 ASP cc_start: 0.7635 (m-30) cc_final: 0.7407 (m-30) REVERT: B 134 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7499 (ptt180) outliers start: 18 outliers final: 8 residues processed: 135 average time/residue: 1.2524 time to fit residues: 180.1817 Evaluate side-chains 119 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 0.0040 chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 88 ASN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8806 Z= 0.238 Angle : 0.557 8.448 11958 Z= 0.295 Chirality : 0.042 0.140 1403 Planarity : 0.004 0.062 1500 Dihedral : 5.054 47.414 1229 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.99 % Allowed : 13.73 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.12 (0.25), residues: 1115 helix: 1.86 (0.28), residues: 353 sheet: -0.53 (0.30), residues: 280 loop : -0.84 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 36 HIS 0.005 0.001 HIS S 35 PHE 0.013 0.001 PHE B 199 TYR 0.012 0.002 TYR R 165 ARG 0.005 0.000 ARG Y 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7677 (m-30) cc_final: 0.7446 (m-30) REVERT: B 43 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8313 (mp) REVERT: B 134 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7463 (ptt180) REVERT: B 205 ASP cc_start: 0.6656 (t0) cc_final: 0.6446 (t0) REVERT: B 325 MET cc_start: 0.7528 (mmt) cc_final: 0.7262 (mmm) outliers start: 27 outliers final: 12 residues processed: 138 average time/residue: 1.1611 time to fit residues: 171.3564 Evaluate side-chains 131 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 207 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 27 optimal weight: 0.0980 chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8806 Z= 0.171 Angle : 0.532 10.889 11958 Z= 0.276 Chirality : 0.042 0.158 1403 Planarity : 0.004 0.058 1500 Dihedral : 4.912 44.599 1229 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.10 % Allowed : 14.40 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.23 (0.25), residues: 1115 helix: 1.85 (0.28), residues: 360 sheet: -0.42 (0.30), residues: 278 loop : -0.76 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.003 0.001 HIS S 35 PHE 0.014 0.001 PHE B 199 TYR 0.011 0.001 TYR S 191 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8298 (mttm) cc_final: 0.8094 (mttp) REVERT: A 308 GLU cc_start: 0.7828 (tt0) cc_final: 0.7599 (mt-10) REVERT: A 309 ASP cc_start: 0.7652 (m-30) cc_final: 0.7425 (m-30) REVERT: B 23 LYS cc_start: 0.7973 (tppt) cc_final: 0.7696 (mmpt) REVERT: B 134 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7457 (ptt180) REVERT: B 205 ASP cc_start: 0.6570 (t0) cc_final: 0.6330 (t0) REVERT: B 226 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: B 325 MET cc_start: 0.7536 (mmt) cc_final: 0.7273 (mmm) REVERT: R 134 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7517 (tp) outliers start: 28 outliers final: 12 residues processed: 146 average time/residue: 1.1903 time to fit residues: 185.8374 Evaluate side-chains 141 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 216 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8806 Z= 0.241 Angle : 0.554 8.829 11958 Z= 0.293 Chirality : 0.043 0.147 1403 Planarity : 0.004 0.061 1500 Dihedral : 5.073 50.254 1229 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.32 % Allowed : 15.17 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.21 (0.25), residues: 1115 helix: 1.79 (0.28), residues: 361 sheet: -0.45 (0.30), residues: 280 loop : -0.73 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 36 HIS 0.006 0.001 HIS S 35 PHE 0.014 0.001 PHE B 199 TYR 0.011 0.001 TYR R 165 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 308 GLU cc_start: 0.7877 (tt0) cc_final: 0.7506 (mt-10) REVERT: A 309 ASP cc_start: 0.7663 (m-30) cc_final: 0.7432 (m-30) REVERT: A 345 LYS cc_start: 0.7430 (mtpt) cc_final: 0.7168 (mtmt) REVERT: B 43 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8222 (mp) REVERT: B 134 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7409 (ptt180) REVERT: B 205 ASP cc_start: 0.6523 (t0) cc_final: 0.6278 (t0) REVERT: B 226 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: B 325 MET cc_start: 0.7526 (mmt) cc_final: 0.7285 (mmm) outliers start: 30 outliers final: 18 residues processed: 145 average time/residue: 1.1624 time to fit residues: 182.1797 Evaluate side-chains 144 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 216 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 42 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8806 Z= 0.174 Angle : 0.520 8.007 11958 Z= 0.276 Chirality : 0.042 0.199 1403 Planarity : 0.004 0.058 1500 Dihedral : 4.927 50.912 1229 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.99 % Allowed : 16.50 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.31 (0.25), residues: 1115 helix: 1.93 (0.28), residues: 361 sheet: -0.39 (0.30), residues: 279 loop : -0.73 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE B 199 TYR 0.011 0.001 TYR S 191 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 GLU cc_start: 0.7826 (tt0) cc_final: 0.7466 (mt-10) REVERT: A 309 ASP cc_start: 0.7666 (m-30) cc_final: 0.7434 (m-30) REVERT: A 345 LYS cc_start: 0.7414 (mtpt) cc_final: 0.7136 (mtmt) REVERT: B 23 LYS cc_start: 0.7992 (tppt) cc_final: 0.7678 (mmpt) REVERT: B 134 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7403 (ptt180) REVERT: B 205 ASP cc_start: 0.6409 (t0) cc_final: 0.6168 (t0) REVERT: B 226 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6874 (mp0) REVERT: B 325 MET cc_start: 0.7594 (mmt) cc_final: 0.7305 (mmm) REVERT: R 134 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7523 (tp) outliers start: 27 outliers final: 16 residues processed: 138 average time/residue: 1.1666 time to fit residues: 172.2816 Evaluate side-chains 137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 216 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.0670 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 97 optimal weight: 0.0030 chunk 102 optimal weight: 0.0060 chunk 93 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.5146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8806 Z= 0.140 Angle : 0.508 7.493 11958 Z= 0.266 Chirality : 0.041 0.176 1403 Planarity : 0.004 0.051 1500 Dihedral : 4.704 48.907 1229 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.10 % Allowed : 17.72 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.25), residues: 1115 helix: 2.20 (0.28), residues: 359 sheet: -0.25 (0.30), residues: 283 loop : -0.68 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE B 199 TYR 0.011 0.001 TYR S 191 ARG 0.006 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: A 308 GLU cc_start: 0.7832 (tt0) cc_final: 0.7492 (mt-10) REVERT: A 309 ASP cc_start: 0.7652 (m-30) cc_final: 0.7421 (m-30) REVERT: B 23 LYS cc_start: 0.7924 (tppt) cc_final: 0.7644 (mmpt) REVERT: B 130 GLU cc_start: 0.7539 (mp0) cc_final: 0.7120 (mp0) REVERT: B 205 ASP cc_start: 0.6307 (t0) cc_final: 0.6050 (t0) REVERT: B 325 MET cc_start: 0.7530 (mmt) cc_final: 0.7266 (mmm) REVERT: R 134 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7487 (tp) outliers start: 19 outliers final: 10 residues processed: 131 average time/residue: 1.1650 time to fit residues: 163.8054 Evaluate side-chains 120 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 216 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8806 Z= 0.216 Angle : 0.557 10.166 11958 Z= 0.292 Chirality : 0.043 0.170 1403 Planarity : 0.004 0.058 1500 Dihedral : 4.904 51.559 1229 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.66 % Allowed : 19.16 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1115 helix: 2.05 (0.28), residues: 360 sheet: -0.34 (0.30), residues: 279 loop : -0.69 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 36 HIS 0.005 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.011 0.001 TYR B 124 ARG 0.007 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 308 GLU cc_start: 0.7896 (tt0) cc_final: 0.7541 (mt-10) REVERT: A 309 ASP cc_start: 0.7679 (m-30) cc_final: 0.7450 (m-30) REVERT: B 217 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.7090 (ppp) REVERT: R 134 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7543 (tp) outliers start: 15 outliers final: 11 residues processed: 134 average time/residue: 1.1690 time to fit residues: 167.5994 Evaluate side-chains 131 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 216 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 69 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8806 Z= 0.228 Angle : 0.570 9.500 11958 Z= 0.300 Chirality : 0.043 0.210 1403 Planarity : 0.004 0.058 1500 Dihedral : 4.978 53.169 1229 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.99 % Allowed : 19.05 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.38 (0.25), residues: 1115 helix: 1.97 (0.28), residues: 360 sheet: -0.32 (0.30), residues: 284 loop : -0.69 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 36 HIS 0.005 0.001 HIS S 35 PHE 0.014 0.001 PHE B 199 TYR 0.011 0.001 TYR R 165 ARG 0.007 0.000 ARG B 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 308 GLU cc_start: 0.7885 (tt0) cc_final: 0.7545 (mt-10) REVERT: A 309 ASP cc_start: 0.7682 (m-30) cc_final: 0.7453 (m-30) REVERT: B 217 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.7116 (ppp) REVERT: R 134 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7520 (tp) outliers start: 18 outliers final: 15 residues processed: 136 average time/residue: 1.1209 time to fit residues: 163.4958 Evaluate side-chains 137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 244 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.0570 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.184905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145067 restraints weight = 8984.169| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.10 r_work: 0.3402 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8806 Z= 0.148 Angle : 0.533 9.637 11958 Z= 0.276 Chirality : 0.042 0.205 1403 Planarity : 0.004 0.051 1500 Dihedral : 4.710 50.188 1229 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.66 % Allowed : 19.60 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.58 (0.25), residues: 1115 helix: 2.20 (0.28), residues: 358 sheet: -0.20 (0.30), residues: 283 loop : -0.61 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.002 0.001 HIS S 35 PHE 0.013 0.001 PHE B 199 TYR 0.013 0.001 TYR S 191 ARG 0.007 0.000 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3491.50 seconds wall clock time: 63 minutes 19.14 seconds (3799.14 seconds total)