Starting phenix.real_space_refine on Sat Dec 28 10:01:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y24_33585/12_2024/7y24_33585.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y24_33585/12_2024/7y24_33585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y24_33585/12_2024/7y24_33585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y24_33585/12_2024/7y24_33585.map" model { file = "/net/cci-nas-00/data/ceres_data/7y24_33585/12_2024/7y24_33585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y24_33585/12_2024/7y24_33585.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5251 2.51 5 N 1381 2.21 5 O 1540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8229 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1605 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2449 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 117 Chain: "G" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 360 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "S" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1722 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Classifications: {'peptide': 3} Modifications used: {'PEPT-D': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'DPN%PEPT-D:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Classifications: {'peptide': 5} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 4} Chain: "E" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2027 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 11, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 97 Time building chain proxies: 5.12, per 1000 atoms: 0.62 Number of scatterers: 8229 At special positions: 0 Unit cell: (91.308, 120.657, 125.005, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1540 8.00 N 1381 7.00 C 5251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Simple disulfide: pdb=" SG CYS C 2 " - pdb=" SG CYS C 7 " distance=2.03 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 193 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " DTR C 4 " - " PHE C 3 " Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN C 1 " pdb=" CB DTR C 4 " Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 15 sheets defined 37.2% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 44 through 53 removed outlier: 4.471A pdb=" N THR A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.577A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 256 removed outlier: 4.126A pdb=" N HIS A 245 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 280 removed outlier: 4.306A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.695A pdb=" N VAL A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.784A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.930A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 72 Processing helix chain 'E' and resid 76 through 105 Proline residue: E 97 - end of helix removed outlier: 3.626A pdb=" N ALA E 100 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN E 102 " --> pdb=" O PHE E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 146 Processing helix chain 'E' and resid 146 through 154 Processing helix chain 'E' and resid 155 through 180 Proline residue: E 176 - end of helix Processing helix chain 'E' and resid 203 through 219 Processing helix chain 'E' and resid 219 through 237 Processing helix chain 'E' and resid 244 through 282 removed outlier: 4.438A pdb=" N LYS E 248 " --> pdb=" O SER E 244 " (cutoff:3.500A) Proline residue: E 271 - end of helix Processing helix chain 'E' and resid 287 through 314 Proline residue: E 309 - end of helix Processing helix chain 'E' and resid 316 through 325 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192 removed outlier: 9.228A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.953A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.870A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.676A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.894A 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: 3.573A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.635A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.568A 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 234 removed outlier: 6.738A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.315A 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: 3.869A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 5.256A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.583A pdb=" N VAL S 143 " --> pdb=" O ILE S 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 Processing sheet with id=AB4, first strand: chain 'S' and resid 182 through 183 removed outlier: 5.706A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL S 214 " --> pdb=" O GLN S 167 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 2 through 3 removed outlier: 3.619A pdb=" N PHE C 3 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 6 " --> pdb=" O PHE C 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 182 through 185 457 hydrogen bonds defined for protein. 1323 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: 2.84 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1543 1.33 - 1.45: 2200 1.45 - 1.57: 4584 1.57 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 8405 Sorted by residual: bond pdb=" N LEU S 221 " pdb=" CA LEU S 221 " ideal model delta sigma weight residual 1.459 1.401 0.058 1.23e-02 6.61e+03 2.21e+01 bond pdb=" N TYR S 223 " pdb=" CA TYR S 223 " ideal model delta sigma weight residual 1.461 1.422 0.039 9.20e-03 1.18e+04 1.82e+01 bond pdb=" CA TYR S 223 " pdb=" C TYR S 223 " ideal model delta sigma weight residual 1.520 1.469 0.051 1.23e-02 6.61e+03 1.74e+01 bond pdb=" CA PRO S 224 " pdb=" CB PRO S 224 " ideal model delta sigma weight residual 1.532 1.481 0.051 1.33e-02 5.65e+03 1.49e+01 bond pdb=" CA LEU S 221 " pdb=" C LEU S 221 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.29e-02 6.01e+03 1.04e+01 ... (remaining 8400 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 11331 2.53 - 5.05: 121 5.05 - 7.58: 12 7.58 - 10.11: 2 10.11 - 12.64: 2 Bond angle restraints: 11468 Sorted by residual: angle pdb=" N TYR S 223 " pdb=" CA TYR S 223 " pdb=" C TYR S 223 " ideal model delta sigma weight residual 112.75 125.39 -12.64 1.36e+00 5.41e-01 8.63e+01 angle pdb=" CA TYR S 223 " pdb=" CB TYR S 223 " pdb=" CG TYR S 223 " ideal model delta sigma weight residual 113.90 103.75 10.15 1.80e+00 3.09e-01 3.18e+01 angle pdb=" O TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " ideal model delta sigma weight residual 120.48 124.22 -3.74 8.90e-01 1.26e+00 1.76e+01 angle pdb=" N PRO S 224 " pdb=" CA PRO S 224 " pdb=" C PRO S 224 " ideal model delta sigma weight residual 111.03 105.02 6.01 1.54e+00 4.22e-01 1.52e+01 angle pdb=" C GLU S 222 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " ideal model delta sigma weight residual 120.26 115.51 4.75 1.34e+00 5.57e-01 1.25e+01 ... (remaining 11463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4513 17.95 - 35.91: 305 35.91 - 53.86: 55 53.86 - 71.81: 12 71.81 - 89.77: 5 Dihedral angle restraints: 4890 sinusoidal: 1628 harmonic: 3262 Sorted by residual: dihedral pdb=" N TYR S 223 " pdb=" C TYR S 223 " pdb=" CA TYR S 223 " pdb=" CB TYR S 223 " ideal model delta harmonic sigma weight residual 122.80 147.56 -24.76 0 2.50e+00 1.60e-01 9.81e+01 dihedral pdb=" C TYR S 223 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " pdb=" CB TYR S 223 " ideal model delta harmonic sigma weight residual -122.60 -146.50 23.90 0 2.50e+00 1.60e-01 9.14e+01 dihedral pdb=" CB CYS E 115 " pdb=" SG CYS E 115 " pdb=" SG CYS E 193 " pdb=" CB CYS E 193 " ideal model delta sinusoidal sigma weight residual 93.00 179.61 -86.61 1 1.00e+01 1.00e-02 9.03e+01 ... (remaining 4887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.247: 1353 0.247 - 0.494: 0 0.494 - 0.740: 1 0.740 - 0.987: 0 0.987 - 1.234: 1 Chirality restraints: 1355 Sorted by residual: chirality pdb=" CA TYR S 223 " pdb=" N TYR S 223 " pdb=" C TYR S 223 " pdb=" CB TYR S 223 " both_signs ideal model delta sigma weight residual False 2.51 1.28 1.23 2.00e-01 2.50e+01 3.81e+01 chirality pdb=" CA GLU S 222 " pdb=" N GLU S 222 " pdb=" C GLU S 222 " pdb=" CB GLU S 222 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.18e+00 chirality pdb=" CA LEU S 221 " pdb=" N LEU S 221 " pdb=" C LEU S 221 " pdb=" CB LEU S 221 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 1352 not shown) Planarity restraints: 1453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR S 223 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C TYR S 223 " -0.061 2.00e-02 2.50e+03 pdb=" O TYR S 223 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO S 224 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 223 " 0.033 2.00e-02 2.50e+03 2.22e-02 9.89e+00 pdb=" CG TYR S 223 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR S 223 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR S 223 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR S 223 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR S 223 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR S 223 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR S 223 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP S 164 " 0.018 2.00e-02 2.50e+03 1.52e-02 5.80e+00 pdb=" CG TRP S 164 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP S 164 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP S 164 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP S 164 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP S 164 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP S 164 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 164 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 164 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP S 164 " 0.006 2.00e-02 2.50e+03 ... (remaining 1450 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 886 2.75 - 3.29: 8456 3.29 - 3.82: 14065 3.82 - 4.36: 15802 4.36 - 4.90: 27828 Nonbonded interactions: 67037 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.208 3.040 nonbonded pdb=" OE2 GLU A 9 " pdb=" ND2 ASN S 157 " model vdw 2.234 3.120 nonbonded pdb=" O SER S 52 " pdb=" NH1 ARG S 72 " model vdw 2.249 3.120 nonbonded pdb=" O ASP B 228 " pdb=" OG SER B 245 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.255 3.040 ... (remaining 67032 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.030 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8405 Z= 0.250 Angle : 0.675 12.637 11468 Z= 0.382 Chirality : 0.057 1.234 1355 Planarity : 0.005 0.055 1452 Dihedral : 12.927 89.767 2776 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.37 % Allowed : 0.25 % Favored : 99.38 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1107 helix: 1.98 (0.26), residues: 389 sheet: -0.01 (0.30), residues: 279 loop : -0.56 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP S 164 HIS 0.004 0.001 HIS S 35 PHE 0.026 0.002 PHE E 92 TYR 0.045 0.002 TYR S 223 ARG 0.009 0.001 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 220 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8206 (tm-30) REVERT: A 305 GLN cc_start: 0.8572 (mt0) cc_final: 0.8117 (tm-30) REVERT: A 313 ARG cc_start: 0.8559 (ttp-170) cc_final: 0.8278 (ttm110) REVERT: A 322 HIS cc_start: 0.7067 (t-90) cc_final: 0.6677 (t-90) REVERT: G 40 TYR cc_start: 0.7716 (t80) cc_final: 0.7312 (t80) REVERT: S 148 ARG cc_start: 0.6574 (ttp80) cc_final: 0.6284 (ttp80) REVERT: S 218 MET cc_start: 0.6506 (mtp) cc_final: 0.6271 (mtp) REVERT: S 222 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8305 (mm-30) REVERT: E 122 ASP cc_start: 0.7856 (t70) cc_final: 0.7413 (m-30) outliers start: 3 outliers final: 1 residues processed: 221 average time/residue: 0.2082 time to fit residues: 63.6961 Evaluate side-chains 189 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 0.0980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 259 GLN S 182 ASN E 308 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8405 Z= 0.201 Angle : 0.566 6.403 11468 Z= 0.302 Chirality : 0.043 0.201 1355 Planarity : 0.004 0.053 1452 Dihedral : 4.751 59.182 1204 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.83 % Allowed : 9.98 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1107 helix: 2.25 (0.25), residues: 393 sheet: -0.01 (0.30), residues: 281 loop : -0.66 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 153 HIS 0.005 0.001 HIS E 107 PHE 0.020 0.002 PHE E 92 TYR 0.023 0.001 TYR S 223 ARG 0.004 0.001 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 GLN cc_start: 0.8459 (mt0) cc_final: 0.8093 (tm-30) REVERT: A 341 ASP cc_start: 0.8296 (t0) cc_final: 0.7981 (m-30) REVERT: B 101 MET cc_start: 0.8720 (mtp) cc_final: 0.8412 (mtp) REVERT: S 125 ASP cc_start: 0.7894 (p0) cc_final: 0.7687 (p0) REVERT: S 218 MET cc_start: 0.6428 (mtp) cc_final: 0.6224 (mtp) outliers start: 23 outliers final: 16 residues processed: 223 average time/residue: 0.1973 time to fit residues: 61.3286 Evaluate side-chains 213 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 308 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 34 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN S 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8405 Z= 0.221 Angle : 0.564 5.732 11468 Z= 0.303 Chirality : 0.043 0.171 1355 Planarity : 0.004 0.050 1452 Dihedral : 4.186 24.500 1199 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.83 % Allowed : 13.67 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1107 helix: 2.08 (0.25), residues: 399 sheet: -0.01 (0.29), residues: 287 loop : -0.61 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 197 HIS 0.004 0.001 HIS B 91 PHE 0.020 0.001 PHE E 92 TYR 0.026 0.002 TYR S 223 ARG 0.004 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 198 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 GLN cc_start: 0.8501 (mt0) cc_final: 0.8108 (tm-30) REVERT: A 333 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7673 (tm-30) REVERT: A 337 ASP cc_start: 0.8563 (m-30) cc_final: 0.8357 (m-30) REVERT: S 223 TYR cc_start: 0.7414 (t80) cc_final: 0.7171 (t80) REVERT: E 92 PHE cc_start: 0.8177 (t80) cc_final: 0.7803 (t80) REVERT: E 139 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.7031 (t0) outliers start: 23 outliers final: 15 residues processed: 208 average time/residue: 0.1995 time to fit residues: 58.1230 Evaluate side-chains 201 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 59 CYS Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 227 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8405 Z= 0.180 Angle : 0.534 6.468 11468 Z= 0.285 Chirality : 0.042 0.179 1355 Planarity : 0.004 0.049 1452 Dihedral : 4.043 23.187 1199 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.45 % Allowed : 15.39 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1107 helix: 2.16 (0.25), residues: 400 sheet: -0.06 (0.30), residues: 290 loop : -0.58 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 197 HIS 0.003 0.001 HIS E 107 PHE 0.016 0.001 PHE E 92 TYR 0.021 0.001 TYR S 223 ARG 0.003 0.000 ARG E 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 GLN cc_start: 0.8486 (mt0) cc_final: 0.8106 (tm-30) REVERT: A 333 GLN cc_start: 0.7868 (tm-30) cc_final: 0.7362 (tm-30) REVERT: A 337 ASP cc_start: 0.8480 (m-30) cc_final: 0.8278 (m-30) REVERT: A 341 ASP cc_start: 0.8327 (t0) cc_final: 0.8094 (m-30) REVERT: S 12 VAL cc_start: 0.4259 (OUTLIER) cc_final: 0.3656 (m) REVERT: E 93 MET cc_start: 0.8089 (mmm) cc_final: 0.7471 (mmm) REVERT: E 139 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.7030 (t0) outliers start: 28 outliers final: 17 residues processed: 217 average time/residue: 0.1826 time to fit residues: 55.7706 Evaluate side-chains 205 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 59 CYS Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain E residue 227 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 50.0000 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 8405 Z= 0.414 Angle : 0.678 9.322 11468 Z= 0.362 Chirality : 0.047 0.167 1355 Planarity : 0.005 0.054 1452 Dihedral : 4.466 24.703 1199 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.93 % Allowed : 17.73 % Favored : 77.34 % 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: 0.41 (0.25), residues: 1107 helix: 1.69 (0.25), residues: 398 sheet: -0.22 (0.29), residues: 298 loop : -0.68 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 212 HIS 0.009 0.002 HIS B 91 PHE 0.030 0.002 PHE E 92 TYR 0.024 0.002 TYR S 223 ARG 0.006 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8290 (mp0) cc_final: 0.7926 (mp0) REVERT: A 305 GLN cc_start: 0.8546 (mt0) cc_final: 0.7903 (tm-30) REVERT: A 341 ASP cc_start: 0.8528 (t0) cc_final: 0.8326 (t70) REVERT: S 36 TRP cc_start: 0.7747 (m100) cc_final: 0.7526 (m100) REVERT: E 122 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: E 139 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7285 (t0) outliers start: 40 outliers final: 30 residues processed: 226 average time/residue: 0.1829 time to fit residues: 58.0735 Evaluate side-chains 222 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 59 CYS Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 231 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 50.0000 chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 88 optimal weight: 0.0370 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8405 Z= 0.223 Angle : 0.584 7.015 11468 Z= 0.310 Chirality : 0.042 0.173 1355 Planarity : 0.004 0.054 1452 Dihedral : 4.307 25.520 1199 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.94 % Allowed : 19.33 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1107 helix: 1.88 (0.26), residues: 398 sheet: -0.23 (0.29), residues: 289 loop : -0.57 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 197 HIS 0.004 0.001 HIS B 91 PHE 0.038 0.002 PHE E 92 TYR 0.029 0.002 TYR E 273 ARG 0.007 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8246 (mp0) cc_final: 0.7917 (mp0) REVERT: A 341 ASP cc_start: 0.8267 (t0) cc_final: 0.7843 (m-30) REVERT: S 12 VAL cc_start: 0.4146 (OUTLIER) cc_final: 0.3518 (m) REVERT: S 36 TRP cc_start: 0.7707 (m100) cc_final: 0.7499 (m100) REVERT: S 148 ARG cc_start: 0.6356 (ttp80) cc_final: 0.6149 (ttp80) REVERT: S 220 HIS cc_start: 0.8064 (OUTLIER) cc_final: 0.7771 (t-90) REVERT: S 223 TYR cc_start: 0.7538 (t80) cc_final: 0.7278 (t80) REVERT: E 122 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7639 (m-30) REVERT: E 139 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7084 (t0) outliers start: 32 outliers final: 22 residues processed: 218 average time/residue: 0.1953 time to fit residues: 58.7589 Evaluate side-chains 216 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.4980 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8405 Z= 0.297 Angle : 0.623 7.932 11468 Z= 0.332 Chirality : 0.044 0.188 1355 Planarity : 0.004 0.056 1452 Dihedral : 4.361 25.906 1199 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.19 % Allowed : 20.07 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1107 helix: 1.87 (0.26), residues: 390 sheet: -0.24 (0.29), residues: 298 loop : -0.61 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 212 HIS 0.006 0.001 HIS B 91 PHE 0.033 0.002 PHE E 92 TYR 0.020 0.002 TYR S 223 ARG 0.005 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8274 (mp0) cc_final: 0.7898 (mp0) REVERT: A 322 HIS cc_start: 0.7050 (t-90) cc_final: 0.6778 (t-90) REVERT: A 341 ASP cc_start: 0.8323 (t0) cc_final: 0.7861 (m-30) REVERT: B 283 ARG cc_start: 0.8024 (tpt170) cc_final: 0.7823 (tpt170) REVERT: B 325 MET cc_start: 0.7231 (ttm) cc_final: 0.7017 (ttt) REVERT: S 36 TRP cc_start: 0.7810 (m100) cc_final: 0.7563 (m100) REVERT: S 220 HIS cc_start: 0.8159 (OUTLIER) cc_final: 0.7812 (t-90) REVERT: E 122 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7571 (m-30) REVERT: E 139 ASP cc_start: 0.7411 (t70) cc_final: 0.7111 (t0) outliers start: 34 outliers final: 29 residues processed: 216 average time/residue: 0.2000 time to fit residues: 59.4767 Evaluate side-chains 219 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.0970 chunk 83 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8405 Z= 0.202 Angle : 0.588 8.012 11468 Z= 0.312 Chirality : 0.042 0.157 1355 Planarity : 0.004 0.056 1452 Dihedral : 4.235 25.419 1199 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.69 % Allowed : 21.31 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.26), residues: 1107 helix: 2.07 (0.26), residues: 390 sheet: -0.26 (0.30), residues: 287 loop : -0.59 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 197 HIS 0.003 0.001 HIS E 107 PHE 0.035 0.002 PHE E 92 TYR 0.033 0.002 TYR S 223 ARG 0.008 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8229 (mp0) cc_final: 0.7863 (mp0) REVERT: A 322 HIS cc_start: 0.7073 (t-90) cc_final: 0.6766 (t-90) REVERT: B 325 MET cc_start: 0.7110 (ttm) cc_final: 0.6900 (ttt) REVERT: S 12 VAL cc_start: 0.4243 (OUTLIER) cc_final: 0.3614 (m) REVERT: S 36 TRP cc_start: 0.7713 (m100) cc_final: 0.7468 (m100) REVERT: S 220 HIS cc_start: 0.7967 (OUTLIER) cc_final: 0.7730 (t-90) REVERT: E 122 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7583 (m-30) REVERT: E 139 ASP cc_start: 0.7327 (t70) cc_final: 0.7041 (t0) REVERT: E 257 MET cc_start: 0.6903 (mmt) cc_final: 0.6623 (mmt) outliers start: 30 outliers final: 23 residues processed: 223 average time/residue: 0.1892 time to fit residues: 59.0106 Evaluate side-chains 220 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 333 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8405 Z= 0.231 Angle : 0.623 9.627 11468 Z= 0.325 Chirality : 0.043 0.175 1355 Planarity : 0.004 0.056 1452 Dihedral : 4.228 25.851 1199 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.06 % Allowed : 21.06 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1107 helix: 1.97 (0.26), residues: 389 sheet: -0.22 (0.30), residues: 287 loop : -0.62 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 212 HIS 0.006 0.001 HIS S 35 PHE 0.030 0.002 PHE E 92 TYR 0.028 0.002 TYR S 223 ARG 0.011 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8250 (mp0) cc_final: 0.7860 (mp0) REVERT: A 322 HIS cc_start: 0.7097 (t-90) cc_final: 0.6768 (t-90) REVERT: B 57 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7279 (mtmt) REVERT: B 325 MET cc_start: 0.7183 (ttm) cc_final: 0.6966 (ttt) REVERT: G 40 TYR cc_start: 0.8140 (t80) cc_final: 0.7913 (t80) REVERT: S 36 TRP cc_start: 0.7778 (m100) cc_final: 0.7549 (m100) REVERT: S 218 MET cc_start: 0.6788 (OUTLIER) cc_final: 0.6322 (ttp) REVERT: E 122 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7545 (m-30) REVERT: E 139 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.7031 (t0) REVERT: E 257 MET cc_start: 0.6795 (mmt) cc_final: 0.6560 (mmt) outliers start: 33 outliers final: 26 residues processed: 215 average time/residue: 0.1932 time to fit residues: 57.8563 Evaluate side-chains 221 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 333 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8405 Z= 0.208 Angle : 0.622 11.692 11468 Z= 0.326 Chirality : 0.043 0.186 1355 Planarity : 0.004 0.056 1452 Dihedral : 4.199 25.685 1199 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.57 % Allowed : 21.80 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1107 helix: 2.01 (0.26), residues: 389 sheet: -0.23 (0.30), residues: 287 loop : -0.60 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 212 HIS 0.007 0.001 HIS S 35 PHE 0.030 0.002 PHE E 92 TYR 0.022 0.002 TYR S 223 ARG 0.004 0.000 ARG B 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8230 (mp0) cc_final: 0.7852 (mp0) REVERT: A 322 HIS cc_start: 0.7043 (t-90) cc_final: 0.6689 (t-90) REVERT: B 57 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7252 (mtmt) REVERT: B 280 LYS cc_start: 0.8557 (tptt) cc_final: 0.8295 (tttp) REVERT: S 12 VAL cc_start: 0.4275 (OUTLIER) cc_final: 0.3654 (m) REVERT: S 36 TRP cc_start: 0.7731 (m100) cc_final: 0.7457 (m100) REVERT: S 67 ARG cc_start: 0.6134 (OUTLIER) cc_final: 0.5708 (mtp180) REVERT: E 122 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7531 (m-30) REVERT: E 139 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6827 (t0) REVERT: E 257 MET cc_start: 0.6769 (mmt) cc_final: 0.6554 (mmt) outliers start: 29 outliers final: 23 residues processed: 210 average time/residue: 0.1972 time to fit residues: 57.2727 Evaluate side-chains 215 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.2980 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 0.0570 chunk 63 optimal weight: 0.9980 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.184831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.148185 restraints weight = 11484.784| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 3.14 r_work: 0.3762 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8405 Z= 0.211 Angle : 0.625 11.495 11468 Z= 0.328 Chirality : 0.044 0.248 1355 Planarity : 0.004 0.056 1452 Dihedral : 4.153 25.168 1199 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.08 % Allowed : 22.41 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1107 helix: 1.98 (0.26), residues: 390 sheet: -0.22 (0.30), residues: 287 loop : -0.56 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 212 HIS 0.006 0.001 HIS S 35 PHE 0.029 0.002 PHE E 92 TYR 0.023 0.001 TYR S 223 ARG 0.004 0.001 ARG S 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2137.93 seconds wall clock time: 39 minutes 40.83 seconds (2380.83 seconds total)