Starting phenix.real_space_refine on Wed Mar 12 08:54:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ind_60703/03_2025/9ind_60703.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ind_60703/03_2025/9ind_60703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ind_60703/03_2025/9ind_60703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ind_60703/03_2025/9ind_60703.map" model { file = "/net/cci-nas-00/data/ceres_data/9ind_60703/03_2025/9ind_60703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ind_60703/03_2025/9ind_60703.cif" } resolution = 2.88 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= 0.023 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 37 5.16 5 C 4854 2.51 5 N 1269 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7644 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3267 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 21, 'TRANS': 418} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 89 Chain: "H" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 913 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 782 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2565 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 139 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 117 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.59, per 1000 atoms: 0.73 Number of scatterers: 7644 At special positions: 0 Unit cell: (72.15, 95.55, 126.1, 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 37 16.00 O 1484 8.00 N 1269 7.00 C 4854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.02 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 377 " 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 ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 501 " - " ASN A 44 " " NAG A 502 " - " ASN A 260 " " NAG B 501 " - " ASN B 389 " " NAG B 502 " - " ASN B 414 " " NAG C 1 " - " ASN A 266 " Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 1.2 seconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1838 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 19 sheets defined 14.4% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.511A pdb=" N THR A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.794A pdb=" N LYS A 370 " --> pdb=" O GLU A 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.912A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.987A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 123 Processing helix chain 'B' and resid 126 through 135 removed outlier: 4.593A pdb=" N SER B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 172 removed outlier: 3.598A pdb=" N ILE B 165 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR B 172 " --> pdb=" O GLN B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.580A pdb=" N PHE B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.638A pdb=" N GLN B 220 " --> pdb=" O ASP B 216 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 250 through 256 removed outlier: 3.920A pdb=" N LYS B 253 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 293 removed outlier: 3.642A pdb=" N LYS B 289 " --> pdb=" O GLN B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 removed outlier: 3.747A pdb=" N TYR B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 313 " --> pdb=" O TYR B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 345 removed outlier: 3.511A pdb=" N VAL B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 343 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 345 " --> pdb=" O LYS B 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.527A pdb=" N TYR A 11 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 431 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASP A 421 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 411 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 407 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 7.200A pdb=" N ASP A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 101 removed outlier: 3.556A pdb=" N LYS A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.519A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 225 through 229 removed outlier: 3.701A pdb=" N SER A 225 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE A 255 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 283 Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 348 removed outlier: 5.650A pdb=" N ASP A 357 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AB3, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.110A pdb=" N GLY H 33 " --> pdb=" O ASN H 99 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.611A pdb=" N TYR H 108 " --> pdb=" O LEU H 98 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N TYR H 100 " --> pdb=" O PHE H 106 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N PHE H 106 " --> pdb=" O TYR H 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 6 through 7 removed outlier: 3.629A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.615A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LYS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU L 33 " --> pdb=" O LYS L 49 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AB9, first strand: chain 'B' and resid 80 through 82 removed outlier: 6.428A pdb=" N VAL B 81 " --> pdb=" O HIS B 420 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 182 through 189 removed outlier: 7.040A pdb=" N VAL B 185 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N SER B 148 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N SER B 187 " --> pdb=" O PHE B 146 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N PHE B 146 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYR B 103 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP B 141 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU B 237 " --> pdb=" O PRO B 104 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 106 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU B 239 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR B 108 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N MET B 241 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU B 110 " --> pdb=" O MET B 241 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ILE B 320 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 297 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLY B 322 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N PHE B 299 " --> pdb=" O GLY B 322 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 669 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: 2.65 Time building geometry restraints manager: 2.50 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: 1865 1.33 - 1.45: 1808 1.45 - 1.57: 4090 1.57 - 1.70: 0 1.70 - 1.82: 57 Bond restraints: 7820 Sorted by residual: bond pdb=" C GLN B 168 " pdb=" N CYS B 169 " ideal model delta sigma weight residual 1.335 1.242 0.093 1.31e-02 5.83e+03 5.03e+01 bond pdb=" N ASN B 173 " pdb=" CA ASN B 173 " ideal model delta sigma weight residual 1.462 1.395 0.066 1.44e-02 4.82e+03 2.12e+01 bond pdb=" CA ASN B 173 " pdb=" C ASN B 173 " ideal model delta sigma weight residual 1.528 1.500 0.028 1.04e-02 9.25e+03 7.31e+00 bond pdb=" C5 MAN C 4 " pdb=" O5 MAN C 4 " ideal model delta sigma weight residual 1.418 1.470 -0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" CA ASN B 173 " pdb=" CB ASN B 173 " ideal model delta sigma weight residual 1.526 1.488 0.038 1.51e-02 4.39e+03 6.39e+00 ... (remaining 7815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 10182 2.35 - 4.69: 403 4.69 - 7.04: 46 7.04 - 9.38: 15 9.38 - 11.73: 6 Bond angle restraints: 10652 Sorted by residual: angle pdb=" O GLN B 168 " pdb=" C GLN B 168 " pdb=" N CYS B 169 " ideal model delta sigma weight residual 122.15 111.65 10.50 1.14e+00 7.69e-01 8.48e+01 angle pdb=" O ASN B 167 " pdb=" C ASN B 167 " pdb=" N GLN B 168 " ideal model delta sigma weight residual 122.27 133.39 -11.12 1.23e+00 6.61e-01 8.18e+01 angle pdb=" CA ASN B 167 " pdb=" C ASN B 167 " pdb=" N GLN B 168 " ideal model delta sigma weight residual 117.72 105.99 11.73 1.31e+00 5.83e-01 8.01e+01 angle pdb=" C GLN B 168 " pdb=" N CYS B 169 " pdb=" CA CYS B 169 " ideal model delta sigma weight residual 120.28 131.75 -11.47 1.34e+00 5.57e-01 7.32e+01 angle pdb=" CA GLN B 168 " pdb=" C GLN B 168 " pdb=" N CYS B 169 " ideal model delta sigma weight residual 117.39 127.88 -10.49 1.24e+00 6.50e-01 7.16e+01 ... (remaining 10647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 4562 21.89 - 43.78: 114 43.78 - 65.68: 8 65.68 - 87.57: 10 87.57 - 109.46: 7 Dihedral angle restraints: 4701 sinusoidal: 1815 harmonic: 2886 Sorted by residual: dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual -86.00 -4.27 -81.73 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 160.44 -67.44 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CA ASN H 99 " pdb=" C ASN H 99 " pdb=" N TYR H 100 " pdb=" CA TYR H 100 " ideal model delta harmonic sigma weight residual 180.00 148.76 31.24 0 5.00e+00 4.00e-02 3.90e+01 ... (remaining 4698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 845 0.058 - 0.115: 287 0.115 - 0.172: 69 0.172 - 0.229: 11 0.229 - 0.287: 4 Chirality restraints: 1216 Sorted by residual: chirality pdb=" CB ILE A 433 " pdb=" CA ILE A 433 " pdb=" CG1 ILE A 433 " pdb=" CG2 ILE A 433 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.37 0.03 2.00e-02 2.50e+03 1.77e+00 chirality pdb=" CB VAL B 348 " pdb=" CA VAL B 348 " pdb=" CG1 VAL B 348 " pdb=" CG2 VAL B 348 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1213 not shown) Planarity restraints: 1385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 294 " -0.025 2.00e-02 2.50e+03 2.55e-02 1.14e+01 pdb=" CG PHE A 294 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 294 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 294 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 294 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE A 294 " -0.020 2.00e-02 2.50e+03 pdb=" CZ PHE A 294 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 114 " 0.019 2.00e-02 2.50e+03 1.68e-02 7.04e+00 pdb=" CG TRP A 114 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 114 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 114 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 114 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 114 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 114 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 114 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 114 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 272 " 0.017 2.00e-02 2.50e+03 1.74e-02 6.05e+00 pdb=" CG TYR B 272 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR B 272 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 272 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 272 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 272 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 272 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 272 " 0.002 2.00e-02 2.50e+03 ... (remaining 1382 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1963 2.79 - 3.32: 6258 3.32 - 3.85: 13035 3.85 - 4.37: 15722 4.37 - 4.90: 26957 Nonbonded interactions: 63935 Sorted by model distance: nonbonded pdb=" OD1 ASN A 377 " pdb=" OG SER A 388 " model vdw 2.266 3.040 nonbonded pdb=" OG SER A 279 " pdb=" O SER A 342 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR A 275 " pdb=" OD1 ASP B 251 " model vdw 2.297 3.040 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.308 3.040 nonbonded pdb=" NE2 GLN A 156 " pdb=" O LEU B 254 " model vdw 2.335 3.120 ... (remaining 63930 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: 3.550 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.480 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 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 : 0.011 0.099 7820 Z= 0.715 Angle : 1.090 11.728 10652 Z= 0.623 Chirality : 0.062 0.287 1216 Planarity : 0.007 0.055 1380 Dihedral : 11.527 109.461 2839 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.26 % Allowed : 1.30 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.25 (0.22), residues: 1000 helix: -4.46 (0.24), residues: 96 sheet: -1.53 (0.24), residues: 372 loop : -2.15 (0.22), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.005 TRP A 114 HIS 0.011 0.003 HIS B 161 PHE 0.054 0.004 PHE A 294 TYR 0.043 0.004 TYR B 272 ARG 0.015 0.002 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 0.798 Fit side-chains REVERT: A 46 THR cc_start: 0.7771 (t) cc_final: 0.7545 (m) REVERT: A 232 ASN cc_start: 0.8049 (p0) cc_final: 0.7776 (p0) REVERT: A 406 TYR cc_start: 0.8080 (t80) cc_final: 0.7732 (t80) REVERT: A 408 MET cc_start: 0.7470 (mtm) cc_final: 0.7253 (ptp) REVERT: A 427 PHE cc_start: 0.7750 (p90) cc_final: 0.7500 (p90) REVERT: A 438 ARG cc_start: 0.6759 (mtm180) cc_final: 0.5819 (tmt170) REVERT: L 36 TYR cc_start: 0.8201 (m-80) cc_final: 0.7964 (m-80) REVERT: L 48 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7452 (mm) REVERT: B 179 PRO cc_start: 0.7759 (Cg_endo) cc_final: 0.7429 (Cg_exo) REVERT: B 223 VAL cc_start: 0.8401 (p) cc_final: 0.8191 (t) REVERT: B 244 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7617 (mm110) REVERT: B 251 ASP cc_start: 0.7897 (m-30) cc_final: 0.7672 (m-30) REVERT: B 259 VAL cc_start: 0.8101 (p) cc_final: 0.7765 (t) REVERT: B 311 ASP cc_start: 0.7873 (m-30) cc_final: 0.7631 (m-30) outliers start: 2 outliers final: 0 residues processed: 218 average time/residue: 0.8633 time to fit residues: 202.7948 Evaluate side-chains 195 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 40 optimal weight: 0.0010 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 131 GLN A 207 GLN A 271 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 42 GLN ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN B 270 ASN B 340 GLN B 360 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.120664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109299 restraints weight = 10248.725| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.58 r_work: 0.3331 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7820 Z= 0.249 Angle : 0.632 8.048 10652 Z= 0.335 Chirality : 0.047 0.212 1216 Planarity : 0.005 0.036 1380 Dihedral : 9.977 90.072 1264 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.25 % Allowed : 10.00 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -2.26 (0.24), residues: 1000 helix: -2.72 (0.37), residues: 96 sheet: -0.85 (0.26), residues: 366 loop : -1.71 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 114 HIS 0.005 0.002 HIS B 307 PHE 0.029 0.002 PHE A 294 TYR 0.021 0.002 TYR H 32 ARG 0.004 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.755 Fit side-chains REVERT: A 46 THR cc_start: 0.7985 (t) cc_final: 0.7742 (m) REVERT: A 168 ARG cc_start: 0.7697 (mtp85) cc_final: 0.7397 (mtt-85) REVERT: A 232 ASN cc_start: 0.7943 (p0) cc_final: 0.7480 (p0) REVERT: A 438 ARG cc_start: 0.7145 (mtm180) cc_final: 0.5964 (tmt170) REVERT: L 36 TYR cc_start: 0.8247 (m-80) cc_final: 0.7987 (m-80) REVERT: L 52 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.8156 (m) REVERT: L 86 TYR cc_start: 0.8220 (m-80) cc_final: 0.7950 (m-80) REVERT: B 203 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7242 (mtmp) REVERT: B 251 ASP cc_start: 0.8237 (m-30) cc_final: 0.7984 (m-30) REVERT: B 258 VAL cc_start: 0.8412 (m) cc_final: 0.8083 (t) REVERT: B 259 VAL cc_start: 0.8256 (p) cc_final: 0.7954 (t) REVERT: B 278 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7199 (mtt) REVERT: B 311 ASP cc_start: 0.7991 (m-30) cc_final: 0.7774 (m-30) REVERT: B 348 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8142 (t) outliers start: 25 outliers final: 9 residues processed: 201 average time/residue: 0.8889 time to fit residues: 192.5319 Evaluate side-chains 203 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 190 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 285 GLN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 0.0570 chunk 23 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 overall best weight: 0.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 77 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN L 42 GLN B 92 ASN B 166 HIS B 244 GLN B 340 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.120758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109451 restraints weight = 10343.723| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.60 r_work: 0.3323 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7820 Z= 0.283 Angle : 0.626 9.667 10652 Z= 0.326 Chirality : 0.047 0.207 1216 Planarity : 0.004 0.034 1380 Dihedral : 8.753 74.127 1262 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.12 % Allowed : 12.73 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.25), residues: 1000 helix: -1.40 (0.46), residues: 96 sheet: -0.38 (0.27), residues: 362 loop : -1.36 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 395 HIS 0.006 0.002 HIS B 280 PHE 0.023 0.002 PHE A 294 TYR 0.024 0.002 TYR H 32 ARG 0.003 0.001 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.843 Fit side-chains REVERT: A 46 THR cc_start: 0.7990 (t) cc_final: 0.7753 (m) REVERT: A 168 ARG cc_start: 0.7645 (mtp85) cc_final: 0.7332 (mtt-85) REVERT: A 232 ASN cc_start: 0.7778 (p0) cc_final: 0.7272 (p0) REVERT: A 376 PHE cc_start: 0.7917 (m-80) cc_final: 0.7640 (m-80) REVERT: A 438 ARG cc_start: 0.7174 (mtm180) cc_final: 0.5944 (tmt170) REVERT: H 46 GLU cc_start: 0.7831 (tp30) cc_final: 0.7252 (tp30) REVERT: L 86 TYR cc_start: 0.8302 (m-80) cc_final: 0.7956 (m-80) REVERT: L 102 THR cc_start: 0.8629 (t) cc_final: 0.8352 (t) REVERT: B 72 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7459 (mt) REVERT: B 114 SER cc_start: 0.8716 (m) cc_final: 0.8475 (p) REVERT: B 226 SER cc_start: 0.8076 (p) cc_final: 0.7826 (m) REVERT: B 251 ASP cc_start: 0.8264 (m-30) cc_final: 0.8032 (m-30) REVERT: B 258 VAL cc_start: 0.8375 (m) cc_final: 0.8063 (t) REVERT: B 259 VAL cc_start: 0.8220 (OUTLIER) cc_final: 0.7922 (t) REVERT: B 278 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7148 (mtt) REVERT: B 348 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8179 (t) REVERT: B 390 VAL cc_start: 0.7976 (t) cc_final: 0.7647 (m) outliers start: 24 outliers final: 9 residues processed: 195 average time/residue: 0.9058 time to fit residues: 189.8450 Evaluate side-chains 194 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 55 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.0970 chunk 13 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN B 92 ASN B 200 HIS B 220 GLN B 340 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.121540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110361 restraints weight = 10222.540| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.53 r_work: 0.3335 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7820 Z= 0.309 Angle : 0.626 9.840 10652 Z= 0.324 Chirality : 0.047 0.214 1216 Planarity : 0.004 0.044 1380 Dihedral : 7.580 58.757 1262 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.90 % Allowed : 12.99 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.26), residues: 1000 helix: -0.67 (0.51), residues: 96 sheet: -0.12 (0.27), residues: 362 loop : -1.22 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 395 HIS 0.007 0.002 HIS B 280 PHE 0.016 0.002 PHE B 142 TYR 0.022 0.002 TYR L 50 ARG 0.003 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 25 PHE cc_start: 0.8076 (m-80) cc_final: 0.7863 (m-80) REVERT: A 46 THR cc_start: 0.7933 (t) cc_final: 0.7709 (m) REVERT: A 168 ARG cc_start: 0.7667 (mtp85) cc_final: 0.7414 (mtt-85) REVERT: A 232 ASN cc_start: 0.7729 (p0) cc_final: 0.7229 (p0) REVERT: A 358 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.6986 (mp) REVERT: A 438 ARG cc_start: 0.7192 (mtm180) cc_final: 0.6011 (tmt170) REVERT: H 46 GLU cc_start: 0.7888 (tp30) cc_final: 0.7301 (tp30) REVERT: H 70 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7690 (mtt) REVERT: H 104 ARG cc_start: 0.8608 (mtm180) cc_final: 0.8379 (mpp-170) REVERT: L 86 TYR cc_start: 0.8286 (m-80) cc_final: 0.7912 (m-80) REVERT: L 102 THR cc_start: 0.8575 (t) cc_final: 0.8315 (t) REVERT: B 203 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7278 (mtmp) REVERT: B 226 SER cc_start: 0.8078 (p) cc_final: 0.7871 (m) REVERT: B 251 ASP cc_start: 0.8255 (m-30) cc_final: 0.7984 (m-30) REVERT: B 258 VAL cc_start: 0.8326 (m) cc_final: 0.8052 (t) REVERT: B 259 VAL cc_start: 0.8206 (p) cc_final: 0.7840 (t) REVERT: B 278 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7094 (mtt) REVERT: B 348 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8165 (t) outliers start: 30 outliers final: 14 residues processed: 195 average time/residue: 0.9005 time to fit residues: 188.5742 Evaluate side-chains 198 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 1 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 152 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN B 349 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110257 restraints weight = 10173.305| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.57 r_work: 0.3334 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7820 Z= 0.306 Angle : 0.624 9.005 10652 Z= 0.320 Chirality : 0.047 0.163 1216 Planarity : 0.004 0.043 1380 Dihedral : 6.509 46.567 1262 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.29 % Allowed : 13.90 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.95 (0.26), residues: 1000 helix: -0.40 (0.52), residues: 98 sheet: -0.05 (0.27), residues: 364 loop : -1.06 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 395 HIS 0.006 0.002 HIS B 280 PHE 0.018 0.002 PHE B 142 TYR 0.022 0.002 TYR L 50 ARG 0.003 0.001 ARG H 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 25 PHE cc_start: 0.8107 (m-80) cc_final: 0.7824 (m-80) REVERT: A 46 THR cc_start: 0.7966 (t) cc_final: 0.7733 (m) REVERT: A 168 ARG cc_start: 0.7651 (mtp85) cc_final: 0.7332 (mtt-85) REVERT: A 206 ASN cc_start: 0.7984 (m-40) cc_final: 0.7604 (m110) REVERT: A 358 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7002 (mp) REVERT: A 404 PHE cc_start: 0.7585 (t80) cc_final: 0.7369 (t80) REVERT: A 438 ARG cc_start: 0.7266 (mtm180) cc_final: 0.5977 (tmt170) REVERT: H 46 GLU cc_start: 0.7983 (tp30) cc_final: 0.7388 (tp30) REVERT: H 104 ARG cc_start: 0.8604 (mtm180) cc_final: 0.8402 (mpp-170) REVERT: L 86 TYR cc_start: 0.8307 (m-80) cc_final: 0.7932 (m-80) REVERT: L 102 THR cc_start: 0.8675 (t) cc_final: 0.8425 (t) REVERT: B 72 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7561 (mt) REVERT: B 112 ASP cc_start: 0.7910 (t0) cc_final: 0.7574 (t0) REVERT: B 202 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7818 (tp40) REVERT: B 203 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7307 (mtmp) REVERT: B 251 ASP cc_start: 0.8268 (m-30) cc_final: 0.7974 (m-30) REVERT: B 258 VAL cc_start: 0.8259 (m) cc_final: 0.8006 (t) REVERT: B 278 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.7109 (mtt) REVERT: B 348 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8129 (t) REVERT: B 391 THR cc_start: 0.8282 (m) cc_final: 0.7797 (p) outliers start: 33 outliers final: 15 residues processed: 192 average time/residue: 0.9193 time to fit residues: 189.2139 Evaluate side-chains 202 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 77 ASN A 152 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 340 GLN B 349 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.122156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110949 restraints weight = 10110.281| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.55 r_work: 0.3348 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7820 Z= 0.272 Angle : 0.604 9.226 10652 Z= 0.310 Chirality : 0.046 0.148 1216 Planarity : 0.004 0.042 1380 Dihedral : 5.793 45.304 1262 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.90 % Allowed : 14.29 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.74 (0.26), residues: 1000 helix: -0.23 (0.53), residues: 98 sheet: 0.08 (0.27), residues: 360 loop : -0.91 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 395 HIS 0.005 0.001 HIS B 280 PHE 0.015 0.002 PHE B 142 TYR 0.020 0.002 TYR L 50 ARG 0.003 0.000 ARG H 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 25 PHE cc_start: 0.8092 (m-80) cc_final: 0.7825 (m-80) REVERT: A 46 THR cc_start: 0.7950 (t) cc_final: 0.7725 (m) REVERT: A 206 ASN cc_start: 0.7978 (m-40) cc_final: 0.7668 (m110) REVERT: A 358 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.6994 (mp) REVERT: A 438 ARG cc_start: 0.7275 (mtm180) cc_final: 0.5985 (tmt170) REVERT: H 46 GLU cc_start: 0.7974 (tp30) cc_final: 0.7380 (tp30) REVERT: L 86 TYR cc_start: 0.8288 (m-80) cc_final: 0.7812 (m-80) REVERT: L 102 THR cc_start: 0.8634 (t) cc_final: 0.8399 (t) REVERT: B 72 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7568 (mt) REVERT: B 112 ASP cc_start: 0.7887 (t0) cc_final: 0.7565 (t0) REVERT: B 124 LEU cc_start: 0.8443 (mp) cc_final: 0.8182 (mt) REVERT: B 202 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7821 (tp40) REVERT: B 203 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7291 (mtmp) REVERT: B 251 ASP cc_start: 0.8281 (m-30) cc_final: 0.7975 (m-30) REVERT: B 278 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7092 (mtt) REVERT: B 348 VAL cc_start: 0.8394 (OUTLIER) cc_final: 0.8145 (t) REVERT: B 391 THR cc_start: 0.8294 (m) cc_final: 0.7808 (p) outliers start: 30 outliers final: 15 residues processed: 193 average time/residue: 0.9228 time to fit residues: 190.9269 Evaluate side-chains 195 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN B 119 ASN B 220 GLN B 285 GLN B 340 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.110667 restraints weight = 10099.195| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.55 r_work: 0.3340 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7820 Z= 0.302 Angle : 0.625 9.745 10652 Z= 0.318 Chirality : 0.047 0.145 1216 Planarity : 0.004 0.042 1380 Dihedral : 5.606 45.916 1262 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.77 % Allowed : 15.06 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.26), residues: 1000 helix: -0.14 (0.54), residues: 98 sheet: 0.07 (0.27), residues: 362 loop : -0.83 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 230 HIS 0.006 0.002 HIS B 280 PHE 0.017 0.002 PHE L 98 TYR 0.022 0.002 TYR L 50 ARG 0.004 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 25 PHE cc_start: 0.8081 (m-80) cc_final: 0.7829 (m-80) REVERT: A 46 THR cc_start: 0.7946 (t) cc_final: 0.7725 (m) REVERT: A 358 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7006 (mp) REVERT: A 438 ARG cc_start: 0.7302 (mtm180) cc_final: 0.5977 (tmt170) REVERT: H 46 GLU cc_start: 0.7967 (tp30) cc_final: 0.7215 (tp30) REVERT: L 86 TYR cc_start: 0.8292 (m-80) cc_final: 0.7982 (m-80) REVERT: L 91 SER cc_start: 0.7922 (t) cc_final: 0.7550 (t) REVERT: L 102 THR cc_start: 0.8676 (t) cc_final: 0.8405 (t) REVERT: B 202 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7830 (tp40) REVERT: B 203 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7311 (mtmp) REVERT: B 251 ASP cc_start: 0.8278 (m-30) cc_final: 0.7977 (m-30) REVERT: B 258 VAL cc_start: 0.8231 (m) cc_final: 0.7986 (t) REVERT: B 278 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7098 (mtt) REVERT: B 285 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7684 (tp-100) REVERT: B 348 VAL cc_start: 0.8377 (OUTLIER) cc_final: 0.8117 (t) REVERT: B 391 THR cc_start: 0.8275 (m) cc_final: 0.7791 (p) outliers start: 29 outliers final: 18 residues processed: 187 average time/residue: 0.9404 time to fit residues: 188.9270 Evaluate side-chains 196 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 285 GLN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.0770 chunk 19 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 356 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 285 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN B 349 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.122480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111133 restraints weight = 10260.051| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.57 r_work: 0.3347 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7820 Z= 0.259 Angle : 0.608 10.038 10652 Z= 0.309 Chirality : 0.046 0.148 1216 Planarity : 0.004 0.042 1380 Dihedral : 5.489 45.708 1262 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.90 % Allowed : 15.32 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.61 (0.26), residues: 1000 helix: -0.07 (0.54), residues: 98 sheet: 0.10 (0.27), residues: 362 loop : -0.78 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 395 HIS 0.005 0.001 HIS B 280 PHE 0.015 0.002 PHE L 98 TYR 0.020 0.002 TYR L 50 ARG 0.002 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 25 PHE cc_start: 0.8081 (m-80) cc_final: 0.7814 (m-80) REVERT: A 358 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.6990 (mp) REVERT: A 424 VAL cc_start: 0.7935 (m) cc_final: 0.7727 (p) REVERT: A 438 ARG cc_start: 0.7291 (mtm180) cc_final: 0.5960 (tmt170) REVERT: H 46 GLU cc_start: 0.7992 (tp30) cc_final: 0.7227 (tp30) REVERT: L 86 TYR cc_start: 0.8292 (m-80) cc_final: 0.7794 (m-80) REVERT: L 91 SER cc_start: 0.7934 (t) cc_final: 0.7550 (t) REVERT: L 102 THR cc_start: 0.8664 (t) cc_final: 0.8401 (t) REVERT: B 112 ASP cc_start: 0.7893 (t0) cc_final: 0.7558 (t0) REVERT: B 202 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7771 (tp40) REVERT: B 203 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7278 (mtmp) REVERT: B 251 ASP cc_start: 0.8288 (m-30) cc_final: 0.7984 (m-30) REVERT: B 258 VAL cc_start: 0.8234 (m) cc_final: 0.7975 (t) REVERT: B 278 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7081 (mtt) REVERT: B 348 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.8112 (t) REVERT: B 391 THR cc_start: 0.8255 (m) cc_final: 0.7759 (p) outliers start: 30 outliers final: 19 residues processed: 181 average time/residue: 1.2365 time to fit residues: 241.0158 Evaluate side-chains 189 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 74 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 77 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 340 GLN B 349 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.122217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110969 restraints weight = 10301.026| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.56 r_work: 0.3344 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7820 Z= 0.300 Angle : 0.626 10.161 10652 Z= 0.319 Chirality : 0.047 0.145 1216 Planarity : 0.004 0.043 1380 Dihedral : 5.498 46.068 1262 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.12 % Allowed : 16.49 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.26), residues: 1000 helix: -0.05 (0.54), residues: 98 sheet: 0.15 (0.26), residues: 370 loop : -0.79 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 395 HIS 0.006 0.001 HIS B 280 PHE 0.016 0.002 PHE B 142 TYR 0.021 0.002 TYR L 50 ARG 0.003 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 25 PHE cc_start: 0.8067 (m-80) cc_final: 0.7776 (m-80) REVERT: A 358 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7011 (mp) REVERT: A 391 LEU cc_start: 0.8536 (mt) cc_final: 0.8255 (mp) REVERT: A 438 ARG cc_start: 0.7296 (mtm180) cc_final: 0.5865 (tmt170) REVERT: H 46 GLU cc_start: 0.8002 (tp30) cc_final: 0.7222 (tp30) REVERT: L 86 TYR cc_start: 0.8302 (m-80) cc_final: 0.7801 (m-80) REVERT: L 91 SER cc_start: 0.7938 (t) cc_final: 0.7534 (t) REVERT: L 102 THR cc_start: 0.8672 (t) cc_final: 0.8406 (t) REVERT: B 112 ASP cc_start: 0.7878 (t0) cc_final: 0.7524 (t0) REVERT: B 202 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7772 (tp40) REVERT: B 258 VAL cc_start: 0.8224 (m) cc_final: 0.7971 (t) REVERT: B 278 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7116 (mtt) REVERT: B 391 THR cc_start: 0.8256 (m) cc_final: 0.7743 (p) outliers start: 24 outliers final: 21 residues processed: 176 average time/residue: 1.0657 time to fit residues: 200.6331 Evaluate side-chains 186 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 84 optimal weight: 0.0060 chunk 66 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 77 ASN A 356 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN B 220 GLN B 340 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.123170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111921 restraints weight = 10263.195| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.56 r_work: 0.3359 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7820 Z= 0.231 Angle : 0.595 10.831 10652 Z= 0.303 Chirality : 0.045 0.151 1216 Planarity : 0.004 0.044 1380 Dihedral : 5.316 44.653 1262 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.73 % Allowed : 16.49 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.46 (0.27), residues: 1000 helix: 0.16 (0.55), residues: 98 sheet: 0.21 (0.27), residues: 370 loop : -0.73 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 395 HIS 0.004 0.001 HIS B 280 PHE 0.013 0.002 PHE L 98 TYR 0.017 0.002 TYR L 50 ARG 0.004 0.000 ARG A 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 8 PRO cc_start: 0.7568 (Cg_endo) cc_final: 0.7358 (Cg_exo) REVERT: A 25 PHE cc_start: 0.8036 (m-80) cc_final: 0.7787 (m-80) REVERT: A 358 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.6967 (mp) REVERT: A 391 LEU cc_start: 0.8523 (mt) cc_final: 0.8254 (mp) REVERT: A 438 ARG cc_start: 0.7307 (mtm180) cc_final: 0.5905 (tmt170) REVERT: H 46 GLU cc_start: 0.7980 (tp30) cc_final: 0.7233 (tp30) REVERT: L 86 TYR cc_start: 0.8271 (m-80) cc_final: 0.7986 (m-80) REVERT: L 91 SER cc_start: 0.7954 (t) cc_final: 0.7576 (t) REVERT: L 98 PHE cc_start: 0.8366 (m-80) cc_final: 0.7937 (m-80) REVERT: L 102 THR cc_start: 0.8642 (t) cc_final: 0.8347 (t) REVERT: B 112 ASP cc_start: 0.7845 (t0) cc_final: 0.7500 (t0) REVERT: B 202 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7840 (tp40) REVERT: B 258 VAL cc_start: 0.8223 (m) cc_final: 0.7976 (t) REVERT: B 278 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.7064 (mtt) REVERT: B 348 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8054 (t) REVERT: B 391 THR cc_start: 0.8256 (m) cc_final: 0.7756 (p) outliers start: 21 outliers final: 14 residues processed: 183 average time/residue: 1.4886 time to fit residues: 291.2286 Evaluate side-chains 186 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 15 optimal weight: 0.2980 chunk 38 optimal weight: 0.3980 chunk 46 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 chunk 56 optimal weight: 0.0670 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 77 ASN A 327 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN B 119 ASN B 220 GLN B 340 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.124086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.112822 restraints weight = 10211.869| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.56 r_work: 0.3373 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7820 Z= 0.188 Angle : 0.584 11.391 10652 Z= 0.296 Chirality : 0.045 0.151 1216 Planarity : 0.004 0.042 1380 Dihedral : 5.156 42.367 1262 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.34 % Allowed : 17.66 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.37 (0.27), residues: 1000 helix: 0.23 (0.55), residues: 98 sheet: 0.30 (0.27), residues: 369 loop : -0.69 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 395 HIS 0.004 0.001 HIS B 118 PHE 0.012 0.001 PHE L 98 TYR 0.016 0.001 TYR B 272 ARG 0.004 0.000 ARG A 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6120.76 seconds wall clock time: 107 minutes 50.63 seconds (6470.63 seconds total)