Starting phenix.real_space_refine on Thu Jul 2 02:18:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ef2_47968/07_2026/9ef2_47968.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ef2_47968/07_2026/9ef2_47968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ef2_47968/07_2026/9ef2_47968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ef2_47968/07_2026/9ef2_47968.map" model { file = "/net/cci-nas-00/data/ceres_data/9ef2_47968/07_2026/9ef2_47968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ef2_47968/07_2026/9ef2_47968.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 Mn 3 7.51 5 S 20 5.16 5 C 3658 2.51 5 N 932 2.21 5 O 1140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5756 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3227 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 31, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASP:plan': 9, 'ARG:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 91 Chain: "B" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1861 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 229} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 426 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 46 Chain: "D" 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: "E" 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: "F" 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: "G" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 42 Ad-hoc single atom residues: {' MN': 3} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.62, per 1000 atoms: 0.28 Number of scatterers: 5756 At special positions: 0 Unit cell: (70.686, 92.004, 93.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 3 24.99 Ca 3 19.99 S 20 16.00 O 1140 8.00 N 932 7.00 C 3658 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 187 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 281 " 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 G 3 " - " MAN G 6 " " MAN G 4 " - " MAN G 5 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " BETA1-6 " NAG H 1 " - " FUC H 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG B 801 " - " ASN B 192 " " NAG B 802 " - " ASN B 249 " " NAG B 803 " - " ASN B 343 " " NAG D 1 " - " ASN A 43 " " NAG E 1 " - " ASN A 256 " " NAG F 1 " - " ASN A 266 " " NAG G 1 " - " ASN A 275 " " NAG H 1 " - " ASN A 141 " Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 162.4 milliseconds 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1322 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 11 sheets defined 20.7% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 138 through 157 removed outlier: 3.800A pdb=" N ASN B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG B 155 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 4.012A pdb=" N ARG B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.683A pdb=" N PHE B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 241 removed outlier: 4.387A pdb=" N ALA B 234 " --> pdb=" O GLY B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 removed outlier: 3.800A pdb=" N ILE B 245 " --> pdb=" O CYS B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 298 through 310 Processing helix chain 'B' and resid 321 through 332 removed outlier: 3.594A pdb=" N LEU B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 Processing helix chain 'C' and resid 12 through 26 removed outlier: 3.925A pdb=" N LEU C 16 " --> pdb=" O PRO C 12 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 18 " --> pdb=" O SER C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 57 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 12 removed outlier: 8.953A pdb=" N ALA A 7 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ARG A 447 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG A 423 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE A 434 " --> pdb=" O GLY A 421 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLY A 421 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY A 436 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 419 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 removed outlier: 3.879A pdb=" N THR A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 3.730A pdb=" N SER A 120 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 108 removed outlier: 3.646A pdb=" N ARG A 144 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.688A pdb=" N SER A 169 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 238 removed outlier: 4.264A pdb=" N PHE A 248 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 262 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN A 275 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 264 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 289 through 292 Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 312 Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 359 removed outlier: 5.823A pdb=" N ASP A 368 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 200 through 206 removed outlier: 6.836A pdb=" N VAL B 202 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N SER B 166 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N SER B 204 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N PHE B 164 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG B 161 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 163 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG B 252 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ILE B 314 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU B 254 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA B 316 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE B 256 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 317 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 5 200 hydrogen bonds defined for protein. 522 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: 0.78 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1704 1.33 - 1.45: 1026 1.45 - 1.57: 3123 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 5883 Sorted by residual: bond pdb=" N ASN A 266 " pdb=" CA ASN A 266 " ideal model delta sigma weight residual 1.457 1.490 -0.034 1.33e-02 5.65e+03 6.41e+00 bond pdb=" N LYS C 40 " pdb=" CA LYS C 40 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.23e-02 6.61e+03 4.73e+00 bond pdb=" N SER B 344 " pdb=" CA SER B 344 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.32e-02 5.74e+03 4.47e+00 bond pdb=" N GLU A 81 " pdb=" CA GLU A 81 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.22e-02 6.72e+03 4.27e+00 bond pdb=" N ASN B 343 " pdb=" CA ASN B 343 " ideal model delta sigma weight residual 1.462 1.485 -0.024 1.27e-02 6.20e+03 3.54e+00 ... (remaining 5878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 7742 1.44 - 2.89: 218 2.89 - 4.33: 47 4.33 - 5.77: 9 5.77 - 7.21: 1 Bond angle restraints: 8017 Sorted by residual: angle pdb=" CA ASN A 266 " pdb=" CB ASN A 266 " pdb=" CG ASN A 266 " ideal model delta sigma weight residual 112.60 119.81 -7.21 1.00e+00 1.00e+00 5.20e+01 angle pdb=" C ASN A 141 " pdb=" CA ASN A 141 " pdb=" CB ASN A 141 " ideal model delta sigma weight residual 116.54 111.56 4.98 1.15e+00 7.56e-01 1.88e+01 angle pdb=" CA ARG C 35 " pdb=" C ARG C 35 " pdb=" O ARG C 35 " ideal model delta sigma weight residual 121.54 117.28 4.26 1.16e+00 7.43e-01 1.35e+01 angle pdb=" N ASN A 266 " pdb=" CA ASN A 266 " pdb=" C ASN A 266 " ideal model delta sigma weight residual 112.89 108.48 4.41 1.24e+00 6.50e-01 1.27e+01 angle pdb=" N SER B 344 " pdb=" CA SER B 344 " pdb=" C SER B 344 " ideal model delta sigma weight residual 113.02 109.53 3.49 1.20e+00 6.94e-01 8.46e+00 ... (remaining 8012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.37: 3507 24.37 - 48.74: 122 48.74 - 73.11: 20 73.11 - 97.48: 4 97.48 - 121.85: 6 Dihedral angle restraints: 3659 sinusoidal: 1562 harmonic: 2097 Sorted by residual: dihedral pdb=" CA LYS C 40 " pdb=" C LYS C 40 " pdb=" N GLY C 41 " pdb=" CA GLY C 41 " ideal model delta harmonic sigma weight residual 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" C2 MAN G 6 " pdb=" C1 MAN G 6 " pdb=" O5 MAN G 6 " pdb=" C5 MAN G 6 " ideal model delta sinusoidal sigma weight residual -57.62 64.23 -121.85 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C2 MAN G 5 " pdb=" C1 MAN G 5 " pdb=" O5 MAN G 5 " pdb=" C5 MAN G 5 " ideal model delta sinusoidal sigma weight residual -57.62 60.66 -118.28 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 3656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 715 0.047 - 0.094: 167 0.094 - 0.141: 59 0.141 - 0.188: 5 0.188 - 0.235: 1 Chirality restraints: 947 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.58e+01 chirality pdb=" C1 NAG B 802 " pdb=" ND2 ASN B 249 " pdb=" C2 NAG B 802 " pdb=" O5 NAG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 266 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.51e-01 ... (remaining 944 not shown) Planarity restraints: 1028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 803 " -0.256 2.00e-02 2.50e+03 2.15e-01 5.78e+02 pdb=" C7 NAG B 803 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG B 803 " -0.171 2.00e-02 2.50e+03 pdb=" N2 NAG B 803 " 0.363 2.00e-02 2.50e+03 pdb=" O7 NAG B 803 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.135 2.00e-02 2.50e+03 1.15e-01 1.65e+02 pdb=" C7 NAG F 1 " -0.024 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.031 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.186 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.121 2.00e-02 2.50e+03 9.88e-02 1.22e+02 pdb=" C7 NAG F 2 " 0.034 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.091 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.156 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.022 2.00e-02 2.50e+03 ... (remaining 1025 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 32 2.57 - 3.15: 4725 3.15 - 3.73: 8489 3.73 - 4.32: 11728 4.32 - 4.90: 20443 Nonbonded interactions: 45417 Sorted by model distance: nonbonded pdb=" OD1 ASN B 224 " pdb="MN MN B 806 " model vdw 1.985 3.060 nonbonded pdb=" O PRO B 228 " pdb="MN MN B 806 " model vdw 2.015 3.060 nonbonded pdb=" OD1 ASP B 226 " pdb="MN MN B 806 " model vdw 2.061 3.060 nonbonded pdb=" OD2 ASP B 259 " pdb="MN MN B 805 " model vdw 2.074 3.060 nonbonded pdb=" OD1 ASP B 137 " pdb="MN MN B 805 " model vdw 2.085 3.060 ... (remaining 45412 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 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.000 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 0.034 5906 Z= 0.193 Angle : 0.635 7.578 8081 Z= 0.353 Chirality : 0.046 0.235 947 Planarity : 0.009 0.215 1020 Dihedral : 13.747 121.847 2322 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.29 % Allowed : 7.05 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.31), residues: 734 helix: 0.53 (0.48), residues: 116 sheet: -0.95 (0.36), residues: 202 loop : -1.08 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 220 TYR 0.009 0.001 TYR A 327 PHE 0.011 0.001 PHE B 264 TRP 0.006 0.001 TRP A 121 HIS 0.003 0.001 HIS B 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 ( 5883) covalent geometry : angle 0.61799 / 0.35 ( 8017) SS BOND : bond 0.00327 / 0.16 ( 5) SS BOND : angle 1.08930 / 0.64 ( 10) hydrogen bonds : bond 0.15703 / 11.16 ( 200) hydrogen bonds : angle 7.58652 / 5.42 ( 522) link_ALPHA1-3 : bond 0.00250 / 0.13 ( 2) link_ALPHA1-3 : angle 1.69429 / 1.31 ( 6) link_ALPHA1-6 : bond 0.00185 / 0.10 ( 1) link_ALPHA1-6 : angle 1.51632 / 1.28 ( 3) link_BETA1-4 : bond 0.00839 / 0.42 ( 6) link_BETA1-4 : angle 2.15080 / 1.32 ( 18) link_BETA1-6 : bond 0.00703 / 0.37 ( 1) link_BETA1-6 : angle 1.51352 / 0.88 ( 3) link_NAG-ASN : bond 0.00539 / 0.27 ( 8) link_NAG-ASN : angle 1.74502 / 1.14 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 211 ASN cc_start: 0.8401 (t0) cc_final: 0.7930 (t0) REVERT: A 284 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.7984 (m-80) REVERT: B 152 GLU cc_start: 0.8632 (tp30) cc_final: 0.8416 (tp30) REVERT: B 153 MET cc_start: 0.8185 (ttp) cc_final: 0.7742 (ttm) REVERT: B 183 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7958 (mm) REVERT: B 287 MET cc_start: 0.8382 (ttt) cc_final: 0.8148 (ttm) REVERT: C 49 GLU cc_start: 0.8969 (tp30) cc_final: 0.8683 (tp30) REVERT: C 50 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8936 (mm) outliers start: 13 outliers final: 7 residues processed: 61 average time/residue: 0.0658 time to fit residues: 5.3528 Evaluate side-chains 53 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 61 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 ASN B 286 ASN B 301 HIS B 312 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.081251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.066876 restraints weight = 12853.168| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.15 r_work: 0.2778 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5906 Z= 0.175 Angle : 0.599 7.881 8081 Z= 0.295 Chirality : 0.046 0.221 947 Planarity : 0.004 0.028 1020 Dihedral : 10.410 108.904 1181 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.65 % Allowed : 10.93 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.31), residues: 734 helix: 1.04 (0.48), residues: 122 sheet: -0.90 (0.35), residues: 203 loop : -1.14 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 35 TYR 0.012 0.001 TYR B 325 PHE 0.014 0.002 PHE B 164 TRP 0.009 0.001 TRP A 121 HIS 0.005 0.001 HIS C 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 5883) covalent geometry : angle 0.58159 / 0.29 ( 8017) SS BOND : bond 0.00346 / 0.17 ( 5) SS BOND : angle 0.69406 / 0.41 ( 10) hydrogen bonds : bond 0.04465 / 3.15 ( 200) hydrogen bonds : angle 6.06480 / 4.31 ( 522) link_ALPHA1-3 : bond 0.00567 / 0.29 ( 2) link_ALPHA1-3 : angle 2.68392 / 1.97 ( 6) link_ALPHA1-6 : bond 0.00210 / 0.11 ( 1) link_ALPHA1-6 : angle 1.76923 / 1.55 ( 3) link_BETA1-4 : bond 0.00795 / 0.39 ( 6) link_BETA1-4 : angle 2.15206 / 1.32 ( 18) link_BETA1-6 : bond 0.00828 / 0.44 ( 1) link_BETA1-6 : angle 1.60152 / 0.92 ( 3) link_NAG-ASN : bond 0.00467 / 0.24 ( 8) link_NAG-ASN : angle 1.33174 / 0.84 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.138 Fit side-chains REVERT: A 78 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7987 (mtm180) REVERT: A 211 ASN cc_start: 0.8343 (t0) cc_final: 0.7874 (t0) REVERT: A 284 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.8023 (m-80) REVERT: B 183 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7982 (mm) REVERT: B 287 MET cc_start: 0.8458 (ttt) cc_final: 0.8229 (ttm) outliers start: 15 outliers final: 5 residues processed: 58 average time/residue: 0.0590 time to fit residues: 4.6191 Evaluate side-chains 53 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 301 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.081416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.067032 restraints weight = 12784.083| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.07 r_work: 0.2780 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5906 Z= 0.168 Angle : 0.593 8.431 8081 Z= 0.287 Chirality : 0.045 0.211 947 Planarity : 0.003 0.035 1020 Dihedral : 9.363 96.984 1173 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.23 % Allowed : 11.29 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.31), residues: 734 helix: 1.07 (0.47), residues: 128 sheet: -1.01 (0.35), residues: 205 loop : -1.21 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 35 TYR 0.014 0.001 TYR B 325 PHE 0.011 0.002 PHE B 264 TRP 0.008 0.001 TRP A 121 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 5883) covalent geometry : angle 0.57440 / 0.28 ( 8017) SS BOND : bond 0.00355 / 0.19 ( 5) SS BOND : angle 0.81861 / 0.49 ( 10) hydrogen bonds : bond 0.03817 / 2.64 ( 200) hydrogen bonds : angle 5.73870 / 4.12 ( 522) link_ALPHA1-3 : bond 0.00781 / 0.40 ( 2) link_ALPHA1-3 : angle 2.95456 / 2.17 ( 6) link_ALPHA1-6 : bond 0.00088 / 0.05 ( 1) link_ALPHA1-6 : angle 1.86327 / 1.65 ( 3) link_BETA1-4 : bond 0.00805 / 0.40 ( 6) link_BETA1-4 : angle 2.11127 / 1.31 ( 18) link_BETA1-6 : bond 0.00733 / 0.39 ( 1) link_BETA1-6 : angle 1.49392 / 0.86 ( 3) link_NAG-ASN : bond 0.00408 / 0.21 ( 8) link_NAG-ASN : angle 1.25956 / 0.77 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.134 Fit side-chains REVERT: A 78 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8029 (mtm180) REVERT: A 211 ASN cc_start: 0.8256 (t0) cc_final: 0.7853 (t0) REVERT: A 284 TYR cc_start: 0.8944 (OUTLIER) cc_final: 0.8114 (m-80) REVERT: B 153 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7881 (ttm) REVERT: B 183 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8242 (mt) REVERT: B 287 MET cc_start: 0.8433 (ttt) cc_final: 0.8222 (ttm) REVERT: B 290 MET cc_start: 0.9033 (tpp) cc_final: 0.8759 (tpp) REVERT: B 327 GLU cc_start: 0.8624 (tp30) cc_final: 0.8172 (tp30) REVERT: C 49 GLU cc_start: 0.8982 (tp30) cc_final: 0.8761 (tp30) REVERT: C 56 LYS cc_start: 0.8625 (tppp) cc_final: 0.8357 (tppt) outliers start: 24 outliers final: 13 residues processed: 68 average time/residue: 0.0675 time to fit residues: 6.0170 Evaluate side-chains 65 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 61 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 23 optimal weight: 0.0010 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 301 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.082362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.067768 restraints weight = 12668.806| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.15 r_work: 0.2784 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 0.023 5906 Z= 0.129 Angle : 0.576 8.546 8081 Z= 0.274 Chirality : 0.045 0.209 947 Planarity : 0.004 0.041 1020 Dihedral : 8.611 90.866 1173 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.88 % Allowed : 12.87 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.31), residues: 734 helix: 1.24 (0.48), residues: 128 sheet: -1.00 (0.35), residues: 199 loop : -1.19 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 35 TYR 0.015 0.001 TYR B 325 PHE 0.010 0.001 PHE B 264 TRP 0.006 0.001 TRP A 121 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 5883) covalent geometry : angle 0.55688 / 0.27 ( 8017) SS BOND : bond 0.00355 / 0.22 ( 5) SS BOND : angle 0.99426 / 0.57 ( 10) hydrogen bonds : bond 0.03399 / 2.35 ( 200) hydrogen bonds : angle 5.48108 / 3.95 ( 522) link_ALPHA1-3 : bond 0.01028 / 0.52 ( 2) link_ALPHA1-3 : angle 3.12048 / 2.26 ( 6) link_ALPHA1-6 : bond 0.00187 / 0.10 ( 1) link_ALPHA1-6 : angle 1.75254 / 1.56 ( 3) link_BETA1-4 : bond 0.00834 / 0.41 ( 6) link_BETA1-4 : angle 2.05926 / 1.28 ( 18) link_BETA1-6 : bond 0.00732 / 0.39 ( 1) link_BETA1-6 : angle 1.32559 / 0.78 ( 3) link_NAG-ASN : bond 0.00408 / 0.20 ( 8) link_NAG-ASN : angle 1.16288 / 0.72 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7978 (mtm180) REVERT: A 211 ASN cc_start: 0.8244 (t0) cc_final: 0.7843 (t0) REVERT: A 284 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: A 342 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8335 (mm) REVERT: B 153 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7781 (ttm) REVERT: B 287 MET cc_start: 0.8427 (ttt) cc_final: 0.8204 (ttm) REVERT: B 290 MET cc_start: 0.9043 (tpp) cc_final: 0.8799 (tpp) REVERT: C 32 ARG cc_start: 0.8584 (ttt-90) cc_final: 0.8311 (tpt-90) REVERT: C 49 GLU cc_start: 0.8938 (tp30) cc_final: 0.8678 (tp30) REVERT: C 56 LYS cc_start: 0.8579 (tppp) cc_final: 0.8327 (tppt) outliers start: 22 outliers final: 9 residues processed: 69 average time/residue: 0.0666 time to fit residues: 5.9591 Evaluate side-chains 62 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 61 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 301 HIS B 309 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.082212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.067872 restraints weight = 13105.951| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.11 r_work: 0.2819 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 5906 Z= 0.182 Angle : 0.661 9.914 8081 Z= 0.324 Chirality : 0.046 0.193 947 Planarity : 0.004 0.033 1020 Dihedral : 7.834 85.718 1170 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.06 % Allowed : 13.05 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.30), residues: 734 helix: 1.06 (0.47), residues: 128 sheet: -0.94 (0.35), residues: 203 loop : -1.25 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 35 TYR 0.014 0.001 TYR B 325 PHE 0.012 0.001 PHE B 264 TRP 0.007 0.001 TRP A 121 HIS 0.004 0.001 HIS B 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 5883) covalent geometry : angle 0.63927 / 0.32 ( 8017) SS BOND : bond 0.00509 / 0.34 ( 5) SS BOND : angle 2.42837 / 1.36 ( 10) hydrogen bonds : bond 0.04104 / 2.80 ( 200) hydrogen bonds : angle 5.54101 / 4.02 ( 522) link_ALPHA1-3 : bond 0.01116 / 0.58 ( 2) link_ALPHA1-3 : angle 3.13327 / 2.32 ( 6) link_ALPHA1-6 : bond 0.00119 / 0.06 ( 1) link_ALPHA1-6 : angle 1.87592 / 1.70 ( 3) link_BETA1-4 : bond 0.00841 / 0.40 ( 6) link_BETA1-4 : angle 2.14300 / 1.32 ( 18) link_BETA1-6 : bond 0.00720 / 0.38 ( 1) link_BETA1-6 : angle 1.46947 / 0.85 ( 3) link_NAG-ASN : bond 0.00399 / 0.20 ( 8) link_NAG-ASN : angle 1.26291 / 0.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.137 Fit side-chains REVERT: A 78 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8046 (mtm180) REVERT: A 211 ASN cc_start: 0.8135 (t0) cc_final: 0.7737 (t0) REVERT: A 284 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8153 (m-80) REVERT: A 342 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8363 (mm) REVERT: B 287 MET cc_start: 0.8489 (ttt) cc_final: 0.8284 (ttm) REVERT: B 290 MET cc_start: 0.9051 (tpp) cc_final: 0.8823 (tpp) REVERT: B 327 GLU cc_start: 0.8644 (tp30) cc_final: 0.8101 (tp30) REVERT: C 20 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8359 (mt-10) REVERT: C 32 ARG cc_start: 0.8628 (ttt-90) cc_final: 0.7809 (tpt-90) REVERT: C 49 GLU cc_start: 0.8950 (tp30) cc_final: 0.8688 (tp30) REVERT: C 56 LYS cc_start: 0.8649 (tppp) cc_final: 0.8413 (tppt) outliers start: 23 outliers final: 13 residues processed: 69 average time/residue: 0.0665 time to fit residues: 5.8924 Evaluate side-chains 66 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 61 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 301 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.081309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.066525 restraints weight = 12992.989| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.19 r_work: 0.2763 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5906 Z= 0.176 Angle : 0.635 8.944 8081 Z= 0.306 Chirality : 0.046 0.193 947 Planarity : 0.003 0.035 1020 Dihedral : 7.060 78.759 1170 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.59 % Allowed : 13.58 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.30), residues: 734 helix: 1.11 (0.47), residues: 128 sheet: -0.98 (0.35), residues: 204 loop : -1.26 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 35 TYR 0.014 0.001 TYR B 325 PHE 0.012 0.002 PHE B 264 TRP 0.007 0.001 TRP A 121 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 5883) covalent geometry : angle 0.61597 / 0.30 ( 8017) SS BOND : bond 0.00386 / 0.23 ( 5) SS BOND : angle 2.06661 / 1.15 ( 10) hydrogen bonds : bond 0.03956 / 2.71 ( 200) hydrogen bonds : angle 5.51580 / 3.99 ( 522) link_ALPHA1-3 : bond 0.01459 / 0.75 ( 2) link_ALPHA1-3 : angle 2.70594 / 2.07 ( 6) link_ALPHA1-6 : bond 0.00199 / 0.10 ( 1) link_ALPHA1-6 : angle 1.63494 / 1.50 ( 3) link_BETA1-4 : bond 0.00831 / 0.43 ( 6) link_BETA1-4 : angle 2.12409 / 1.31 ( 18) link_BETA1-6 : bond 0.00753 / 0.40 ( 1) link_BETA1-6 : angle 1.46089 / 0.84 ( 3) link_NAG-ASN : bond 0.00387 / 0.20 ( 8) link_NAG-ASN : angle 1.21935 / 0.75 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.173 Fit side-chains REVERT: A 78 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7940 (mtm180) REVERT: A 211 ASN cc_start: 0.8259 (t0) cc_final: 0.7852 (t0) REVERT: A 284 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.8065 (m-80) REVERT: A 342 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8345 (mm) REVERT: B 154 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7587 (ttm110) REVERT: B 287 MET cc_start: 0.8469 (ttt) cc_final: 0.8246 (ttm) REVERT: B 290 MET cc_start: 0.9011 (tpp) cc_final: 0.8765 (tpp) REVERT: B 327 GLU cc_start: 0.8708 (tp30) cc_final: 0.8155 (tp30) REVERT: C 20 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8279 (mt-10) REVERT: C 32 ARG cc_start: 0.8628 (ttt-90) cc_final: 0.7803 (tpt-90) REVERT: C 35 ARG cc_start: 0.7962 (ttm110) cc_final: 0.7601 (ttp-110) REVERT: C 49 GLU cc_start: 0.8966 (tp30) cc_final: 0.8694 (tp30) REVERT: C 56 LYS cc_start: 0.8622 (tppp) cc_final: 0.8390 (tppt) outliers start: 26 outliers final: 16 residues processed: 70 average time/residue: 0.0738 time to fit residues: 6.5430 Evaluate side-chains 69 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 61 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 GLN B 301 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.082318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.068191 restraints weight = 13030.546| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.06 r_work: 0.2824 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5906 Z= 0.161 Angle : 0.617 9.430 8081 Z= 0.296 Chirality : 0.045 0.187 947 Planarity : 0.003 0.033 1020 Dihedral : 6.222 61.955 1170 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.76 % Allowed : 13.93 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.30), residues: 734 helix: 1.14 (0.47), residues: 128 sheet: -0.96 (0.36), residues: 197 loop : -1.23 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 35 TYR 0.015 0.001 TYR B 325 PHE 0.011 0.001 PHE B 264 TRP 0.007 0.001 TRP A 121 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 5883) covalent geometry : angle 0.59727 / 0.29 ( 8017) SS BOND : bond 0.00385 / 0.24 ( 5) SS BOND : angle 1.88921 / 1.06 ( 10) hydrogen bonds : bond 0.03762 / 2.58 ( 200) hydrogen bonds : angle 5.46289 / 3.96 ( 522) link_ALPHA1-3 : bond 0.01319 / 0.67 ( 2) link_ALPHA1-3 : angle 2.86327 / 2.10 ( 6) link_ALPHA1-6 : bond 0.00213 / 0.11 ( 1) link_ALPHA1-6 : angle 1.73043 / 1.60 ( 3) link_BETA1-4 : bond 0.00844 / 0.44 ( 6) link_BETA1-4 : angle 2.09336 / 1.29 ( 18) link_BETA1-6 : bond 0.00753 / 0.40 ( 1) link_BETA1-6 : angle 1.41264 / 0.82 ( 3) link_NAG-ASN : bond 0.00365 / 0.18 ( 8) link_NAG-ASN : angle 1.20105 / 0.75 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 51 time to evaluate : 0.144 Fit side-chains REVERT: A 78 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7990 (mtm180) REVERT: A 211 ASN cc_start: 0.8191 (t0) cc_final: 0.7802 (t0) REVERT: A 284 TYR cc_start: 0.8954 (OUTLIER) cc_final: 0.8119 (m-80) REVERT: A 342 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8296 (mm) REVERT: B 154 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7680 (ttm110) REVERT: B 287 MET cc_start: 0.8485 (ttt) cc_final: 0.8279 (ttm) REVERT: B 290 MET cc_start: 0.9046 (tpp) cc_final: 0.8823 (tpp) REVERT: B 327 GLU cc_start: 0.8700 (tp30) cc_final: 0.8129 (tp30) REVERT: C 17 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8052 (mp0) REVERT: C 20 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8305 (mt-10) REVERT: C 32 ARG cc_start: 0.8618 (ttt-90) cc_final: 0.7822 (tpt-90) REVERT: C 35 ARG cc_start: 0.7954 (ttm110) cc_final: 0.7606 (ttp-110) REVERT: C 49 GLU cc_start: 0.8970 (tp30) cc_final: 0.8693 (tp30) REVERT: C 56 LYS cc_start: 0.8632 (tppp) cc_final: 0.8407 (tppt) outliers start: 27 outliers final: 18 residues processed: 72 average time/residue: 0.0767 time to fit residues: 7.1092 Evaluate side-chains 71 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 61 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 32 optimal weight: 0.0570 chunk 40 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.083238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.069073 restraints weight = 12950.543| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.07 r_work: 0.2837 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5906 Z= 0.130 Angle : 0.586 8.686 8081 Z= 0.282 Chirality : 0.044 0.182 947 Planarity : 0.003 0.033 1020 Dihedral : 5.502 59.062 1170 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.53 % Allowed : 15.17 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.30), residues: 734 helix: 1.19 (0.47), residues: 128 sheet: -0.94 (0.36), residues: 197 loop : -1.19 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 35 TYR 0.016 0.001 TYR B 325 PHE 0.010 0.001 PHE B 264 TRP 0.006 0.001 TRP A 121 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 5883) covalent geometry : angle 0.56864 / 0.28 ( 8017) SS BOND : bond 0.00300 / 0.17 ( 5) SS BOND : angle 1.52882 / 0.86 ( 10) hydrogen bonds : bond 0.03531 / 2.41 ( 200) hydrogen bonds : angle 5.38885 / 3.90 ( 522) link_ALPHA1-3 : bond 0.01427 / 0.71 ( 2) link_ALPHA1-3 : angle 2.62366 / 1.75 ( 6) link_ALPHA1-6 : bond 0.00252 / 0.13 ( 1) link_ALPHA1-6 : angle 1.72984 / 1.60 ( 3) link_BETA1-4 : bond 0.00892 / 0.45 ( 6) link_BETA1-4 : angle 2.04357 / 1.27 ( 18) link_BETA1-6 : bond 0.00781 / 0.41 ( 1) link_BETA1-6 : angle 1.29962 / 0.76 ( 3) link_NAG-ASN : bond 0.00358 / 0.18 ( 8) link_NAG-ASN : angle 1.10645 / 0.70 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.158 Fit side-chains REVERT: A 78 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8073 (mtm180) REVERT: A 211 ASN cc_start: 0.8153 (t0) cc_final: 0.7777 (t0) REVERT: A 284 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: A 342 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8320 (mm) REVERT: B 121 TYR cc_start: 0.7849 (m-10) cc_final: 0.7627 (m-10) REVERT: B 287 MET cc_start: 0.8480 (ttt) cc_final: 0.8280 (ttm) REVERT: B 290 MET cc_start: 0.9019 (tpp) cc_final: 0.8794 (tpp) REVERT: C 20 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8281 (mt-10) REVERT: C 32 ARG cc_start: 0.8622 (ttt-90) cc_final: 0.7838 (tpt-90) REVERT: C 35 ARG cc_start: 0.8008 (ttm110) cc_final: 0.7693 (ttp-110) REVERT: C 49 GLU cc_start: 0.8960 (tp30) cc_final: 0.8690 (tp30) REVERT: C 56 LYS cc_start: 0.8652 (tppp) cc_final: 0.8439 (tppt) outliers start: 20 outliers final: 15 residues processed: 67 average time/residue: 0.0731 time to fit residues: 6.3404 Evaluate side-chains 69 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 8 optimal weight: 0.0270 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.083758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.069779 restraints weight = 12911.460| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.04 r_work: 0.2857 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5906 Z= 0.120 Angle : 0.581 8.598 8081 Z= 0.279 Chirality : 0.045 0.179 947 Planarity : 0.003 0.032 1020 Dihedral : 5.218 59.813 1170 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.70 % Allowed : 14.99 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.30), residues: 734 helix: 0.95 (0.47), residues: 134 sheet: -0.92 (0.36), residues: 198 loop : -1.21 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 35 TYR 0.016 0.001 TYR B 325 PHE 0.009 0.001 PHE B 264 TRP 0.005 0.001 TRP C 60 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 5883) covalent geometry : angle 0.56413 / 0.27 ( 8017) SS BOND : bond 0.00279 / 0.16 ( 5) SS BOND : angle 1.38946 / 0.78 ( 10) hydrogen bonds : bond 0.03440 / 2.33 ( 200) hydrogen bonds : angle 5.34930 / 3.90 ( 522) link_ALPHA1-3 : bond 0.01247 / 0.62 ( 2) link_ALPHA1-3 : angle 2.54941 / 1.57 ( 6) link_ALPHA1-6 : bond 0.00197 / 0.10 ( 1) link_ALPHA1-6 : angle 1.79980 / 1.68 ( 3) link_BETA1-4 : bond 0.00860 / 0.44 ( 6) link_BETA1-4 : angle 2.02733 / 1.26 ( 18) link_BETA1-6 : bond 0.00751 / 0.40 ( 1) link_BETA1-6 : angle 1.22560 / 0.72 ( 3) link_NAG-ASN : bond 0.00351 / 0.17 ( 8) link_NAG-ASN : angle 1.09700 / 0.70 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8058 (mtm180) REVERT: A 211 ASN cc_start: 0.8198 (t0) cc_final: 0.7826 (t0) REVERT: A 284 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: A 342 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8349 (mm) REVERT: B 121 TYR cc_start: 0.7824 (m-10) cc_final: 0.7601 (m-10) REVERT: B 287 MET cc_start: 0.8480 (ttt) cc_final: 0.8275 (ttm) REVERT: B 290 MET cc_start: 0.9036 (tpp) cc_final: 0.8810 (tpp) REVERT: B 313 THR cc_start: 0.9294 (m) cc_final: 0.9032 (t) REVERT: C 17 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8067 (mp0) REVERT: C 20 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8271 (mt-10) REVERT: C 32 ARG cc_start: 0.8612 (ttt-90) cc_final: 0.7893 (tpt-90) REVERT: C 35 ARG cc_start: 0.8067 (ttm110) cc_final: 0.7730 (ttp-110) REVERT: C 49 GLU cc_start: 0.9005 (tp30) cc_final: 0.8693 (tp30) REVERT: C 56 LYS cc_start: 0.8505 (tppp) cc_final: 0.8300 (tppt) outliers start: 21 outliers final: 16 residues processed: 66 average time/residue: 0.0645 time to fit residues: 5.5229 Evaluate side-chains 69 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 50 optimal weight: 0.0370 chunk 20 optimal weight: 0.6980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.083516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.069479 restraints weight = 13140.323| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.07 r_work: 0.2849 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5906 Z= 0.127 Angle : 0.573 8.796 8081 Z= 0.278 Chirality : 0.045 0.264 947 Planarity : 0.003 0.033 1020 Dihedral : 5.123 59.985 1170 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.88 % Allowed : 14.46 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.30), residues: 734 helix: 0.96 (0.47), residues: 134 sheet: -0.98 (0.36), residues: 192 loop : -1.17 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 35 TYR 0.015 0.001 TYR B 325 PHE 0.010 0.001 PHE B 264 TRP 0.006 0.001 TRP A 121 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 5883) covalent geometry : angle 0.55630 / 0.27 ( 8017) SS BOND : bond 0.00307 / 0.18 ( 5) SS BOND : angle 1.31492 / 0.74 ( 10) hydrogen bonds : bond 0.03446 / 2.34 ( 200) hydrogen bonds : angle 5.33197 / 3.89 ( 522) link_ALPHA1-3 : bond 0.00921 / 0.46 ( 2) link_ALPHA1-3 : angle 2.25003 / 1.41 ( 6) link_ALPHA1-6 : bond 0.00087 / 0.05 ( 1) link_ALPHA1-6 : angle 1.94925 / 1.82 ( 3) link_BETA1-4 : bond 0.00840 / 0.42 ( 6) link_BETA1-4 : angle 2.03322 / 1.26 ( 18) link_BETA1-6 : bond 0.00751 / 0.40 ( 1) link_BETA1-6 : angle 1.24077 / 0.73 ( 3) link_NAG-ASN : bond 0.00328 / 0.16 ( 8) link_NAG-ASN : angle 1.11758 / 0.71 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.131 Fit side-chains REVERT: A 78 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8078 (mtm180) REVERT: A 122 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8069 (ttt90) REVERT: A 211 ASN cc_start: 0.8204 (t0) cc_final: 0.7822 (t0) REVERT: A 284 TYR cc_start: 0.8976 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: A 342 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8354 (mm) REVERT: B 121 TYR cc_start: 0.7842 (m-10) cc_final: 0.7620 (m-10) REVERT: B 154 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7526 (ttm110) REVERT: B 290 MET cc_start: 0.9047 (tpp) cc_final: 0.8821 (tpp) REVERT: C 20 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8286 (mt-10) REVERT: C 32 ARG cc_start: 0.8549 (ttt-90) cc_final: 0.7834 (tpt-90) REVERT: C 35 ARG cc_start: 0.8031 (ttm110) cc_final: 0.7726 (ttp-110) REVERT: C 49 GLU cc_start: 0.9025 (tp30) cc_final: 0.8725 (tp30) outliers start: 22 outliers final: 14 residues processed: 69 average time/residue: 0.0688 time to fit residues: 6.0289 Evaluate side-chains 68 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 301 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.083400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.069340 restraints weight = 12860.358| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.03 r_work: 0.2852 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5906 Z= 0.133 Angle : 0.580 8.763 8081 Z= 0.281 Chirality : 0.045 0.248 947 Planarity : 0.003 0.036 1020 Dihedral : 5.088 59.893 1169 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.35 % Allowed : 14.99 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.31), residues: 734 helix: 1.28 (0.48), residues: 128 sheet: -0.93 (0.36), residues: 198 loop : -1.08 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 35 TYR 0.015 0.001 TYR B 325 PHE 0.010 0.001 PHE B 264 TRP 0.006 0.001 TRP A 121 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 5883) covalent geometry : angle 0.56392 / 0.28 ( 8017) SS BOND : bond 0.00296 / 0.17 ( 5) SS BOND : angle 1.25944 / 0.71 ( 10) hydrogen bonds : bond 0.03433 / 2.34 ( 200) hydrogen bonds : angle 5.29683 / 3.84 ( 522) link_ALPHA1-3 : bond 0.00836 / 0.42 ( 2) link_ALPHA1-3 : angle 2.17247 / 1.38 ( 6) link_ALPHA1-6 : bond 0.00057 / 0.03 ( 1) link_ALPHA1-6 : angle 1.92883 / 1.79 ( 3) link_BETA1-4 : bond 0.00829 / 0.41 ( 6) link_BETA1-4 : angle 2.03148 / 1.26 ( 18) link_BETA1-6 : bond 0.00752 / 0.40 ( 1) link_BETA1-6 : angle 1.25737 / 0.73 ( 3) link_NAG-ASN : bond 0.00332 / 0.17 ( 8) link_NAG-ASN : angle 1.12560 / 0.72 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 898.85 seconds wall clock time: 16 minutes 9.58 seconds (969.58 seconds total)