Starting phenix.real_space_refine on Wed Sep 17 06:06:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ef2_47968/09_2025/9ef2_47968.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ef2_47968/09_2025/9ef2_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ef2_47968/09_2025/9ef2_47968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ef2_47968/09_2025/9ef2_47968.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ef2_47968/09_2025/9ef2_47968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ef2_47968/09_2025/9ef2_47968.map" } 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-2.0-5805/lib/python3.9/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, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Unusual residues: {' MN': 3, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.72, per 1000 atoms: 0.30 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: 0.70 Conformation dependent library (CDL) restraints added in 334.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.19 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: 0.81 Time building geometry restraints manager: 0.87 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 2.320 nonbonded pdb=" O PRO B 228 " pdb="MN MN B 806 " model vdw 2.015 2.320 nonbonded pdb=" OD1 ASP B 226 " pdb="MN MN B 806 " model vdw 2.061 2.320 nonbonded pdb=" OD2 ASP B 259 " pdb="MN MN B 805 " model vdw 2.074 2.320 nonbonded pdb=" OD1 ASP B 137 " pdb="MN MN B 805 " model vdw 2.085 2.320 ... (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: 2.960 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.700 Find NCS groups from input model: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 aren 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 covalent geometry : bond 0.00394 ( 5883) covalent geometry : angle 0.61799 ( 8017) SS BOND : bond 0.00327 ( 5) SS BOND : angle 1.08930 ( 10) hydrogen bonds : bond 0.15703 ( 200) hydrogen bonds : angle 7.58652 ( 522) link_ALPHA1-3 : bond 0.00250 ( 2) link_ALPHA1-3 : angle 1.69429 ( 6) link_ALPHA1-6 : bond 0.00185 ( 1) link_ALPHA1-6 : angle 1.51632 ( 3) link_BETA1-4 : bond 0.00839 ( 6) link_BETA1-4 : angle 2.15080 ( 18) link_BETA1-6 : bond 0.00703 ( 1) link_BETA1-6 : angle 1.51352 ( 3) link_NAG-ASN : bond 0.00539 ( 8) link_NAG-ASN : angle 1.74502 ( 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 : 0.222 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: 0.8937 (mm) outliers start: 13 outliers final: 7 residues processed: 61 average time/residue: 0.0952 time to fit residues: 7.5811 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 : 0.223 ------------------------------------------------------------------------------- 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: 0.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN B 301 HIS B 312 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.080665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.066272 restraints weight = 13083.513| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.16 r_work: 0.2764 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5906 Z= 0.201 Angle : 0.618 8.249 8081 Z= 0.303 Chirality : 0.046 0.217 947 Planarity : 0.004 0.030 1020 Dihedral : 10.296 107.070 1181 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.00 % Allowed : 10.58 % 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 aren not related in a simple way. whole: -1.03 (0.31), residues: 734 helix: 1.00 (0.48), residues: 122 sheet: -0.92 (0.36), residues: 203 loop : -1.06 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 35 TYR 0.013 0.001 TYR B 325 PHE 0.014 0.002 PHE B 164 TRP 0.010 0.001 TRP A 121 HIS 0.005 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 5883) covalent geometry : angle 0.59944 ( 8017) SS BOND : bond 0.00379 ( 5) SS BOND : angle 0.76880 ( 10) hydrogen bonds : bond 0.04409 ( 200) hydrogen bonds : angle 6.02684 ( 522) link_ALPHA1-3 : bond 0.00519 ( 2) link_ALPHA1-3 : angle 2.81443 ( 6) link_ALPHA1-6 : bond 0.00095 ( 1) link_ALPHA1-6 : angle 1.87923 ( 3) link_BETA1-4 : bond 0.00836 ( 6) link_BETA1-4 : angle 2.19003 ( 18) link_BETA1-6 : bond 0.00697 ( 1) link_BETA1-6 : angle 1.58411 ( 3) link_NAG-ASN : bond 0.00438 ( 8) link_NAG-ASN : angle 1.36595 ( 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 63 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7986 (mtm180) REVERT: A 211 ASN cc_start: 0.8370 (t0) cc_final: 0.7909 (t0) REVERT: A 284 TYR cc_start: 0.8907 (OUTLIER) cc_final: 0.8033 (m-80) REVERT: B 183 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8087 (mm) REVERT: B 287 MET cc_start: 0.8428 (ttt) cc_final: 0.8197 (ttm) REVERT: C 49 GLU cc_start: 0.9013 (tp30) cc_final: 0.8715 (tp30) outliers start: 17 outliers final: 7 residues processed: 59 average time/residue: 0.0884 time to fit residues: 6.9914 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 : 0.205 ------------------------------------------------------------------------------- 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 A residue 434 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 313 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.079398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.064946 restraints weight = 13016.430| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.08 r_work: 0.2738 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 5906 Z= 0.242 Angle : 0.657 9.191 8081 Z= 0.318 Chirality : 0.047 0.209 947 Planarity : 0.004 0.037 1020 Dihedral : 9.363 97.278 1173 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.47 % Allowed : 10.05 % 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 aren not related in a simple way. whole: -1.23 (0.31), residues: 734 helix: 0.94 (0.47), residues: 128 sheet: -1.09 (0.35), residues: 210 loop : -1.22 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 35 TYR 0.015 0.001 TYR B 325 PHE 0.015 0.002 PHE B 264 TRP 0.010 0.001 TRP A 121 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 5883) covalent geometry : angle 0.63765 ( 8017) SS BOND : bond 0.00434 ( 5) SS BOND : angle 0.82974 ( 10) hydrogen bonds : bond 0.04287 ( 200) hydrogen bonds : angle 5.86653 ( 522) link_ALPHA1-3 : bond 0.00683 ( 2) link_ALPHA1-3 : angle 3.13953 ( 6) link_ALPHA1-6 : bond 0.00073 ( 1) link_ALPHA1-6 : angle 2.09915 ( 3) link_BETA1-4 : bond 0.00787 ( 6) link_BETA1-4 : angle 2.24974 ( 18) link_BETA1-6 : bond 0.00794 ( 1) link_BETA1-6 : angle 1.78647 ( 3) link_NAG-ASN : bond 0.00452 ( 8) link_NAG-ASN : angle 1.46587 ( 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 82 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 51 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8117 (mtm180) REVERT: A 211 ASN cc_start: 0.8346 (t0) cc_final: 0.7930 (t0) REVERT: A 284 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: B 124 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7795 (t0) REVERT: B 183 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8123 (mm) REVERT: B 287 MET cc_start: 0.8441 (ttt) cc_final: 0.8218 (ttm) REVERT: B 290 MET cc_start: 0.9014 (tpp) cc_final: 0.8756 (tpp) REVERT: B 327 GLU cc_start: 0.8640 (tp30) cc_final: 0.8208 (tp30) REVERT: C 49 GLU cc_start: 0.9049 (tp30) cc_final: 0.8745 (tp30) outliers start: 31 outliers final: 16 residues processed: 74 average time/residue: 0.1068 time to fit residues: 9.9219 Evaluate side-chains 66 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 411 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 124 ASP 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 B residue 318 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 8 ARG 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: 0.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.080835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.066340 restraints weight = 12857.897| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.07 r_work: 0.2769 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1193 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= 0.145 Angle : 0.594 8.947 8081 Z= 0.284 Chirality : 0.045 0.214 947 Planarity : 0.004 0.038 1020 Dihedral : 8.478 91.891 1173 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.70 % Allowed : 13.58 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.31), residues: 734 helix: 1.10 (0.47), residues: 129 sheet: -1.04 (0.35), residues: 199 loop : -1.15 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 32 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 C 34 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 5883) covalent geometry : angle 0.57547 ( 8017) SS BOND : bond 0.00297 ( 5) SS BOND : angle 0.60188 ( 10) hydrogen bonds : bond 0.03567 ( 200) hydrogen bonds : angle 5.60632 ( 522) link_ALPHA1-3 : bond 0.01034 ( 2) link_ALPHA1-3 : angle 3.12520 ( 6) link_ALPHA1-6 : bond 0.00122 ( 1) link_ALPHA1-6 : angle 1.76223 ( 3) link_BETA1-4 : bond 0.00830 ( 6) link_BETA1-4 : angle 2.10838 ( 18) link_BETA1-6 : bond 0.00789 ( 1) link_BETA1-6 : angle 1.44333 ( 3) link_NAG-ASN : bond 0.00398 ( 8) link_NAG-ASN : angle 1.21501 ( 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 72 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8028 (mtm180) REVERT: A 211 ASN cc_start: 0.8211 (t0) cc_final: 0.7818 (t0) REVERT: A 284 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.8068 (m-80) REVERT: A 342 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8474 (mm) REVERT: B 183 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8212 (mt) REVERT: B 287 MET cc_start: 0.8451 (ttt) cc_final: 0.8246 (ttm) REVERT: B 290 MET cc_start: 0.8942 (tpp) cc_final: 0.8724 (tpp) REVERT: B 327 GLU cc_start: 0.8647 (tp30) cc_final: 0.8134 (tp30) outliers start: 21 outliers final: 9 residues processed: 64 average time/residue: 0.0975 time to fit residues: 8.1956 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 : 0.182 ------------------------------------------------------------------------------- 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 342 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 215 LEU 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: 0.8980 chunk 23 optimal weight: 0.0020 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3142 r_free = 0.3142 target = 0.080832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.066163 restraints weight = 13109.459| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.16 r_work: 0.2760 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5906 Z= 0.151 Angle : 0.597 8.800 8081 Z= 0.283 Chirality : 0.045 0.198 947 Planarity : 0.003 0.035 1020 Dihedral : 7.339 83.508 1173 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.76 % Allowed : 13.76 % Favored : 81.48 % 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 aren not related in a simple way. whole: -1.05 (0.31), residues: 734 helix: 1.18 (0.48), residues: 129 sheet: -1.01 (0.36), residues: 197 loop : -1.13 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 35 TYR 0.014 0.001 TYR B 325 PHE 0.011 0.001 PHE B 264 TRP 0.006 0.001 TRP A 121 HIS 0.003 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 5883) covalent geometry : angle 0.57976 ( 8017) SS BOND : bond 0.00306 ( 5) SS BOND : angle 0.61857 ( 10) hydrogen bonds : bond 0.03479 ( 200) hydrogen bonds : angle 5.45923 ( 522) link_ALPHA1-3 : bond 0.01346 ( 2) link_ALPHA1-3 : angle 2.89081 ( 6) link_ALPHA1-6 : bond 0.00206 ( 1) link_ALPHA1-6 : angle 1.73469 ( 3) link_BETA1-4 : bond 0.00806 ( 6) link_BETA1-4 : angle 2.12279 ( 18) link_BETA1-6 : bond 0.00765 ( 1) link_BETA1-6 : angle 1.39850 ( 3) link_NAG-ASN : bond 0.00379 ( 8) link_NAG-ASN : angle 1.21700 ( 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 79 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7952 (mtm180) REVERT: A 211 ASN cc_start: 0.8226 (t0) cc_final: 0.7833 (t0) REVERT: A 284 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8067 (m-80) REVERT: A 342 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8391 (mm) REVERT: B 154 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7661 (ttm110) REVERT: B 287 MET cc_start: 0.8458 (ttt) cc_final: 0.8240 (ttm) REVERT: B 290 MET cc_start: 0.8983 (tpp) cc_final: 0.8763 (tpp) REVERT: B 327 GLU cc_start: 0.8678 (tp30) cc_final: 0.8148 (tp30) REVERT: C 49 GLU cc_start: 0.8975 (tp30) cc_final: 0.8754 (tp30) outliers start: 27 outliers final: 16 residues processed: 73 average time/residue: 0.1021 time to fit residues: 9.4521 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 : 0.227 ------------------------------------------------------------------------------- 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 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 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 43 SER 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: 0.9980 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 0.0270 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 0.0770 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.081613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.066945 restraints weight = 12955.373| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.15 r_work: 0.2768 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5906 Z= 0.129 Angle : 0.565 9.196 8081 Z= 0.270 Chirality : 0.044 0.194 947 Planarity : 0.003 0.034 1020 Dihedral : 6.352 69.728 1171 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.70 % Allowed : 14.46 % 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 aren not related in a simple way. whole: -0.99 (0.31), residues: 734 helix: 1.24 (0.48), residues: 129 sheet: -1.02 (0.35), residues: 199 loop : -1.07 (0.30), residues: 406 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 0.005 0.001 TRP A 121 HIS 0.002 0.000 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5883) covalent geometry : angle 0.54942 ( 8017) SS BOND : bond 0.00270 ( 5) SS BOND : angle 0.50676 ( 10) hydrogen bonds : bond 0.03212 ( 200) hydrogen bonds : angle 5.34711 ( 522) link_ALPHA1-3 : bond 0.01478 ( 2) link_ALPHA1-3 : angle 2.61091 ( 6) link_ALPHA1-6 : bond 0.00356 ( 1) link_ALPHA1-6 : angle 1.51365 ( 3) link_BETA1-4 : bond 0.00921 ( 6) link_BETA1-4 : angle 2.07084 ( 18) link_BETA1-6 : bond 0.00770 ( 1) link_BETA1-6 : angle 1.29348 ( 3) link_NAG-ASN : bond 0.00378 ( 8) link_NAG-ASN : angle 1.12615 ( 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 74 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8025 (mtm180) REVERT: A 211 ASN cc_start: 0.8215 (t0) cc_final: 0.7816 (t0) REVERT: A 284 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8077 (m-80) REVERT: A 342 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8432 (mm) REVERT: B 154 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7633 (ttm110) REVERT: B 287 MET cc_start: 0.8455 (ttt) cc_final: 0.8243 (ttm) REVERT: B 290 MET cc_start: 0.8958 (tpp) cc_final: 0.8749 (tpp) REVERT: C 35 ARG cc_start: 0.8139 (tpp80) cc_final: 0.7908 (ttp-110) REVERT: C 49 GLU cc_start: 0.8942 (tp30) cc_final: 0.8687 (tp30) outliers start: 21 outliers final: 12 residues processed: 69 average time/residue: 0.1031 time to fit residues: 9.0214 Evaluate side-chains 68 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 342 LEU Chi-restraints excluded: chain A residue 369 VAL 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 28 LEU Chi-restraints excluded: chain C residue 30 VAL 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: 0.2980 chunk 21 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 13 optimal weight: 0.0980 chunk 55 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.081933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.067228 restraints weight = 12941.615| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.17 r_work: 0.2775 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1518 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= 0.123 Angle : 0.567 9.528 8081 Z= 0.269 Chirality : 0.044 0.187 947 Planarity : 0.003 0.032 1020 Dihedral : 5.820 59.113 1170 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.59 % Allowed : 13.76 % 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 aren not related in a simple way. whole: -0.94 (0.31), residues: 734 helix: 1.26 (0.47), residues: 129 sheet: -0.98 (0.36), residues: 197 loop : -1.04 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 35 TYR 0.015 0.001 TYR B 325 PHE 0.009 0.001 PHE B 264 TRP 0.005 0.001 TRP A 121 HIS 0.002 0.000 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 5883) covalent geometry : angle 0.55049 ( 8017) SS BOND : bond 0.00261 ( 5) SS BOND : angle 0.50727 ( 10) hydrogen bonds : bond 0.03131 ( 200) hydrogen bonds : angle 5.28880 ( 522) link_ALPHA1-3 : bond 0.01421 ( 2) link_ALPHA1-3 : angle 2.76958 ( 6) link_ALPHA1-6 : bond 0.00283 ( 1) link_ALPHA1-6 : angle 1.65840 ( 3) link_BETA1-4 : bond 0.00869 ( 6) link_BETA1-4 : angle 2.04143 ( 18) link_BETA1-6 : bond 0.00760 ( 1) link_BETA1-6 : angle 1.25201 ( 3) link_NAG-ASN : bond 0.00362 ( 8) link_NAG-ASN : angle 1.11944 ( 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 79 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 53 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8043 (mtm180) REVERT: A 211 ASN cc_start: 0.8263 (t0) cc_final: 0.7876 (t0) REVERT: A 284 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.7977 (m-80) REVERT: A 342 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8416 (mm) REVERT: B 121 TYR cc_start: 0.7826 (m-10) cc_final: 0.7598 (m-10) REVERT: B 154 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7577 (ttm110) REVERT: B 287 MET cc_start: 0.8445 (ttt) cc_final: 0.8230 (ttm) REVERT: B 290 MET cc_start: 0.8980 (tpp) cc_final: 0.8775 (tpp) REVERT: C 35 ARG cc_start: 0.8202 (tpp80) cc_final: 0.7964 (ttp-110) REVERT: C 49 GLU cc_start: 0.8972 (tp30) cc_final: 0.8722 (tp30) outliers start: 26 outliers final: 16 residues processed: 74 average time/residue: 0.1012 time to fit residues: 9.5681 Evaluate side-chains 72 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 57 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.081468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.066821 restraints weight = 12958.395| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.16 r_work: 0.2767 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1567 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= 0.139 Angle : 0.575 8.892 8081 Z= 0.274 Chirality : 0.044 0.179 947 Planarity : 0.003 0.033 1020 Dihedral : 5.426 59.177 1170 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.76 % Allowed : 13.58 % 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 aren not related in a simple way. whole: -0.95 (0.31), residues: 734 helix: 1.25 (0.47), residues: 129 sheet: -1.02 (0.36), residues: 192 loop : -1.03 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 35 TYR 0.014 0.001 TYR B 325 PHE 0.010 0.001 PHE B 264 TRP 0.005 0.001 TRP A 121 HIS 0.002 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5883) covalent geometry : angle 0.55883 ( 8017) SS BOND : bond 0.00278 ( 5) SS BOND : angle 0.50479 ( 10) hydrogen bonds : bond 0.03227 ( 200) hydrogen bonds : angle 5.30743 ( 522) link_ALPHA1-3 : bond 0.01386 ( 2) link_ALPHA1-3 : angle 2.77007 ( 6) link_ALPHA1-6 : bond 0.00224 ( 1) link_ALPHA1-6 : angle 1.77781 ( 3) link_BETA1-4 : bond 0.00846 ( 6) link_BETA1-4 : angle 2.06228 ( 18) link_BETA1-6 : bond 0.00761 ( 1) link_BETA1-6 : angle 1.29438 ( 3) link_NAG-ASN : bond 0.00351 ( 8) link_NAG-ASN : angle 1.15311 ( 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 81 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 54 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8025 (mtm180) REVERT: A 211 ASN cc_start: 0.8228 (t0) cc_final: 0.7847 (t0) REVERT: A 284 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8006 (m-80) REVERT: A 342 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8425 (mm) REVERT: B 121 TYR cc_start: 0.7832 (m-10) cc_final: 0.7606 (m-10) REVERT: B 154 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7595 (ttm110) REVERT: B 287 MET cc_start: 0.8442 (ttt) cc_final: 0.8223 (ttm) REVERT: B 290 MET cc_start: 0.8988 (tpp) cc_final: 0.8786 (tpp) REVERT: C 17 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8072 (mp0) REVERT: C 32 ARG cc_start: 0.8478 (ttt-90) cc_final: 0.8166 (tpt-90) REVERT: C 49 GLU cc_start: 0.8979 (tp30) cc_final: 0.8728 (tp30) outliers start: 27 outliers final: 17 residues processed: 75 average time/residue: 0.1003 time to fit residues: 9.6140 Evaluate side-chains 73 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 47 optimal weight: 0.0060 chunk 40 optimal weight: 0.0020 chunk 22 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.082283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.067827 restraints weight = 12922.972| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.13 r_work: 0.2788 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5906 Z= 0.113 Angle : 0.564 8.679 8081 Z= 0.270 Chirality : 0.044 0.181 947 Planarity : 0.003 0.035 1020 Dihedral : 5.198 59.590 1170 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.88 % Allowed : 15.17 % Favored : 80.95 % 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 aren not related in a simple way. whole: -1.01 (0.31), residues: 734 helix: 1.04 (0.47), residues: 135 sheet: -0.98 (0.36), residues: 197 loop : -1.07 (0.30), residues: 402 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 0.009 0.001 PHE B 264 TRP 0.005 0.001 TRP A 121 HIS 0.002 0.000 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 5883) covalent geometry : angle 0.54897 ( 8017) SS BOND : bond 0.00212 ( 5) SS BOND : angle 0.40792 ( 10) hydrogen bonds : bond 0.03068 ( 200) hydrogen bonds : angle 5.28212 ( 522) link_ALPHA1-3 : bond 0.01298 ( 2) link_ALPHA1-3 : angle 2.56892 ( 6) link_ALPHA1-6 : bond 0.00239 ( 1) link_ALPHA1-6 : angle 1.76712 ( 3) link_BETA1-4 : bond 0.00858 ( 6) link_BETA1-4 : angle 2.00566 ( 18) link_BETA1-6 : bond 0.00758 ( 1) link_BETA1-6 : angle 1.19701 ( 3) link_NAG-ASN : bond 0.00360 ( 8) link_NAG-ASN : angle 1.08758 ( 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 75 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8038 (mtm180) REVERT: A 211 ASN cc_start: 0.8238 (t0) cc_final: 0.7874 (t0) REVERT: A 284 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: A 342 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8378 (mm) REVERT: B 121 TYR cc_start: 0.7802 (m-10) cc_final: 0.7587 (m-10) REVERT: B 154 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7500 (ttm110) REVERT: B 287 MET cc_start: 0.8433 (ttt) cc_final: 0.8214 (ttm) REVERT: C 35 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7718 (ttp-110) REVERT: C 49 GLU cc_start: 0.8999 (tp30) cc_final: 0.8744 (tp30) outliers start: 22 outliers final: 15 residues processed: 69 average time/residue: 0.1001 time to fit residues: 8.8642 Evaluate side-chains 71 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 5 optimal weight: 0.0270 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 50 optimal weight: 0.0070 chunk 20 optimal weight: 0.9980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.083321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.069341 restraints weight = 13060.791| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.06 r_work: 0.2838 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5906 Z= 0.115 Angle : 0.557 8.682 8081 Z= 0.269 Chirality : 0.044 0.256 947 Planarity : 0.003 0.032 1020 Dihedral : 5.047 59.835 1170 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.35 % Allowed : 15.34 % 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 aren not related in a simple way. whole: -0.96 (0.31), residues: 734 helix: 1.08 (0.47), residues: 135 sheet: -0.98 (0.36), residues: 197 loop : -1.02 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 35 TYR 0.014 0.001 TYR B 325 PHE 0.009 0.001 PHE B 264 TRP 0.005 0.001 TRP A 121 HIS 0.002 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 5883) covalent geometry : angle 0.54276 ( 8017) SS BOND : bond 0.00223 ( 5) SS BOND : angle 0.40216 ( 10) hydrogen bonds : bond 0.03033 ( 200) hydrogen bonds : angle 5.23511 ( 522) link_ALPHA1-3 : bond 0.01032 ( 2) link_ALPHA1-3 : angle 2.26718 ( 6) link_ALPHA1-6 : bond 0.00133 ( 1) link_ALPHA1-6 : angle 1.87690 ( 3) link_BETA1-4 : bond 0.00846 ( 6) link_BETA1-4 : angle 2.00553 ( 18) link_BETA1-6 : bond 0.00767 ( 1) link_BETA1-6 : angle 1.20279 ( 3) link_NAG-ASN : bond 0.00334 ( 8) link_NAG-ASN : angle 1.09295 ( 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: 19 poor density : 55 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8097 (mtm180) REVERT: A 211 ASN cc_start: 0.8180 (t0) cc_final: 0.7820 (t0) REVERT: A 284 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: A 342 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8384 (mm) REVERT: B 121 TYR cc_start: 0.7836 (m-10) cc_final: 0.7625 (m-10) REVERT: B 287 MET cc_start: 0.8446 (ttt) cc_final: 0.8239 (ttm) REVERT: C 17 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8105 (mp0) REVERT: C 32 ARG cc_start: 0.8426 (ttt-90) cc_final: 0.8143 (tpt-90) REVERT: C 34 HIS cc_start: 0.7306 (t-170) cc_final: 0.6406 (t-170) REVERT: C 35 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.7763 (ttp-110) REVERT: C 49 GLU cc_start: 0.9016 (tp30) cc_final: 0.8711 (tp30) outliers start: 19 outliers final: 14 residues processed: 69 average time/residue: 0.1056 time to fit residues: 9.3127 Evaluate side-chains 71 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 0.0570 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 0.0770 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 0.0040 chunk 24 optimal weight: 0.9980 overall best weight: 0.4268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.083761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.069890 restraints weight = 12787.876| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.02 r_work: 0.2859 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5906 Z= 0.108 Angle : 0.551 8.624 8081 Z= 0.266 Chirality : 0.044 0.239 947 Planarity : 0.003 0.032 1020 Dihedral : 4.961 59.472 1170 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.00 % Allowed : 15.52 % Favored : 81.48 % 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 aren not related in a simple way. whole: -0.93 (0.31), residues: 734 helix: 1.14 (0.47), residues: 135 sheet: -1.01 (0.36), residues: 198 loop : -0.98 (0.30), residues: 401 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 0.008 0.001 PHE B 264 TRP 0.004 0.001 TRP A 121 HIS 0.002 0.000 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 5883) covalent geometry : angle 0.53673 ( 8017) SS BOND : bond 0.00211 ( 5) SS BOND : angle 0.38249 ( 10) hydrogen bonds : bond 0.02960 ( 200) hydrogen bonds : angle 5.20288 ( 522) link_ALPHA1-3 : bond 0.00908 ( 2) link_ALPHA1-3 : angle 2.10567 ( 6) link_ALPHA1-6 : bond 0.00156 ( 1) link_ALPHA1-6 : angle 1.85443 ( 3) link_BETA1-4 : bond 0.00864 ( 6) link_BETA1-4 : angle 1.98434 ( 18) link_BETA1-6 : bond 0.00767 ( 1) link_BETA1-6 : angle 1.17559 ( 3) link_NAG-ASN : bond 0.00343 ( 8) link_NAG-ASN : angle 1.06391 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1295.54 seconds wall clock time: 22 minutes 59.76 seconds (1379.76 seconds total)