Starting phenix.real_space_refine on Thu Jul 2 03:28:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rtt_24688/07_2026/7rtt_24688.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtt_24688/07_2026/7rtt_24688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7rtt_24688/07_2026/7rtt_24688.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rtt_24688/07_2026/7rtt_24688.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rtt_24688/07_2026/7rtt_24688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtt_24688/07_2026/7rtt_24688.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rtt_24688/07_2026/7rtt_24688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtt_24688/07_2026/7rtt_24688.map" } resolution = 3.5 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 50 5.16 5 C 4027 2.51 5 N 1013 2.21 5 O 1176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s 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: 6268 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3058 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 9, 'TRANS': 386} Chain breaks: 1 Chain: "B" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3053 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 9, 'TRANS': 385} Chain breaks: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.80, per 1000 atoms: 0.29 Number of scatterers: 6268 At special positions: 0 Unit cell: (84.138, 70.494, 134.166, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 50 16.00 O 1176 8.00 N 1013 7.00 C 4027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 382 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 382 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 367 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG C 1 " - " ASN A 129 " " NAG D 1 " - " ASN A 352 " " NAG E 1 " - " ASN B 129 " " NAG F 1 " - " ASN B 352 " Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 385.0 milliseconds 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1474 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 85.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 removed outlier: 3.790A pdb=" N LEU A 17 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 19 " --> pdb=" O VAL A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 72 removed outlier: 3.595A pdb=" N PHE A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 158 removed outlier: 3.625A pdb=" N GLY A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 188 removed outlier: 3.555A pdb=" N GLN A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 235 removed outlier: 3.672A pdb=" N THR A 195 " --> pdb=" O TRP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 270 removed outlier: 3.668A pdb=" N ALA A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU A 251 " --> pdb=" O CYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.753A pdb=" N ALA A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 285 removed outlier: 3.581A pdb=" N TYR A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.522A pdb=" N THR A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 330 removed outlier: 3.869A pdb=" N THR A 314 " --> pdb=" O GLN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 340 through 365 removed outlier: 4.006A pdb=" N LEU A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.222A pdb=" N LEU A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 372 " --> pdb=" O ARG A 368 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 410 Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'B' and resid 11 through 19 removed outlier: 3.901A pdb=" N LEU B 17 " --> pdb=" O TRP B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 73 removed outlier: 3.832A pdb=" N GLY B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 160 removed outlier: 3.615A pdb=" N MET B 118 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B 160 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 188 removed outlier: 3.801A pdb=" N LEU B 188 " --> pdb=" O GLN B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 234 removed outlier: 3.840A pdb=" N LYS B 200 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 240 through 276 removed outlier: 4.112A pdb=" N SER B 244 " --> pdb=" O CYS B 240 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 251 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 285 removed outlier: 3.827A pdb=" N TYR B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 299 Processing helix chain 'B' and resid 308 through 332 Processing helix chain 'B' and resid 340 through 365 removed outlier: 4.163A pdb=" N GLY B 346 " --> pdb=" O LYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 383 removed outlier: 4.748A pdb=" N LEU B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 410 523 hydrogen bonds defined for protein. 1569 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: 0.95 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1959 1.34 - 1.46: 1527 1.46 - 1.58: 2836 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 6390 Sorted by residual: bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.04e+00 ... (remaining 6385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 8453 1.63 - 3.26: 193 3.26 - 4.89: 43 4.89 - 6.53: 15 6.53 - 8.16: 2 Bond angle restraints: 8706 Sorted by residual: angle pdb=" C VAL A 30 " pdb=" N ASP A 31 " pdb=" CA ASP A 31 " ideal model delta sigma weight residual 121.54 126.85 -5.31 1.91e+00 2.74e-01 7.74e+00 angle pdb=" CB MET A 118 " pdb=" CG MET A 118 " pdb=" SD MET A 118 " ideal model delta sigma weight residual 112.70 120.86 -8.16 3.00e+00 1.11e-01 7.39e+00 angle pdb=" N GLN A 302 " pdb=" CA GLN A 302 " pdb=" C GLN A 302 " ideal model delta sigma weight residual 110.80 115.75 -4.95 2.13e+00 2.20e-01 5.40e+00 angle pdb=" CA TYR B 207 " pdb=" CB TYR B 207 " pdb=" CG TYR B 207 " ideal model delta sigma weight residual 113.90 117.70 -3.80 1.80e+00 3.09e-01 4.45e+00 angle pdb=" CA GLN A 302 " pdb=" C GLN A 302 " pdb=" N SER A 303 " ideal model delta sigma weight residual 116.84 120.40 -3.56 1.71e+00 3.42e-01 4.33e+00 ... (remaining 8701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 3232 17.45 - 34.90: 355 34.90 - 52.35: 57 52.35 - 69.80: 9 69.80 - 87.25: 4 Dihedral angle restraints: 3657 sinusoidal: 1366 harmonic: 2291 Sorted by residual: dihedral pdb=" CB CYS B 300 " pdb=" SG CYS B 300 " pdb=" SG CYS B 367 " pdb=" CB CYS B 367 " ideal model delta sinusoidal sigma weight residual -86.00 -167.16 81.16 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CA PHE B 273 " pdb=" C PHE B 273 " pdb=" N CYS B 274 " pdb=" CA CYS B 274 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ARG B 237 " pdb=" C ARG B 237 " pdb=" N SER B 238 " pdb=" CA SER B 238 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 3654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1016 0.077 - 0.153: 61 0.153 - 0.230: 0 0.230 - 0.306: 5 0.306 - 0.383: 1 Chirality restraints: 1083 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 129 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1080 not shown) Planarity restraints: 1063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 20 " 0.050 5.00e-02 4.00e+02 7.59e-02 9.21e+00 pdb=" N PRO A 21 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 211 " -0.017 2.00e-02 2.50e+03 1.39e-02 3.84e+00 pdb=" CG TYR B 211 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 211 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 211 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 211 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 211 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 211 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 211 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 315 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C PHE A 315 " -0.030 2.00e-02 2.50e+03 pdb=" O PHE A 315 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN A 316 " 0.010 2.00e-02 2.50e+03 ... (remaining 1060 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1185 2.77 - 3.30: 6518 3.30 - 3.84: 10400 3.84 - 4.37: 10633 4.37 - 4.90: 19086 Nonbonded interactions: 47822 Sorted by model distance: nonbonded pdb=" OH TYR B 41 " pdb=" OD2 ASP B 272 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR B 170 " pdb=" OE1 GLN B 325 " model vdw 2.263 3.040 nonbonded pdb=" O ILE A 226 " pdb=" OG1 THR A 230 " model vdw 2.290 3.040 nonbonded pdb=" NH1 ARG A 156 " pdb=" OD1 ASP A 343 " model vdw 2.296 3.120 nonbonded pdb=" OG SER B 291 " pdb=" NH2 ARG B 295 " model vdw 2.319 3.120 ... (remaining 47817 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 'A' and resid 5 through 601) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ )) selection = (chain 'D' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ )) selection = (chain 'E' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ )) 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 group one per residue 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: 1.080 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.030 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 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 : 0.003 0.045 6406 Z= 0.166 Angle : 0.643 8.157 8750 Z= 0.308 Chirality : 0.044 0.383 1083 Planarity : 0.005 0.076 1059 Dihedral : 14.473 87.252 2171 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 2.65 (0.32), residues: 783 helix: 2.38 (0.21), residues: 649 sheet: None (None), residues: 0 loop : -1.55 (0.61), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 156 TYR 0.034 0.002 TYR B 211 PHE 0.011 0.001 PHE B 395 TRP 0.006 0.001 TRP A 12 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 ( 6390) covalent geometry : angle 0.63207 / 0.30 ( 8706) SS BOND : bond 0.00280 / 0.13 ( 4) SS BOND : angle 1.75512 / 1.08 ( 8) hydrogen bonds : bond 0.11051 / 6.91 ( 523) hydrogen bonds : angle 5.26886 / 3.91 ( 1569) link_BETA1-4 : bond 0.00542 / 0.36 ( 8) link_BETA1-4 : angle 1.60143 / 1.03 ( 24) link_NAG-ASN : bond 0.00465 / 0.15 ( 4) link_NAG-ASN : angle 2.09446 / 1.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.213 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0537 time to fit residues: 4.7043 Evaluate side-chains 50 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.207972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.177795 restraints weight = 7035.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.179460 restraints weight = 6804.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.179813 restraints weight = 6051.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.180423 restraints weight = 4886.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.180617 restraints weight = 4176.581| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6406 Z= 0.148 Angle : 0.566 8.740 8750 Z= 0.280 Chirality : 0.038 0.196 1083 Planarity : 0.004 0.052 1059 Dihedral : 3.812 22.807 845 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.04 % Allowed : 7.01 % Favored : 91.94 % 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: 3.38 (0.32), residues: 783 helix: 2.90 (0.20), residues: 650 sheet: None (None), residues: 0 loop : -1.42 (0.62), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 156 TYR 0.016 0.001 TYR B 211 PHE 0.012 0.001 PHE B 273 TRP 0.006 0.001 TRP B 13 HIS 0.004 0.001 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 6390) covalent geometry : angle 0.55639 / 0.28 ( 8706) SS BOND : bond 0.00295 / 0.13 ( 4) SS BOND : angle 0.90264 / 0.47 ( 8) hydrogen bonds : bond 0.05157 / 3.34 ( 523) hydrogen bonds : angle 3.62562 / 2.69 ( 1569) link_BETA1-4 : bond 0.00582 / 0.36 ( 8) link_BETA1-4 : angle 1.56939 / 1.05 ( 24) link_NAG-ASN : bond 0.00459 / 0.17 ( 4) link_NAG-ASN : angle 1.81116 / 0.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.203 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 64 average time/residue: 0.0601 time to fit residues: 5.6729 Evaluate side-chains 64 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 0.0000 chunk 2 optimal weight: 0.0370 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 42 optimal weight: 0.0470 chunk 3 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.212694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.182028 restraints weight = 6948.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.182332 restraints weight = 5973.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.183983 restraints weight = 5744.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.184579 restraints weight = 4733.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.185438 restraints weight = 3977.139| |-----------------------------------------------------------------------------| r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6406 Z= 0.110 Angle : 0.485 6.717 8750 Z= 0.241 Chirality : 0.035 0.174 1083 Planarity : 0.003 0.040 1059 Dihedral : 3.642 22.253 845 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.60 % Allowed : 11.19 % Favored : 88.21 % 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: 3.80 (0.32), residues: 783 helix: 3.20 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.62 (0.63), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 156 TYR 0.008 0.001 TYR A 211 PHE 0.012 0.001 PHE A 220 TRP 0.006 0.001 TRP B 13 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.11 ( 6390) covalent geometry : angle 0.47574 / 0.24 ( 8706) SS BOND : bond 0.00205 / 0.08 ( 4) SS BOND : angle 0.42024 / 0.21 ( 8) hydrogen bonds : bond 0.04199 / 2.76 ( 523) hydrogen bonds : angle 3.28403 / 2.42 ( 1569) link_BETA1-4 : bond 0.00499 / 0.32 ( 8) link_BETA1-4 : angle 1.44167 / 0.96 ( 24) link_NAG-ASN : bond 0.00218 / 0.07 ( 4) link_NAG-ASN : angle 1.71355 / 0.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.162 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 59 average time/residue: 0.0661 time to fit residues: 5.5830 Evaluate side-chains 54 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.209330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.179293 restraints weight = 7065.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.181506 restraints weight = 6694.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.181908 restraints weight = 5558.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.181991 restraints weight = 4587.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.182322 restraints weight = 4191.841| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6406 Z= 0.125 Angle : 0.498 6.493 8750 Z= 0.248 Chirality : 0.036 0.185 1083 Planarity : 0.003 0.034 1059 Dihedral : 3.643 22.524 845 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.90 % Allowed : 13.13 % Favored : 85.97 % 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: 3.88 (0.32), residues: 783 helix: 3.27 (0.20), residues: 650 sheet: None (None), residues: 0 loop : -1.40 (0.63), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 156 TYR 0.009 0.001 TYR B 374 PHE 0.010 0.001 PHE A 220 TRP 0.006 0.001 TRP B 13 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 6390) covalent geometry : angle 0.48931 / 0.25 ( 8706) SS BOND : bond 0.00270 / 0.11 ( 4) SS BOND : angle 0.62954 / 0.28 ( 8) hydrogen bonds : bond 0.04422 / 2.89 ( 523) hydrogen bonds : angle 3.26035 / 2.41 ( 1569) link_BETA1-4 : bond 0.00506 / 0.32 ( 8) link_BETA1-4 : angle 1.40244 / 0.93 ( 24) link_NAG-ASN : bond 0.00315 / 0.11 ( 4) link_NAG-ASN : angle 1.73048 / 0.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.201 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 0.0520 time to fit residues: 4.8086 Evaluate side-chains 58 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 chunk 40 optimal weight: 0.0370 chunk 1 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.209775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.178976 restraints weight = 7180.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.181040 restraints weight = 6975.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.181573 restraints weight = 5838.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.181872 restraints weight = 4591.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.183967 restraints weight = 4141.614| |-----------------------------------------------------------------------------| r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6406 Z= 0.115 Angle : 0.487 6.702 8750 Z= 0.241 Chirality : 0.035 0.178 1083 Planarity : 0.003 0.032 1059 Dihedral : 3.603 22.203 845 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.49 % Allowed : 14.78 % Favored : 83.73 % 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: 3.90 (0.32), residues: 783 helix: 3.29 (0.20), residues: 651 sheet: None (None), residues: 0 loop : -1.52 (0.63), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 156 TYR 0.010 0.001 TYR B 210 PHE 0.010 0.001 PHE A 173 TRP 0.006 0.001 TRP B 13 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 6390) covalent geometry : angle 0.47887 / 0.24 ( 8706) SS BOND : bond 0.00245 / 0.10 ( 4) SS BOND : angle 0.48501 / 0.22 ( 8) hydrogen bonds : bond 0.04268 / 2.80 ( 523) hydrogen bonds : angle 3.16842 / 2.34 ( 1569) link_BETA1-4 : bond 0.00504 / 0.32 ( 8) link_BETA1-4 : angle 1.35908 / 0.90 ( 24) link_NAG-ASN : bond 0.00258 / 0.08 ( 4) link_NAG-ASN : angle 1.71591 / 0.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.217 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 63 average time/residue: 0.0531 time to fit residues: 5.0172 Evaluate side-chains 59 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 39 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS B 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.208244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.177230 restraints weight = 7084.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.176675 restraints weight = 7313.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.178622 restraints weight = 7043.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.179264 restraints weight = 5164.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.179640 restraints weight = 4419.708| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6406 Z= 0.123 Angle : 0.502 6.489 8750 Z= 0.247 Chirality : 0.036 0.182 1083 Planarity : 0.003 0.036 1059 Dihedral : 3.611 22.282 845 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.79 % Allowed : 15.67 % Favored : 82.54 % 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: 3.84 (0.32), residues: 783 helix: 3.26 (0.20), residues: 651 sheet: None (None), residues: 0 loop : -1.58 (0.62), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 156 TYR 0.010 0.001 TYR B 374 PHE 0.010 0.001 PHE B 273 TRP 0.007 0.001 TRP B 13 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 6390) covalent geometry : angle 0.49403 / 0.25 ( 8706) SS BOND : bond 0.00306 / 0.12 ( 4) SS BOND : angle 0.63256 / 0.29 ( 8) hydrogen bonds : bond 0.04412 / 2.89 ( 523) hydrogen bonds : angle 3.18491 / 2.35 ( 1569) link_BETA1-4 : bond 0.00529 / 0.33 ( 8) link_BETA1-4 : angle 1.34552 / 0.90 ( 24) link_NAG-ASN : bond 0.00280 / 0.09 ( 4) link_NAG-ASN : angle 1.69177 / 0.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.136 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 63 average time/residue: 0.0438 time to fit residues: 4.3103 Evaluate side-chains 63 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 39 optimal weight: 0.0270 chunk 35 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.209928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.180035 restraints weight = 7090.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.181096 restraints weight = 6649.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.182444 restraints weight = 6188.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.182786 restraints weight = 4777.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.183252 restraints weight = 4133.530| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6406 Z= 0.115 Angle : 0.501 7.107 8750 Z= 0.245 Chirality : 0.035 0.177 1083 Planarity : 0.003 0.030 1059 Dihedral : 3.585 22.082 845 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.49 % Allowed : 16.87 % Favored : 81.64 % 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: 3.91 (0.32), residues: 783 helix: 3.33 (0.20), residues: 649 sheet: None (None), residues: 0 loop : -1.63 (0.61), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 156 TYR 0.009 0.001 TYR B 374 PHE 0.009 0.001 PHE B 273 TRP 0.007 0.001 TRP B 13 HIS 0.003 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 6390) covalent geometry : angle 0.49334 / 0.24 ( 8706) SS BOND : bond 0.00242 / 0.09 ( 4) SS BOND : angle 0.51221 / 0.24 ( 8) hydrogen bonds : bond 0.04238 / 2.79 ( 523) hydrogen bonds : angle 3.13652 / 2.32 ( 1569) link_BETA1-4 : bond 0.00487 / 0.31 ( 8) link_BETA1-4 : angle 1.32352 / 0.88 ( 24) link_NAG-ASN : bond 0.00244 / 0.08 ( 4) link_NAG-ASN : angle 1.68931 / 0.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.223 Fit side-chains REVERT: B 245 MET cc_start: 0.6926 (tmm) cc_final: 0.6506 (tpp) outliers start: 10 outliers final: 7 residues processed: 61 average time/residue: 0.0521 time to fit residues: 5.0413 Evaluate side-chains 60 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 7 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.205993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.174049 restraints weight = 7239.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.176675 restraints weight = 6228.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.177108 restraints weight = 5373.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.177550 restraints weight = 4211.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.177976 restraints weight = 3847.219| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6406 Z= 0.138 Angle : 0.544 7.531 8750 Z= 0.265 Chirality : 0.037 0.188 1083 Planarity : 0.003 0.028 1059 Dihedral : 3.686 22.744 845 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.79 % Allowed : 16.42 % Favored : 81.79 % 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: 3.72 (0.32), residues: 783 helix: 3.17 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -1.65 (0.62), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 156 TYR 0.010 0.001 TYR A 374 PHE 0.013 0.001 PHE B 273 TRP 0.008 0.001 TRP B 13 HIS 0.003 0.001 HIS A 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 6390) covalent geometry : angle 0.53679 / 0.26 ( 8706) SS BOND : bond 0.00340 / 0.14 ( 4) SS BOND : angle 0.79587 / 0.37 ( 8) hydrogen bonds : bond 0.04729 / 3.09 ( 523) hydrogen bonds : angle 3.24498 / 2.40 ( 1569) link_BETA1-4 : bond 0.00544 / 0.34 ( 8) link_BETA1-4 : angle 1.33602 / 0.89 ( 24) link_NAG-ASN : bond 0.00317 / 0.11 ( 4) link_NAG-ASN : angle 1.69793 / 0.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.220 Fit side-chains REVERT: B 8 TYR cc_start: 0.7004 (t80) cc_final: 0.6444 (t80) REVERT: B 292 GLU cc_start: 0.6659 (tp30) cc_final: 0.6432 (tp30) outliers start: 12 outliers final: 11 residues processed: 69 average time/residue: 0.0494 time to fit residues: 5.4177 Evaluate side-chains 69 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 69 optimal weight: 0.4980 chunk 51 optimal weight: 0.0770 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.4503 r_free = 0.4503 target = 0.208271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.177392 restraints weight = 7239.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.178971 restraints weight = 7298.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.179148 restraints weight = 6453.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.180590 restraints weight = 5123.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.180661 restraints weight = 4326.543| |-----------------------------------------------------------------------------| r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6406 Z= 0.120 Angle : 0.529 7.888 8750 Z= 0.255 Chirality : 0.036 0.177 1083 Planarity : 0.003 0.029 1059 Dihedral : 3.640 22.323 845 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.79 % Allowed : 17.16 % Favored : 81.04 % 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: 3.87 (0.32), residues: 783 helix: 3.30 (0.20), residues: 649 sheet: None (None), residues: 0 loop : -1.66 (0.61), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 212 TYR 0.008 0.001 TYR B 374 PHE 0.021 0.001 PHE A 173 TRP 0.007 0.001 TRP B 13 HIS 0.003 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 6390) covalent geometry : angle 0.52216 / 0.25 ( 8706) SS BOND : bond 0.00258 / 0.11 ( 4) SS BOND : angle 0.58137 / 0.28 ( 8) hydrogen bonds : bond 0.04428 / 2.90 ( 523) hydrogen bonds : angle 3.19524 / 2.36 ( 1569) link_BETA1-4 : bond 0.00506 / 0.32 ( 8) link_BETA1-4 : angle 1.30836 / 0.87 ( 24) link_NAG-ASN : bond 0.00235 / 0.08 ( 4) link_NAG-ASN : angle 1.71584 / 0.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.228 Fit side-chains REVERT: B 8 TYR cc_start: 0.7085 (t80) cc_final: 0.6530 (t80) REVERT: B 350 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7334 (tp) outliers start: 12 outliers final: 8 residues processed: 65 average time/residue: 0.0526 time to fit residues: 5.4123 Evaluate side-chains 64 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4506 r_free = 0.4506 target = 0.208509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.178580 restraints weight = 7147.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.180284 restraints weight = 6658.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.180787 restraints weight = 5831.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.181144 restraints weight = 4796.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.181453 restraints weight = 4276.861| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6406 Z= 0.118 Angle : 0.524 8.071 8750 Z= 0.252 Chirality : 0.035 0.177 1083 Planarity : 0.003 0.033 1059 Dihedral : 3.615 22.371 845 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.49 % Allowed : 17.16 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.93 (0.32), residues: 783 helix: 3.34 (0.20), residues: 651 sheet: None (None), residues: 0 loop : -1.70 (0.61), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 156 TYR 0.013 0.001 TYR B 210 PHE 0.021 0.001 PHE A 173 TRP 0.007 0.001 TRP B 13 HIS 0.003 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 6390) covalent geometry : angle 0.51650 / 0.25 ( 8706) SS BOND : bond 0.00257 / 0.11 ( 4) SS BOND : angle 0.59237 / 0.27 ( 8) hydrogen bonds : bond 0.04330 / 2.84 ( 523) hydrogen bonds : angle 3.16849 / 2.34 ( 1569) link_BETA1-4 : bond 0.00514 / 0.33 ( 8) link_BETA1-4 : angle 1.29313 / 0.86 ( 24) link_NAG-ASN : bond 0.00246 / 0.08 ( 4) link_NAG-ASN : angle 1.65605 / 0.86 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.230 Fit side-chains REVERT: A 316 GLN cc_start: 0.6983 (tp40) cc_final: 0.6779 (tm-30) REVERT: B 8 TYR cc_start: 0.7118 (t80) cc_final: 0.6554 (t80) REVERT: B 350 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7293 (tp) outliers start: 10 outliers final: 9 residues processed: 64 average time/residue: 0.0610 time to fit residues: 5.7986 Evaluate side-chains 65 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4472 r_free = 0.4472 target = 0.204239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.172998 restraints weight = 7143.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.173128 restraints weight = 7521.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.173972 restraints weight = 7049.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.175379 restraints weight = 5277.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.175418 restraints weight = 4398.671| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6406 Z= 0.146 Angle : 0.565 8.024 8750 Z= 0.273 Chirality : 0.037 0.189 1083 Planarity : 0.003 0.030 1059 Dihedral : 3.712 22.164 845 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.49 % Allowed : 17.16 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.72 (0.32), residues: 783 helix: 3.20 (0.20), residues: 651 sheet: None (None), residues: 0 loop : -1.75 (0.62), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 156 TYR 0.013 0.001 TYR B 210 PHE 0.023 0.002 PHE A 173 TRP 0.007 0.001 TRP A 12 HIS 0.004 0.001 HIS B 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 6390) covalent geometry : angle 0.55789 / 0.27 ( 8706) SS BOND : bond 0.00393 / 0.17 ( 4) SS BOND : angle 0.79516 / 0.38 ( 8) hydrogen bonds : bond 0.04800 / 3.12 ( 523) hydrogen bonds : angle 3.27592 / 2.43 ( 1569) link_BETA1-4 : bond 0.00545 / 0.34 ( 8) link_BETA1-4 : angle 1.31221 / 0.87 ( 24) link_NAG-ASN : bond 0.00324 / 0.12 ( 4) link_NAG-ASN : angle 1.69720 / 0.88 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1002.43 seconds wall clock time: 18 minutes 12.53 seconds (1092.53 seconds total)