Starting phenix.real_space_refine on Thu Jul 2 16:12:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jej_36190/07_2026/8jej_36190.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jej_36190/07_2026/8jej_36190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jej_36190/07_2026/8jej_36190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jej_36190/07_2026/8jej_36190.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8jej_36190/07_2026/8jej_36190.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jej_36190/07_2026/8jej_36190.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jej_36190/07_2026/8jej_36190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jej_36190/07_2026/8jej_36190.map" } resolution = 2.5 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= 0.002 sd= 0.047 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 Fe 6 7.16 5 P 2 5.49 5 S 46 5.16 5 C 5421 2.51 5 N 1490 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8604 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4167 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 503} Chain: "B" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3130 Classifications: {'peptide': 413} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 387} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 167 Unusual residues: {'HEC': 3, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 20 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1767 SG CYS A 226 52.668 65.790 36.133 1.00 17.16 S ATOM 1738 SG CYS A 222 53.574 70.572 32.001 1.00 21.97 S ATOM 1698 SG CYS A 216 52.124 65.227 29.426 1.00 25.68 S Time building chain proxies: 1.91, per 1000 atoms: 0.22 Number of scatterers: 8604 At special positions: 0 Unit cell: (103.53, 109.62, 76.56, 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) Fe 6 26.01 S 46 16.00 P 2 15.00 O 1639 8.00 N 1490 7.00 C 5421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 378.3 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " Number of angles added : 9 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 8 sheets defined 41.1% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.609A pdb=" N LYS A 97 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.744A pdb=" N TRP A 111 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 138 through 154 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.614A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 440 through 462 removed outlier: 4.243A pdb=" N VAL A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 Processing helix chain 'A' and resid 522 through 542 Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 68 through 83 Processing helix chain 'B' and resid 85 through 101 Processing helix chain 'B' and resid 104 through 111 Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'C' and resid 41 through 50 Processing helix chain 'C' and resid 52 through 57 removed outlier: 3.883A pdb=" N HIS C 56 " --> pdb=" O CYS C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 106 removed outlier: 3.532A pdb=" N GLY C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 127 through 142 removed outlier: 4.015A pdb=" N VAL C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.870A pdb=" N TYR C 219 " --> pdb=" O GLN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 256 Processing helix chain 'C' and resid 265 through 274 Processing helix chain 'C' and resid 275 through 278 removed outlier: 3.508A pdb=" N LEU C 278 " --> pdb=" O LEU C 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 275 through 278' Processing helix chain 'C' and resid 279 through 291 Processing helix chain 'C' and resid 317 through 324 removed outlier: 3.915A pdb=" N SER C 322 " --> pdb=" O ASN C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 343 Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 431 through 440 Processing helix chain 'C' and resid 445 through 451 Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.825A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP A 9 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL A 286 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 11 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA A 282 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N THR A 266 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 265 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR A 259 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA A 267 " --> pdb=" O MET A 257 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N MET A 257 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER A 269 " --> pdb=" O TYR A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.825A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP A 9 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL A 286 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 11 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N PHE A 507 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE A 285 " --> pdb=" O PHE A 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.404A pdb=" N ILE A 87 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N HIS A 433 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 157 Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.479A pdb=" N SER A 347 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR A 368 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 366 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY A 328 " --> pdb=" O MET A 469 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N MET A 469 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER A 330 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE A 467 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AA7, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AA8, first strand: chain 'C' and resid 384 through 388 317 hydrogen bonds defined for protein. 867 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: 1.30 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.76: 8745 1.76 - 2.30: 90 2.30 - 2.85: 0 2.85 - 3.39: 0 3.39 - 3.93: 3 Bond restraints: 8838 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.928 -1.628 2.00e-02 2.50e+03 6.63e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.816 -1.558 2.00e-02 2.50e+03 6.06e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.786 -1.553 2.00e-02 2.50e+03 6.03e+03 bond pdb=" C2D HEC C 502 " pdb=" C3D HEC C 502 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC C 503 " pdb=" C3D HEC C 503 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.12e+02 ... (remaining 8833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.50: 12061 9.50 - 19.00: 10 19.00 - 28.50: 1 28.50 - 38.00: 8 38.00 - 47.50: 2 Bond angle restraints: 12082 Sorted by residual: angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 67.25 47.50 3.00e+00 1.11e-01 2.51e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 67.92 44.67 3.00e+00 1.11e-01 2.22e+02 angle pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 103.26 68.73 34.53 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " ideal model delta sigma weight residual 103.25 69.61 33.64 3.00e+00 1.11e-01 1.26e+02 angle pdb="FE1 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 72.09 39.35 32.74 3.00e+00 1.11e-01 1.19e+02 ... (remaining 12077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 4957 35.83 - 71.65: 207 71.65 - 107.47: 17 107.47 - 143.30: 1 143.30 - 179.12: 1 Dihedral angle restraints: 5183 sinusoidal: 2031 harmonic: 3152 Sorted by residual: dihedral pdb=" CA PHE A 80 " pdb=" C PHE A 80 " pdb=" N PRO A 81 " pdb=" CA PRO A 81 " ideal model delta harmonic sigma weight residual -180.00 -105.59 -74.41 0 5.00e+00 4.00e-02 2.21e+02 dihedral pdb=" C27 U10 C 504 " pdb=" C28 U10 C 504 " pdb=" C29 U10 C 504 " pdb=" C31 U10 C 504 " ideal model delta sinusoidal sigma weight residual 181.72 2.59 179.12 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2C HEC C 501 " pdb=" C3C HEC C 501 " pdb=" CAC HEC C 501 " pdb=" CBC HEC C 501 " ideal model delta sinusoidal sigma weight residual 60.00 -11.17 71.17 2 1.00e+01 1.00e-02 4.30e+01 ... (remaining 5180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.460: 1276 3.460 - 6.920: 0 6.920 - 10.380: 0 10.380 - 13.840: 0 13.840 - 17.300: 1 Chirality restraints: 1277 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -6.53 17.30 2.00e-01 2.50e+01 7.48e+03 chirality pdb=" CB ILE C 393 " pdb=" CA ILE C 393 " pdb=" CG1 ILE C 393 " pdb=" CG2 ILE C 393 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA PRO B 160 " pdb=" N PRO B 160 " pdb=" C PRO B 160 " pdb=" CB PRO B 160 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1274 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 C 504 " 0.013 2.00e-02 2.50e+03 1.00e-01 1.75e+02 pdb=" C1M U10 C 504 " -0.117 2.00e-02 2.50e+03 pdb=" C2 U10 C 504 " 0.092 2.00e-02 2.50e+03 pdb=" C3 U10 C 504 " 0.053 2.00e-02 2.50e+03 pdb=" C4 U10 C 504 " -0.184 2.00e-02 2.50e+03 pdb=" C5 U10 C 504 " 0.046 2.00e-02 2.50e+03 pdb=" C6 U10 C 504 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 80 " 0.125 5.00e-02 4.00e+02 1.92e-01 5.92e+01 pdb=" N PRO A 81 " -0.333 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " 0.115 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " 0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CBD HEC C 501 " -0.032 2.00e-02 2.50e+03 6.75e-02 4.56e+01 pdb=" CGD HEC C 501 " 0.117 2.00e-02 2.50e+03 pdb=" O1D HEC C 501 " -0.042 2.00e-02 2.50e+03 pdb=" O2D HEC C 501 " -0.043 2.00e-02 2.50e+03 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 307 2.71 - 3.26: 8611 3.26 - 3.81: 15309 3.81 - 4.35: 20471 4.35 - 4.90: 32177 Nonbonded interactions: 76875 Sorted by model distance: nonbonded pdb=" N GLU C 129 " pdb=" OE1 GLU C 129 " model vdw 2.165 3.120 nonbonded pdb=" OH TYR A 139 " pdb=" O PRO A 168 " model vdw 2.243 3.040 nonbonded pdb=" S4 F3S A 602 " pdb="FE4 F3S A 602 " model vdw 2.259 2.688 nonbonded pdb=" S3 F3S A 602 " pdb="FE3 F3S A 602 " model vdw 2.261 2.688 nonbonded pdb=" S1 F3S A 602 " pdb="FE1 F3S A 602 " model vdw 2.262 2.688 ... (remaining 76870 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.890 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 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 : 0.030 1.628 8853 Z= 1.508 Angle : 1.356 47.497 12091 Z= 0.502 Chirality : 0.486 17.300 1277 Planarity : 0.008 0.192 1569 Dihedral : 18.470 179.124 3171 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.60 % Allowed : 16.70 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.25), residues: 1083 helix: 1.15 (0.27), residues: 379 sheet: 0.08 (0.54), residues: 92 loop : -0.60 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 94 TYR 0.023 0.001 TYR A 443 PHE 0.019 0.001 PHE A 270 TRP 0.010 0.001 TRP A 338 HIS 0.005 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.03034 / 1.51 ( 8838) covalent geometry : angle 1.33580 / 0.50 (12082) hydrogen bonds : bond 0.13801 / 8.97 ( 314) hydrogen bonds : angle 6.84134 / 5.10 ( 867) metal coordination : bond 0.00068 / 0.03 ( 3) metal coordination : angle 8.70977 / 5.53 ( 9) Misc. bond : bond 0.06444 / 3.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: B 164 HIS cc_start: 0.7121 (OUTLIER) cc_final: 0.6242 (m-70) REVERT: C 187 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.6888 (m-30) outliers start: 23 outliers final: 21 residues processed: 123 average time/residue: 0.5980 time to fit residues: 78.4862 Evaluate side-chains 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 449 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.0970 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0060 chunk 33 optimal weight: 0.0270 chunk 65 optimal weight: 0.0060 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 HIS ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.132873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.108710 restraints weight = 8978.673| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.34 r_work: 0.3165 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 8853 Z= 0.206 Angle : 1.529 65.350 12091 Z= 0.487 Chirality : 0.107 3.480 1277 Planarity : 0.006 0.129 1569 Dihedral : 10.711 142.334 1279 Min Nonbonded Distance : 1.550 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.48 % Allowed : 16.25 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.26), residues: 1083 helix: 1.53 (0.27), residues: 391 sheet: 1.24 (0.64), residues: 72 loop : -0.43 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 94 TYR 0.017 0.001 TYR A 443 PHE 0.011 0.001 PHE A 270 TRP 0.008 0.001 TRP A 51 HIS 0.002 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 ( 8838) covalent geometry : angle 1.32083 / 0.48 (12082) hydrogen bonds : bond 0.03489 / 2.48 ( 314) hydrogen bonds : angle 5.31037 / 3.89 ( 867) metal coordination : bond 0.02680 / 1.29 ( 3) metal coordination : angle 28.25815 / 16.94 ( 9) Misc. bond : bond 0.01407 / 1.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.344 Fit side-chains REVERT: A 84 ASN cc_start: 0.7898 (t0) cc_final: 0.7650 (t0) REVERT: A 189 GLU cc_start: 0.7290 (pt0) cc_final: 0.6974 (pt0) REVERT: A 389 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7559 (mttt) REVERT: B 164 HIS cc_start: 0.6873 (OUTLIER) cc_final: 0.5083 (m-70) REVERT: C 110 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7461 (p0) REVERT: C 187 ASP cc_start: 0.7537 (m-30) cc_final: 0.7264 (t70) outliers start: 22 outliers final: 9 residues processed: 127 average time/residue: 0.6382 time to fit residues: 86.2640 Evaluate side-chains 121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 88 optimal weight: 0.0570 chunk 0 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN A 476 ASN B 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.124566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.099277 restraints weight = 8994.749| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.36 r_work: 0.3037 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 8853 Z= 0.272 Angle : 1.515 85.279 12091 Z= 0.476 Chirality : 0.063 1.220 1277 Planarity : 0.007 0.116 1569 Dihedral : 10.593 107.927 1251 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer: Outliers : 2.26 % Allowed : 17.38 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.25), residues: 1083 helix: 1.16 (0.27), residues: 386 sheet: 0.02 (0.54), residues: 94 loop : -0.48 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 94 TYR 0.013 0.002 TYR A 232 PHE 0.029 0.002 PHE A 80 TRP 0.018 0.002 TRP A 338 HIS 0.007 0.002 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.27 ( 8838) covalent geometry : angle 1.17403 / 0.47 (12082) hydrogen bonds : bond 0.05102 / 3.59 ( 314) hydrogen bonds : angle 5.64952 / 4.14 ( 867) metal coordination : bond 0.00928 / 0.47 ( 3) metal coordination : angle 35.09954 / 24.91 ( 9) Misc. bond : bond 0.05032 / 3.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.331 Fit side-chains REVERT: A 84 ASN cc_start: 0.8208 (t0) cc_final: 0.7950 (t0) REVERT: B 164 HIS cc_start: 0.7631 (OUTLIER) cc_final: 0.6431 (m-70) REVERT: C 302 THR cc_start: 0.7252 (OUTLIER) cc_final: 0.6967 (t) outliers start: 20 outliers final: 12 residues processed: 121 average time/residue: 0.6562 time to fit residues: 83.8930 Evaluate side-chains 123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 88 optimal weight: 0.0010 chunk 20 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.127654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.102971 restraints weight = 9163.885| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.33 r_work: 0.3056 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 8853 Z= 0.160 Angle : 1.436 82.148 12091 Z= 0.426 Chirality : 0.062 1.463 1277 Planarity : 0.006 0.095 1569 Dihedral : 9.887 89.488 1251 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.12 % Rotamer: Outliers : 2.93 % Allowed : 17.49 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.26), residues: 1083 helix: 1.37 (0.27), residues: 387 sheet: 1.05 (0.62), residues: 73 loop : -0.45 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 94 TYR 0.015 0.001 TYR A 443 PHE 0.015 0.002 PHE A 80 TRP 0.010 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 8838) covalent geometry : angle 1.09035 / 0.42 (12082) hydrogen bonds : bond 0.03906 / 2.78 ( 314) hydrogen bonds : angle 5.30330 / 3.87 ( 867) metal coordination : bond 0.00338 / 0.17 ( 3) metal coordination : angle 34.27381 / 24.56 ( 9) Misc. bond : bond 0.05404 / 3.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.286 Fit side-chains REVERT: A 84 ASN cc_start: 0.8218 (t0) cc_final: 0.7896 (t0) REVERT: A 247 LYS cc_start: 0.8686 (tttp) cc_final: 0.8414 (tttm) REVERT: A 276 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7163 (tp40) REVERT: A 468 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7997 (mt-10) REVERT: B 154 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7862 (mtt180) REVERT: B 164 HIS cc_start: 0.7555 (OUTLIER) cc_final: 0.6331 (m-70) REVERT: C 110 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7616 (p0) REVERT: C 187 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7249 (t0) REVERT: C 302 THR cc_start: 0.7307 (OUTLIER) cc_final: 0.7038 (t) outliers start: 26 outliers final: 10 residues processed: 121 average time/residue: 0.6413 time to fit residues: 82.2422 Evaluate side-chains 120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 0.9990 chunk 22 optimal weight: 0.0570 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.129018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.104783 restraints weight = 9178.304| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.31 r_work: 0.3092 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 8853 Z= 0.151 Angle : 1.426 82.051 12091 Z= 0.418 Chirality : 0.061 1.475 1277 Planarity : 0.005 0.084 1569 Dihedral : 9.427 87.239 1251 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.75 % Rotamer: Outliers : 2.48 % Allowed : 18.06 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.26), residues: 1083 helix: 1.49 (0.27), residues: 388 sheet: 1.10 (0.63), residues: 73 loop : -0.39 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 94 TYR 0.014 0.001 TYR A 443 PHE 0.015 0.001 PHE A 270 TRP 0.008 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 8838) covalent geometry : angle 1.08416 / 0.41 (12082) hydrogen bonds : bond 0.03651 / 2.60 ( 314) hydrogen bonds : angle 5.14053 / 3.74 ( 867) metal coordination : bond 0.00337 / 0.16 ( 3) metal coordination : angle 33.94446 / 24.80 ( 9) Misc. bond : bond 0.05927 / 3.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.318 Fit side-chains REVERT: A 84 ASN cc_start: 0.8146 (t0) cc_final: 0.7788 (t0) REVERT: A 152 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8099 (tp30) REVERT: A 247 LYS cc_start: 0.8638 (tttp) cc_final: 0.8371 (tttm) REVERT: A 276 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7080 (tp40) REVERT: B 154 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7850 (mtt180) REVERT: B 164 HIS cc_start: 0.7530 (OUTLIER) cc_final: 0.6109 (m-70) REVERT: C 110 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7633 (p0) REVERT: C 187 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7296 (t0) REVERT: C 302 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.7043 (t) REVERT: C 395 MET cc_start: 0.8723 (ttt) cc_final: 0.8465 (ttt) outliers start: 22 outliers final: 10 residues processed: 119 average time/residue: 0.6573 time to fit residues: 82.7510 Evaluate side-chains 123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 449 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 68 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 2 optimal weight: 0.0870 chunk 36 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 19 optimal weight: 0.0870 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.131515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.107628 restraints weight = 9170.053| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.31 r_work: 0.3138 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 8853 Z= 0.138 Angle : 1.405 82.200 12091 Z= 0.408 Chirality : 0.061 1.469 1277 Planarity : 0.005 0.076 1569 Dihedral : 9.098 84.759 1251 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.88 % Favored : 96.03 % Rotamer: Outliers : 2.71 % Allowed : 17.61 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.26), residues: 1083 helix: 1.55 (0.27), residues: 396 sheet: 1.04 (0.63), residues: 73 loop : -0.36 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 94 TYR 0.014 0.001 TYR A 443 PHE 0.015 0.001 PHE C 210 TRP 0.008 0.001 TRP A 51 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 8838) covalent geometry : angle 1.06686 / 0.40 (12082) hydrogen bonds : bond 0.03304 / 2.37 ( 314) hydrogen bonds : angle 4.99256 / 3.62 ( 867) metal coordination : bond 0.00314 / 0.15 ( 3) metal coordination : angle 33.53980 / 24.27 ( 9) Misc. bond : bond 0.04077 / 2.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.553 Fit side-chains REVERT: A 84 ASN cc_start: 0.8081 (t0) cc_final: 0.7703 (t0) REVERT: A 152 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8060 (tp30) REVERT: A 189 GLU cc_start: 0.7217 (pt0) cc_final: 0.6933 (tm-30) REVERT: A 247 LYS cc_start: 0.8555 (tttp) cc_final: 0.8298 (tttm) REVERT: A 276 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7159 (tp40) REVERT: A 468 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: B 154 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7726 (mtt180) REVERT: B 164 HIS cc_start: 0.7414 (OUTLIER) cc_final: 0.5661 (m-70) REVERT: C 110 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7659 (p0) REVERT: C 129 GLU cc_start: 0.7870 (mp0) cc_final: 0.7555 (mp0) REVERT: C 187 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7311 (t0) outliers start: 24 outliers final: 9 residues processed: 129 average time/residue: 0.6439 time to fit residues: 88.2197 Evaluate side-chains 131 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 449 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 103 optimal weight: 0.0870 chunk 10 optimal weight: 0.7980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.130306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.106165 restraints weight = 9286.344| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.33 r_work: 0.3106 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.189 8853 Z= 0.148 Angle : 1.419 82.106 12091 Z= 0.416 Chirality : 0.061 1.472 1277 Planarity : 0.005 0.074 1569 Dihedral : 9.107 87.177 1249 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 2.93 % Allowed : 17.83 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.26), residues: 1083 helix: 1.56 (0.27), residues: 395 sheet: 1.04 (0.63), residues: 73 loop : -0.36 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 94 TYR 0.013 0.001 TYR A 443 PHE 0.015 0.001 PHE C 210 TRP 0.008 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 8838) covalent geometry : angle 1.08111 / 0.41 (12082) hydrogen bonds : bond 0.03481 / 2.48 ( 314) hydrogen bonds : angle 5.01017 / 3.63 ( 867) metal coordination : bond 0.00365 / 0.18 ( 3) metal coordination : angle 33.68412 / 24.63 ( 9) Misc. bond : bond 0.05575 / 2.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8087 (t0) cc_final: 0.7728 (t0) REVERT: A 152 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8096 (tp30) REVERT: A 189 GLU cc_start: 0.7241 (pt0) cc_final: 0.6948 (tm-30) REVERT: A 247 LYS cc_start: 0.8563 (tttp) cc_final: 0.8301 (tttm) REVERT: A 276 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7088 (tp40) REVERT: A 468 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: B 154 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7817 (mtt180) REVERT: B 164 HIS cc_start: 0.7536 (OUTLIER) cc_final: 0.5993 (m-70) REVERT: C 110 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7683 (p0) REVERT: C 129 GLU cc_start: 0.7883 (mp0) cc_final: 0.7565 (mp0) REVERT: C 187 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7275 (t0) outliers start: 26 outliers final: 12 residues processed: 125 average time/residue: 0.6617 time to fit residues: 87.8698 Evaluate side-chains 133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 449 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.130535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.106544 restraints weight = 9145.151| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.31 r_work: 0.3138 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 8853 Z= 0.148 Angle : 1.415 82.118 12091 Z= 0.415 Chirality : 0.061 1.472 1277 Planarity : 0.005 0.073 1569 Dihedral : 9.111 87.455 1249 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.84 % Rotamer: Outliers : 2.93 % Allowed : 17.72 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.26), residues: 1083 helix: 1.62 (0.27), residues: 390 sheet: 0.94 (0.63), residues: 73 loop : -0.33 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 94 TYR 0.025 0.001 TYR A 79 PHE 0.015 0.001 PHE A 80 TRP 0.008 0.001 TRP A 51 HIS 0.005 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 8838) covalent geometry : angle 1.07769 / 0.41 (12082) hydrogen bonds : bond 0.03494 / 2.49 ( 314) hydrogen bonds : angle 4.99340 / 3.61 ( 867) metal coordination : bond 0.00362 / 0.18 ( 3) metal coordination : angle 33.64237 / 24.64 ( 9) Misc. bond : bond 0.04837 / 2.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8103 (t0) cc_final: 0.7755 (t0) REVERT: A 152 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8101 (tp30) REVERT: A 189 GLU cc_start: 0.7244 (pt0) cc_final: 0.6959 (tm-30) REVERT: A 247 LYS cc_start: 0.8584 (tttp) cc_final: 0.8329 (tttm) REVERT: A 276 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7085 (tp40) REVERT: A 468 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: B 154 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7797 (mtt180) REVERT: B 164 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.5990 (m-70) REVERT: C 110 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7664 (p0) REVERT: C 129 GLU cc_start: 0.7885 (mp0) cc_final: 0.7568 (mp0) REVERT: C 187 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7265 (t0) outliers start: 26 outliers final: 11 residues processed: 122 average time/residue: 0.6957 time to fit residues: 90.0272 Evaluate side-chains 123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 449 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 20 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 93 optimal weight: 0.0970 chunk 37 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.131230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.107357 restraints weight = 9124.933| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.31 r_work: 0.3153 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 8853 Z= 0.143 Angle : 1.407 82.231 12091 Z= 0.411 Chirality : 0.061 1.472 1277 Planarity : 0.005 0.071 1569 Dihedral : 9.039 87.195 1249 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % Rotamer: Outliers : 2.60 % Allowed : 17.83 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.26), residues: 1083 helix: 1.68 (0.27), residues: 389 sheet: 0.93 (0.64), residues: 73 loop : -0.33 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 94 TYR 0.026 0.001 TYR A 79 PHE 0.016 0.001 PHE C 210 TRP 0.010 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 8838) covalent geometry : angle 1.07264 / 0.40 (12082) hydrogen bonds : bond 0.03381 / 2.42 ( 314) hydrogen bonds : angle 4.95089 / 3.58 ( 867) metal coordination : bond 0.00359 / 0.18 ( 3) metal coordination : angle 33.40149 / 24.32 ( 9) Misc. bond : bond 0.04778 / 2.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8077 (t0) cc_final: 0.7705 (t0) REVERT: A 152 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8084 (tp30) REVERT: A 189 GLU cc_start: 0.7254 (pt0) cc_final: 0.6988 (tm-30) REVERT: A 247 LYS cc_start: 0.8575 (tttp) cc_final: 0.8297 (tttm) REVERT: A 276 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7068 (tp40) REVERT: A 468 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: B 154 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7720 (mtt180) REVERT: B 164 HIS cc_start: 0.7481 (OUTLIER) cc_final: 0.5901 (m-70) REVERT: C 110 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7634 (p0) REVERT: C 129 GLU cc_start: 0.7847 (mp0) cc_final: 0.7527 (mp0) REVERT: C 187 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7320 (t0) outliers start: 23 outliers final: 11 residues processed: 121 average time/residue: 0.6747 time to fit residues: 86.5785 Evaluate side-chains 125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 449 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 138 ASN B 151 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.132839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109162 restraints weight = 9141.617| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.31 r_work: 0.3147 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.149 8853 Z= 0.136 Angle : 1.397 82.441 12091 Z= 0.407 Chirality : 0.060 1.457 1277 Planarity : 0.005 0.070 1569 Dihedral : 8.930 86.797 1249 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.60 % Favored : 96.31 % Rotamer: Outliers : 2.03 % Allowed : 18.28 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.26), residues: 1083 helix: 1.72 (0.27), residues: 390 sheet: 0.97 (0.64), residues: 73 loop : -0.30 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 94 TYR 0.024 0.001 TYR A 79 PHE 0.016 0.001 PHE C 210 TRP 0.010 0.001 TRP A 51 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 8838) covalent geometry : angle 1.06638 / 0.40 (12082) hydrogen bonds : bond 0.03193 / 2.29 ( 314) hydrogen bonds : angle 4.87534 / 3.53 ( 867) metal coordination : bond 0.00360 / 0.18 ( 3) metal coordination : angle 33.09994 / 23.84 ( 9) Misc. bond : bond 0.04527 / 2.50 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8028 (t0) cc_final: 0.7657 (t0) REVERT: A 152 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8072 (tp30) REVERT: A 189 GLU cc_start: 0.7235 (pt0) cc_final: 0.6938 (tm-30) REVERT: A 247 LYS cc_start: 0.8573 (tttp) cc_final: 0.8280 (tttm) REVERT: A 276 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7056 (tp40) REVERT: A 384 MET cc_start: 0.8845 (mtp) cc_final: 0.8440 (mtp) REVERT: B 154 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7672 (mtt180) REVERT: B 164 HIS cc_start: 0.7346 (OUTLIER) cc_final: 0.5581 (m-70) REVERT: C 110 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7625 (p0) REVERT: C 129 GLU cc_start: 0.7837 (mp0) cc_final: 0.7516 (mp0) REVERT: C 190 ARG cc_start: 0.8087 (mtm-85) cc_final: 0.7802 (mtm110) outliers start: 18 outliers final: 9 residues processed: 119 average time/residue: 0.6657 time to fit residues: 84.1912 Evaluate side-chains 123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.128106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.103700 restraints weight = 9172.517| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.33 r_work: 0.3089 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.220 8853 Z= 0.179 Angle : 1.444 81.677 12091 Z= 0.432 Chirality : 0.063 1.481 1277 Planarity : 0.005 0.077 1569 Dihedral : 9.305 86.846 1249 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % Rotamer: Outliers : 1.92 % Allowed : 18.74 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.26), residues: 1083 helix: 1.56 (0.27), residues: 388 sheet: 0.46 (0.59), residues: 83 loop : -0.37 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 94 TYR 0.030 0.002 TYR A 79 PHE 0.022 0.002 PHE A 80 TRP 0.014 0.002 TRP A 338 HIS 0.006 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 8838) covalent geometry : angle 1.10896 / 0.42 (12082) hydrogen bonds : bond 0.03943 / 2.81 ( 314) hydrogen bonds : angle 5.11523 / 3.71 ( 867) metal coordination : bond 0.00466 / 0.23 ( 3) metal coordination : angle 33.94423 / 25.48 ( 9) Misc. bond : bond 0.06692 / 3.66 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3230.68 seconds wall clock time: 55 minutes 59.67 seconds (3359.67 seconds total)