Starting phenix.real_space_refine on Thu Aug 6 13:13:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30uv_58073/08_2026/30uv_58073_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/30uv_58073/08_2026/30uv_58073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/30uv_58073/08_2026/30uv_58073_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30uv_58073/08_2026/30uv_58073_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/30uv_58073/08_2026/30uv_58073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30uv_58073/08_2026/30uv_58073.map" } resolution = 2.49 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= 0.005 sd= 0.043 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 S 64 5.16 5 C 4908 2.51 5 N 1152 2.21 5 O 1218 1.98 5 H 7668 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15010 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7491 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 29, 'TRANS': 438} Chain breaks: 4 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B Time building chain proxies: 6.55, per 1000 atoms: 0.44 Number of scatterers: 15010 At special positions: 0 Unit cell: (82.644, 109.908, 83.496, 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) S 64 16.00 O 1218 8.00 N 1152 7.00 C 4908 6.00 H 7668 1.00 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=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 562 " " NAG B 601 " - " ASN B 562 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 405.8 milliseconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1780 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 82.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 removed outlier: 4.149A pdb=" N LEU A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE A 18 " --> pdb=" O PHE A 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 13 through 18' Processing helix chain 'A' and resid 20 through 29 Proline residue: A 26 - end of helix Processing helix chain 'A' and resid 33 through 51 removed outlier: 3.641A pdb=" N ARG A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 61 through 67 removed outlier: 3.870A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 84 through 103 removed outlier: 3.718A pdb=" N TRP A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 120 through 137 Processing helix chain 'A' and resid 140 through 158 removed outlier: 3.652A pdb=" N THR A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 202 through 221 removed outlier: 3.691A pdb=" N LYS A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 241 removed outlier: 3.682A pdb=" N VAL A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 277 Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 292 through 308 removed outlier: 4.201A pdb=" N LEU A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 334 removed outlier: 3.758A pdb=" N ILE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP A 334 " --> pdb=" O TRP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 367 removed outlier: 3.876A pdb=" N VAL A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 405 removed outlier: 3.923A pdb=" N THR A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 428 removed outlier: 3.591A pdb=" N VAL A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 436 Processing helix chain 'A' and resid 437 through 443 removed outlier: 3.679A pdb=" N ALA A 442 " --> pdb=" O PRO A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 460 Processing helix chain 'A' and resid 464 through 484 Proline residue: A 474 - end of helix Processing helix chain 'A' and resid 486 through 498 removed outlier: 3.899A pdb=" N ILE A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Proline residue: A 493 - end of helix Processing helix chain 'A' and resid 504 through 507 Processing helix chain 'A' and resid 508 through 516 removed outlier: 3.730A pdb=" N ALA A 512 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 547 removed outlier: 3.711A pdb=" N MET A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A 532 " --> pdb=" O THR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 553 removed outlier: 3.988A pdb=" N ILE A 551 " --> pdb=" O TRP A 547 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 removed outlier: 4.175A pdb=" N PHE B 18 " --> pdb=" O PHE B 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 14 through 18' Processing helix chain 'B' and resid 20 through 29 Proline residue: B 26 - end of helix Processing helix chain 'B' and resid 33 through 51 removed outlier: 3.642A pdb=" N ARG B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 61 through 67 removed outlier: 3.870A pdb=" N LEU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 Processing helix chain 'B' and resid 84 through 103 removed outlier: 3.719A pdb=" N TRP B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 118 Processing helix chain 'B' and resid 120 through 137 Processing helix chain 'B' and resid 140 through 158 removed outlier: 3.651A pdb=" N THR B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Proline residue: B 150 - end of helix Processing helix chain 'B' and resid 202 through 221 removed outlier: 3.691A pdb=" N LYS B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 241 removed outlier: 3.682A pdb=" N VAL B 231 " --> pdb=" O THR B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 277 Proline residue: B 259 - end of helix Processing helix chain 'B' and resid 292 through 308 removed outlier: 4.201A pdb=" N LEU B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 334 removed outlier: 3.757A pdb=" N ILE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASP B 334 " --> pdb=" O TRP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 367 removed outlier: 3.877A pdb=" N VAL B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 405 removed outlier: 3.924A pdb=" N THR B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 428 removed outlier: 3.590A pdb=" N VAL B 411 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 436 Processing helix chain 'B' and resid 437 through 443 removed outlier: 3.680A pdb=" N ALA B 442 " --> pdb=" O PRO B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 460 Processing helix chain 'B' and resid 464 through 484 Proline residue: B 474 - end of helix Processing helix chain 'B' and resid 486 through 498 removed outlier: 3.900A pdb=" N ILE B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Proline residue: B 493 - end of helix Processing helix chain 'B' and resid 504 through 507 Processing helix chain 'B' and resid 508 through 516 removed outlier: 3.729A pdb=" N ALA B 512 " --> pdb=" O THR B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 547 removed outlier: 3.710A pdb=" N MET B 525 " --> pdb=" O LYS B 521 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE B 531 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B 532 " --> pdb=" O THR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 553 removed outlier: 3.988A pdb=" N ILE B 551 " --> pdb=" O TRP B 547 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1392 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: 3.11 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7648 1.03 - 1.23: 114 1.23 - 1.43: 2904 1.43 - 1.63: 4428 1.63 - 1.82: 108 Bond restraints: 15202 Sorted by residual: bond pdb=" C1 NAG B 601 " pdb=" C2 NAG B 601 " ideal model delta sigma weight residual 1.532 1.605 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C1 NAG A 601 " pdb=" C2 NAG A 601 " ideal model delta sigma weight residual 1.532 1.605 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C5 NAG B 601 " pdb=" C6 NAG B 601 " ideal model delta sigma weight residual 1.513 1.569 -0.056 2.00e-02 2.50e+03 7.92e+00 bond pdb=" C5 NAG A 601 " pdb=" C6 NAG A 601 " ideal model delta sigma weight residual 1.513 1.569 -0.056 2.00e-02 2.50e+03 7.87e+00 bond pdb=" C7 NAG B 601 " pdb=" N2 NAG B 601 " ideal model delta sigma weight residual 1.346 1.401 -0.055 2.00e-02 2.50e+03 7.65e+00 ... (remaining 15197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.08: 27440 7.08 - 14.16: 30 14.16 - 21.24: 10 21.24 - 28.31: 120 28.31 - 35.39: 86 Bond angle restraints: 27686 Sorted by residual: angle pdb=" CB VAL B 263 " pdb=" CA VAL B 263 " pdb=" HA VAL B 263 " ideal model delta sigma weight residual 109.00 73.61 35.39 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C SER A 291 " pdb=" CA SER A 291 " pdb=" HA SER A 291 " ideal model delta sigma weight residual 109.00 73.61 35.39 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C SER B 291 " pdb=" CA SER B 291 " pdb=" HA SER B 291 " ideal model delta sigma weight residual 109.00 73.61 35.39 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CB VAL A 263 " pdb=" CA VAL A 263 " pdb=" HA VAL A 263 " ideal model delta sigma weight residual 109.00 73.70 35.30 3.00e+00 1.11e-01 1.38e+02 angle pdb=" N SER B 291 " pdb=" CA SER B 291 " pdb=" HA SER B 291 " ideal model delta sigma weight residual 110.00 74.75 35.25 3.00e+00 1.11e-01 1.38e+02 ... (remaining 27681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 6383 17.05 - 34.09: 496 34.09 - 51.14: 211 51.14 - 68.18: 66 68.18 - 85.23: 14 Dihedral angle restraints: 7170 sinusoidal: 3866 harmonic: 3304 Sorted by residual: dihedral pdb=" CA THR B 225 " pdb=" C THR B 225 " pdb=" N GLY B 226 " pdb=" CA GLY B 226 " ideal model delta harmonic sigma weight residual 180.00 154.44 25.56 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA THR A 225 " pdb=" C THR A 225 " pdb=" N GLY A 226 " pdb=" CA GLY A 226 " ideal model delta harmonic sigma weight residual 180.00 154.48 25.52 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA TYR B 353 " pdb=" C TYR B 353 " pdb=" N VAL B 354 " pdb=" CA VAL B 354 " ideal model delta harmonic sigma weight residual -180.00 -156.82 -23.18 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 7167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.344: 1228 0.344 - 0.688: 4 0.688 - 1.032: 0 1.032 - 1.376: 0 1.376 - 1.720: 16 Chirality restraints: 1248 Sorted by residual: chirality pdb=" CB ILE A 29 " pdb=" CA ILE A 29 " pdb=" CG1 ILE A 29 " pdb=" CG2 ILE A 29 " both_signs ideal model delta sigma weight residual False 2.64 0.92 1.72 2.00e-01 2.50e+01 7.40e+01 chirality pdb=" CB ILE B 29 " pdb=" CA ILE B 29 " pdb=" CG1 ILE B 29 " pdb=" CG2 ILE B 29 " both_signs ideal model delta sigma weight residual False 2.64 0.92 1.72 2.00e-01 2.50e+01 7.40e+01 chirality pdb=" CG LEU A 22 " pdb=" CB LEU A 22 " pdb=" CD1 LEU A 22 " pdb=" CD2 LEU A 22 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.26e+01 ... (remaining 1245 not shown) Planarity restraints: 2100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 20 " -0.026 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO B 21 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 21 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 21 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 20 " 0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO A 21 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 310 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO B 311 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 311 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 311 " -0.021 5.00e-02 4.00e+02 ... (remaining 2097 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1075 2.20 - 2.80: 30202 2.80 - 3.40: 41199 3.40 - 4.00: 52325 4.00 - 4.60: 83144 Nonbonded interactions: 207945 Sorted by model distance: nonbonded pdb=" HA VAL A 263 " pdb=" HB VAL A 263 " model vdw 1.604 1.952 nonbonded pdb=" HA VAL B 263 " pdb=" HB VAL B 263 " model vdw 1.604 1.952 nonbonded pdb=" HB THR A 402 " pdb=" HG1 THR A 402 " model vdw 1.627 1.816 nonbonded pdb=" HB THR B 402 " pdb=" HG1 THR B 402 " model vdw 1.628 1.816 nonbonded pdb=" HB THR B 351 " pdb=" HG1 THR B 351 " model vdw 1.631 1.816 ... (remaining 207940 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.000 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: 0.060 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 16.990 Find NCS groups from input model: 0.070 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:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 7536 Z= 0.174 Angle : 1.071 25.940 10280 Z= 0.472 Chirality : 0.184 1.720 1248 Planarity : 0.005 0.040 1230 Dihedral : 15.474 82.945 2690 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.33 % Favored : 93.56 % Rotamer: Outliers : 2.37 % Allowed : 22.57 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.30), residues: 916 helix: 1.42 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -2.09 (0.47), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 549 TYR 0.014 0.001 TYR A 353 PHE 0.011 0.001 PHE B 35 TRP 0.011 0.001 TRP B 49 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 7534) covalent geometry : angle 1.06836 / 0.47 (10274) hydrogen bonds : bond 0.14278 / 9.05 ( 480) hydrogen bonds : angle 6.09238 / 4.47 ( 1392) link_NAG-ASN : bond 0.00960 / 0.48 ( 2) link_NAG-ASN : angle 3.40666 / 1.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 TYR cc_start: 0.7586 (m-80) cc_final: 0.7288 (m-80) REVERT: B 276 TYR cc_start: 0.7608 (m-80) cc_final: 0.7397 (m-80) outliers start: 19 outliers final: 9 residues processed: 120 average time/residue: 0.6183 time to fit residues: 81.8254 Evaluate side-chains 82 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 555 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.098909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.071847 restraints weight = 50940.909| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.44 r_work: 0.3046 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7536 Z= 0.141 Angle : 1.056 26.293 10280 Z= 0.462 Chirality : 0.181 1.750 1248 Planarity : 0.005 0.043 1230 Dihedral : 5.211 57.901 1030 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.12 % Allowed : 22.07 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.30), residues: 916 helix: 2.26 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -2.01 (0.45), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 108 TYR 0.011 0.001 TYR B 353 PHE 0.015 0.001 PHE B 274 TRP 0.010 0.001 TRP A 49 HIS 0.003 0.001 HIS A 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 7534) covalent geometry : angle 1.05354 / 0.46 (10274) hydrogen bonds : bond 0.04561 / 2.90 ( 480) hydrogen bonds : angle 4.44217 / 3.24 ( 1392) link_NAG-ASN : bond 0.00975 / 0.49 ( 2) link_NAG-ASN : angle 3.12225 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7741 (t80) REVERT: B 31 MET cc_start: 0.7333 (mmm) cc_final: 0.6959 (mmm) outliers start: 25 outliers final: 13 residues processed: 95 average time/residue: 0.5986 time to fit residues: 63.2255 Evaluate side-chains 83 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 555 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.8980 chunk 72 optimal weight: 0.0770 chunk 14 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.094892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.067746 restraints weight = 52060.721| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.41 r_work: 0.2960 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7536 Z= 0.181 Angle : 1.063 25.876 10280 Z= 0.467 Chirality : 0.183 1.731 1248 Planarity : 0.005 0.043 1230 Dihedral : 5.095 59.888 1024 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.24 % Allowed : 22.32 % Favored : 74.44 % 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: 2.00 (0.30), residues: 916 helix: 2.33 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -1.98 (0.47), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 108 TYR 0.011 0.001 TYR A 353 PHE 0.016 0.001 PHE B 314 TRP 0.011 0.001 TRP A 49 HIS 0.003 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 ( 7534) covalent geometry : angle 1.06098 / 0.47 (10274) hydrogen bonds : bond 0.05102 / 3.26 ( 480) hydrogen bonds : angle 4.22997 / 3.05 ( 1392) link_NAG-ASN : bond 0.00678 / 0.34 ( 2) link_NAG-ASN : angle 2.97652 / 1.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7369 (t80) outliers start: 26 outliers final: 8 residues processed: 88 average time/residue: 0.6237 time to fit residues: 60.6708 Evaluate side-chains 78 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 555 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 72 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.094898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.067585 restraints weight = 51508.168| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.44 r_work: 0.2965 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7536 Z= 0.173 Angle : 1.063 25.888 10280 Z= 0.465 Chirality : 0.183 1.714 1248 Planarity : 0.005 0.044 1230 Dihedral : 4.966 57.695 1020 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.99 % Allowed : 22.44 % Favored : 74.56 % 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: 2.02 (0.30), residues: 916 helix: 2.44 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -2.05 (0.44), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 278 TYR 0.012 0.001 TYR A 353 PHE 0.015 0.001 PHE B 314 TRP 0.011 0.001 TRP A 49 HIS 0.003 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 ( 7534) covalent geometry : angle 1.06096 / 0.46 (10274) hydrogen bonds : bond 0.04824 / 3.08 ( 480) hydrogen bonds : angle 4.10543 / 2.97 ( 1392) link_NAG-ASN : bond 0.00698 / 0.35 ( 2) link_NAG-ASN : angle 3.03334 / 1.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8381 (tp) outliers start: 24 outliers final: 12 residues processed: 86 average time/residue: 0.7313 time to fit residues: 69.1555 Evaluate side-chains 79 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 555 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 91 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 88 optimal weight: 30.0000 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.097147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.070148 restraints weight = 51685.826| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.41 r_work: 0.3006 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7536 Z= 0.127 Angle : 1.044 26.110 10280 Z= 0.450 Chirality : 0.182 1.728 1248 Planarity : 0.005 0.044 1230 Dihedral : 4.780 52.864 1020 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.49 % Allowed : 22.94 % Favored : 74.56 % 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: 2.21 (0.30), residues: 916 helix: 2.53 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -2.15 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 549 TYR 0.010 0.001 TYR B 353 PHE 0.010 0.001 PHE B 314 TRP 0.009 0.001 TRP B 49 HIS 0.003 0.000 HIS A 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 7534) covalent geometry : angle 1.04230 / 0.45 (10274) hydrogen bonds : bond 0.03941 / 2.48 ( 480) hydrogen bonds : angle 3.87751 / 2.82 ( 1392) link_NAG-ASN : bond 0.00791 / 0.40 ( 2) link_NAG-ASN : angle 2.91796 / 1.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7391 (mmm) cc_final: 0.7041 (mmm) REVERT: A 276 TYR cc_start: 0.8635 (m-80) cc_final: 0.8398 (m-80) REVERT: A 403 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7858 (tm-30) outliers start: 20 outliers final: 8 residues processed: 79 average time/residue: 0.7496 time to fit residues: 64.6725 Evaluate side-chains 72 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 555 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 71 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.093443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.065789 restraints weight = 51714.458| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.45 r_work: 0.2926 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7536 Z= 0.217 Angle : 1.078 26.112 10280 Z= 0.475 Chirality : 0.184 1.709 1248 Planarity : 0.005 0.044 1230 Dihedral : 4.877 53.522 1020 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.00 % Allowed : 23.82 % Favored : 74.19 % 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: 2.11 (0.30), residues: 916 helix: 2.47 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -2.13 (0.46), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 108 TYR 0.012 0.001 TYR A 353 PHE 0.019 0.001 PHE B 314 TRP 0.010 0.001 TRP B 49 HIS 0.005 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 ( 7534) covalent geometry : angle 1.07549 / 0.47 (10274) hydrogen bonds : bond 0.05252 / 3.36 ( 480) hydrogen bonds : angle 4.10881 / 2.98 ( 1392) link_NAG-ASN : bond 0.00631 / 0.32 ( 2) link_NAG-ASN : angle 3.02045 / 1.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: B 65 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8399 (tp) outliers start: 16 outliers final: 9 residues processed: 79 average time/residue: 0.7141 time to fit residues: 62.2000 Evaluate side-chains 74 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 538 PHE Chi-restraints excluded: chain B residue 555 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.096313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.069059 restraints weight = 51401.679| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.46 r_work: 0.2983 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7536 Z= 0.128 Angle : 1.049 26.042 10280 Z= 0.452 Chirality : 0.182 1.734 1248 Planarity : 0.005 0.043 1230 Dihedral : 4.782 50.048 1020 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.50 % Allowed : 23.57 % Favored : 74.94 % 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: 2.30 (0.30), residues: 916 helix: 2.58 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -2.09 (0.47), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 549 TYR 0.011 0.001 TYR A 353 PHE 0.010 0.001 PHE B 314 TRP 0.010 0.001 TRP A 49 HIS 0.002 0.000 HIS A 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 7534) covalent geometry : angle 1.04669 / 0.45 (10274) hydrogen bonds : bond 0.04046 / 2.55 ( 480) hydrogen bonds : angle 3.84868 / 2.81 ( 1392) link_NAG-ASN : bond 0.00788 / 0.40 ( 2) link_NAG-ASN : angle 2.92117 / 1.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7776 (tm-30) outliers start: 12 outliers final: 6 residues processed: 70 average time/residue: 0.8032 time to fit residues: 61.4951 Evaluate side-chains 68 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 538 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 30.0000 chunk 36 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 27 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.095523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.068121 restraints weight = 52028.482| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.46 r_work: 0.3007 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7536 Z= 0.144 Angle : 1.054 26.115 10280 Z= 0.456 Chirality : 0.183 1.717 1248 Planarity : 0.005 0.043 1230 Dihedral : 4.435 32.705 1018 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.37 % Allowed : 23.69 % Favored : 74.94 % 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: 2.38 (0.30), residues: 916 helix: 2.64 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -2.03 (0.47), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 549 TYR 0.011 0.001 TYR A 353 PHE 0.010 0.001 PHE B 314 TRP 0.010 0.001 TRP B 49 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 ( 7534) covalent geometry : angle 1.05249 / 0.46 (10274) hydrogen bonds : bond 0.04275 / 2.71 ( 480) hydrogen bonds : angle 3.86430 / 2.82 ( 1392) link_NAG-ASN : bond 0.00722 / 0.36 ( 2) link_NAG-ASN : angle 2.89146 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7834 (tm-30) outliers start: 11 outliers final: 5 residues processed: 70 average time/residue: 0.8075 time to fit residues: 61.9343 Evaluate side-chains 69 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 91 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.094180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.066611 restraints weight = 52205.229| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.52 r_work: 0.2935 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7536 Z= 0.169 Angle : 1.059 25.981 10280 Z= 0.461 Chirality : 0.183 1.722 1248 Planarity : 0.005 0.042 1230 Dihedral : 4.537 32.582 1018 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.50 % Allowed : 23.57 % Favored : 74.94 % 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: 2.32 (0.30), residues: 916 helix: 2.64 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.95 (0.45), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 549 TYR 0.012 0.001 TYR A 353 PHE 0.014 0.001 PHE B 314 TRP 0.010 0.001 TRP B 49 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 7534) covalent geometry : angle 1.05674 / 0.46 (10274) hydrogen bonds : bond 0.04689 / 2.98 ( 480) hydrogen bonds : angle 3.96236 / 2.88 ( 1392) link_NAG-ASN : bond 0.00682 / 0.34 ( 2) link_NAG-ASN : angle 2.93865 / 1.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: B 65 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8404 (tp) outliers start: 12 outliers final: 5 residues processed: 73 average time/residue: 0.7909 time to fit residues: 62.6436 Evaluate side-chains 69 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 48 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.095004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.067747 restraints weight = 52051.831| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.45 r_work: 0.2956 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7536 Z= 0.147 Angle : 1.059 26.062 10280 Z= 0.458 Chirality : 0.183 1.724 1248 Planarity : 0.005 0.042 1230 Dihedral : 4.493 32.998 1018 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.87 % Allowed : 24.56 % Favored : 74.56 % 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: 2.39 (0.30), residues: 916 helix: 2.69 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.91 (0.45), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 278 TYR 0.011 0.001 TYR A 353 PHE 0.010 0.001 PHE B 314 TRP 0.010 0.001 TRP A 49 HIS 0.002 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 7534) covalent geometry : angle 1.05709 / 0.46 (10274) hydrogen bonds : bond 0.04370 / 2.76 ( 480) hydrogen bonds : angle 3.88971 / 2.83 ( 1392) link_NAG-ASN : bond 0.00716 / 0.36 ( 2) link_NAG-ASN : angle 2.90045 / 1.31 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7476 (mmm) cc_final: 0.6941 (mmm) REVERT: A 403 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7808 (tm-30) outliers start: 7 outliers final: 5 residues processed: 68 average time/residue: 0.7853 time to fit residues: 58.3462 Evaluate side-chains 67 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 56 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 82 optimal weight: 6.9990 chunk 30 optimal weight: 0.4980 chunk 76 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.095754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.068732 restraints weight = 51630.130| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.42 r_work: 0.2989 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7536 Z= 0.133 Angle : 1.051 26.035 10280 Z= 0.453 Chirality : 0.183 1.731 1248 Planarity : 0.005 0.042 1230 Dihedral : 4.430 33.210 1018 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.00 % Allowed : 24.81 % Favored : 74.19 % 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: 2.49 (0.30), residues: 916 helix: 2.75 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.87 (0.46), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 549 TYR 0.011 0.001 TYR A 353 PHE 0.009 0.001 PHE B 314 TRP 0.010 0.001 TRP B 49 HIS 0.002 0.001 HIS A 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 ( 7534) covalent geometry : angle 1.04948 / 0.45 (10274) hydrogen bonds : bond 0.04037 / 2.54 ( 480) hydrogen bonds : angle 3.82053 / 2.78 ( 1392) link_NAG-ASN : bond 0.00739 / 0.37 ( 2) link_NAG-ASN : angle 2.85646 / 1.29 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4376.78 seconds wall clock time: 74 minutes 41.72 seconds (4481.72 seconds total)