Starting phenix.real_space_refine on Thu Aug 6 14:11:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30ut_58071/08_2026/30ut_58071_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/30ut_58071/08_2026/30ut_58071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/30ut_58071/08_2026/30ut_58071_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30ut_58071/08_2026/30ut_58071_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/30ut_58071/08_2026/30ut_58071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30ut_58071/08_2026/30ut_58071.map" } resolution = 2.53 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= 0.036 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 S 64 5.16 5 Na 4 4.78 5 C 4940 2.51 5 N 1152 2.21 5 O 1228 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 8 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: 15056 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: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {' NA': 2, 'NAG': 1, 'X3M': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 8.63, per 1000 atoms: 0.57 Number of scatterers: 15056 At special positions: 0 Unit cell: (85.0368, 94.944, 84.2112, 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) S 64 16.00 Na 4 11.00 O 1228 8.00 N 1152 7.00 C 4940 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: 1.50 Conformation dependent library (CDL) restraints added in 431.2 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: 56 helices and 0 sheets defined 83.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 removed outlier: 4.369A pdb=" N LEU A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE A 18 " --> pdb=" O PHE A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 24 through 31 removed outlier: 4.434A pdb=" N LEU A 30 " --> pdb=" O PRO A 26 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N MET A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 51 removed outlier: 3.590A pdb=" N ARG A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 Proline residue: A 63 - end of helix Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 84 through 103 removed outlier: 3.684A 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 Proline residue: A 150 - end of helix removed outlier: 3.814A pdb=" N GLN A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 221 removed outlier: 4.103A pdb=" N LYS A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 241 removed outlier: 3.547A 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 307 removed outlier: 3.658A pdb=" N LEU A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 313 through 333 removed outlier: 3.830A pdb=" N ILE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 367 removed outlier: 3.816A pdb=" N VAL A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 405 removed outlier: 4.139A pdb=" N THR A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 428 removed outlier: 3.781A pdb=" N VAL A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 436 Processing helix chain 'A' and resid 437 through 442 removed outlier: 3.645A 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 499 removed outlier: 4.227A pdb=" N ILE A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Proline residue: A 493 - end of helix removed outlier: 3.848A pdb=" N SER A 499 " --> pdb=" O THR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 507 Processing helix chain 'A' and resid 508 through 516 Processing helix chain 'A' and resid 521 through 547 removed outlier: 4.258A pdb=" N ILE A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET A 532 " --> pdb=" O THR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 553 removed outlier: 3.947A pdb=" N ILE A 551 " --> pdb=" O TRP A 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 20 removed outlier: 4.027A pdb=" N PHE B 18 " --> pdb=" O PHE B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 24 through 31 removed outlier: 4.434A pdb=" N LEU B 30 " --> pdb=" O PRO B 26 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N MET B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 51 removed outlier: 3.590A pdb=" N ARG B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 Proline residue: B 63 - end of helix Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 74 through 80 Processing helix chain 'B' and resid 84 through 103 removed outlier: 3.685A 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 Proline residue: B 150 - end of helix removed outlier: 3.813A pdb=" N GLN B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 221 removed outlier: 4.104A pdb=" N LYS B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 241 removed outlier: 3.548A 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 307 removed outlier: 3.658A pdb=" N LEU B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 313 through 333 removed outlier: 3.829A pdb=" N ILE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 367 removed outlier: 3.815A pdb=" N VAL B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 405 removed outlier: 4.137A pdb=" N THR B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 428 removed outlier: 3.781A pdb=" N VAL B 411 " --> pdb=" O PRO B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 436 Processing helix chain 'B' and resid 437 through 442 removed outlier: 3.645A 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 499 removed outlier: 4.227A pdb=" N ILE B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Proline residue: B 493 - end of helix removed outlier: 3.849A pdb=" N SER B 499 " --> pdb=" O THR B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 507 Processing helix chain 'B' and resid 508 through 516 Processing helix chain 'B' and resid 521 through 547 removed outlier: 4.258A pdb=" N ILE B 531 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET B 532 " --> pdb=" O THR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 553 removed outlier: 3.947A pdb=" N ILE B 551 " --> pdb=" O TRP B 547 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1440 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: 3.53 Time building geometry restraints manager: 2.08 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: 25 1.23 - 1.42: 3015 1.42 - 1.62: 4448 1.62 - 1.81: 108 Bond restraints: 15244 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" C2 NAG A 601 " ideal model delta sigma weight residual 1.532 1.600 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1 NAG B 601 " pdb=" C2 NAG B 601 " ideal model delta sigma weight residual 1.532 1.599 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C5 NAG A 601 " pdb=" C6 NAG A 601 " ideal model delta sigma weight residual 1.513 1.571 -0.058 2.00e-02 2.50e+03 8.45e+00 bond pdb=" C5 NAG B 601 " pdb=" C6 NAG B 601 " ideal model delta sigma weight residual 1.513 1.570 -0.057 2.00e-02 2.50e+03 8.24e+00 bond pdb=" C7 NAG B 601 " pdb=" N2 NAG B 601 " ideal model delta sigma weight residual 1.346 1.399 -0.053 2.00e-02 2.50e+03 7.06e+00 ... (remaining 15239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.08: 27514 7.08 - 14.16: 28 14.16 - 21.25: 10 21.25 - 28.33: 114 28.33 - 35.41: 82 Bond angle restraints: 27748 Sorted by residual: angle pdb=" C SER A 291 " pdb=" CA SER A 291 " pdb=" HA SER A 291 " ideal model delta sigma weight residual 109.00 73.59 35.41 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=" N SER A 291 " pdb=" CA SER A 291 " pdb=" HA SER A 291 " ideal model delta sigma weight residual 110.00 74.79 35.21 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 74.82 35.18 3.00e+00 1.11e-01 1.38e+02 angle pdb=" C VAL A 263 " pdb=" CA VAL A 263 " pdb=" HA VAL A 263 " ideal model delta sigma weight residual 109.00 73.99 35.01 3.00e+00 1.11e-01 1.36e+02 ... (remaining 27743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 6372 17.21 - 34.42: 542 34.42 - 51.63: 208 51.63 - 68.84: 62 68.84 - 86.06: 18 Dihedral angle restraints: 7202 sinusoidal: 3898 harmonic: 3304 Sorted by residual: 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 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 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 180.00 151.04 28.96 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA TYR A 353 " pdb=" C TYR A 353 " pdb=" N VAL A 354 " pdb=" CA VAL A 354 " ideal model delta harmonic sigma weight residual -180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 7199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 1230 0.338 - 0.677: 4 0.677 - 1.015: 0 1.015 - 1.354: 0 1.354 - 1.692: 16 Chirality restraints: 1250 Sorted by residual: chirality pdb=" CG LEU B 22 " pdb=" CB LEU B 22 " pdb=" CD1 LEU B 22 " pdb=" CD2 LEU B 22 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.16e+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 -0.90 -1.69 2.00e-01 2.50e+01 7.13e+01 chirality pdb=" CG LEU A 23 " pdb=" CB LEU A 23 " pdb=" CD1 LEU A 23 " pdb=" CD2 LEU A 23 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.11e+01 ... (remaining 1247 not shown) Planarity restraints: 2106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 509 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO B 510 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 510 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 510 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 509 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO A 510 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 406 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A 407 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 407 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 407 " -0.026 5.00e-02 4.00e+02 ... (remaining 2103 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1115 2.19 - 2.80: 30894 2.80 - 3.40: 44447 3.40 - 4.00: 56731 4.00 - 4.60: 89611 Nonbonded interactions: 222798 Sorted by model distance: nonbonded pdb=" HE2 LYS B 352 " pdb=" HZ3 LYS B 352 " model vdw 1.593 1.816 nonbonded pdb=" HE2 LYS A 352 " pdb=" HZ3 LYS A 352 " model vdw 1.593 1.816 nonbonded pdb=" HB THR B 351 " pdb=" HG1 THR B 351 " model vdw 1.628 1.816 nonbonded pdb=" HB THR A 351 " pdb=" HG1 THR A 351 " model vdw 1.628 1.816 nonbonded pdb=" HB THR A 402 " pdb=" HG1 THR A 402 " model vdw 1.631 1.816 ... (remaining 222793 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: 0.02 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: 3.250 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: 0.070 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 22.050 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 0.068 7578 Z= 0.183 Angle : 1.092 26.356 10342 Z= 0.483 Chirality : 0.181 1.692 1250 Planarity : 0.006 0.052 1236 Dihedral : 16.018 86.056 2722 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.74 % Allowed : 21.20 % Favored : 75.06 % Cbeta Deviations : 0.22 % 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: 1.41 (0.30), residues: 916 helix: 1.77 (0.21), residues: 686 sheet: None (None), residues: 0 loop : -1.68 (0.48), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 203 TYR 0.012 0.001 TYR A 353 PHE 0.008 0.001 PHE A 35 TRP 0.010 0.001 TRP B 49 HIS 0.006 0.001 HIS A 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 ( 7576) covalent geometry : angle 1.08860 / 0.48 (10336) hydrogen bonds : bond 0.08595 / 5.69 ( 486) hydrogen bonds : angle 4.84485 / 3.54 ( 1440) link_NAG-ASN : bond 0.01038 / 0.52 ( 2) link_NAG-ASN : angle 3.91231 / 1.90 ( 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 212 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 519 HIS cc_start: 0.5721 (OUTLIER) cc_final: 0.4899 (p90) outliers start: 30 outliers final: 11 residues processed: 207 average time/residue: 0.7560 time to fit residues: 172.0276 Evaluate side-chains 129 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 ASN B 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.093568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.079523 restraints weight = 48780.229| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.88 r_work: 0.3162 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7578 Z= 0.159 Angle : 1.075 26.242 10342 Z= 0.472 Chirality : 0.181 1.701 1250 Planarity : 0.006 0.053 1236 Dihedral : 6.767 71.973 1064 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.37 % Allowed : 24.69 % Favored : 71.95 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.44 (0.30), residues: 916 helix: 1.76 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -1.52 (0.49), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 278 TYR 0.009 0.001 TYR B 276 PHE 0.013 0.001 PHE A 314 TRP 0.011 0.001 TRP A 547 HIS 0.005 0.001 HIS A 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 7576) covalent geometry : angle 1.07267 / 0.47 (10336) hydrogen bonds : bond 0.03805 / 2.43 ( 486) hydrogen bonds : angle 4.26780 / 3.06 ( 1440) link_NAG-ASN : bond 0.00932 / 0.47 ( 2) link_NAG-ASN : angle 3.07210 / 1.42 ( 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 144 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7597 (tm-30) REVERT: B 224 LEU cc_start: 0.8965 (tp) cc_final: 0.8725 (tm) REVERT: B 296 LYS cc_start: 0.8848 (tppt) cc_final: 0.8592 (mmpt) REVERT: B 304 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7867 (tm-30) outliers start: 27 outliers final: 11 residues processed: 140 average time/residue: 0.9032 time to fit residues: 137.0694 Evaluate side-chains 118 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 63 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.091902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.077595 restraints weight = 48999.504| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.93 r_work: 0.3146 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7578 Z= 0.145 Angle : 1.059 26.264 10342 Z= 0.463 Chirality : 0.181 1.707 1250 Planarity : 0.006 0.054 1236 Dihedral : 6.587 75.489 1060 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.90 % Favored : 94.00 % Rotamer: Outliers : 2.12 % Allowed : 23.82 % Favored : 74.06 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.53 (0.30), residues: 916 helix: 1.84 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -1.55 (0.48), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 307 TYR 0.009 0.001 TYR A 276 PHE 0.012 0.001 PHE A 314 TRP 0.010 0.001 TRP A 49 HIS 0.004 0.001 HIS A 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 7576) covalent geometry : angle 1.05665 / 0.46 (10336) hydrogen bonds : bond 0.03631 / 2.30 ( 486) hydrogen bonds : angle 4.18058 / 2.99 ( 1440) link_NAG-ASN : bond 0.00781 / 0.39 ( 2) link_NAG-ASN : angle 2.94534 / 1.33 ( 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 124 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8883 (tppt) cc_final: 0.8653 (mmpt) REVERT: B 224 LEU cc_start: 0.8999 (tp) cc_final: 0.8776 (tm) REVERT: B 296 LYS cc_start: 0.8826 (tppt) cc_final: 0.8597 (mmpt) REVERT: B 307 ARG cc_start: 0.7886 (ptp-110) cc_final: 0.7486 (ptp-110) outliers start: 17 outliers final: 11 residues processed: 123 average time/residue: 0.8422 time to fit residues: 113.1513 Evaluate side-chains 113 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.089079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.074664 restraints weight = 49630.916| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.91 r_work: 0.3076 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7578 Z= 0.177 Angle : 1.058 26.372 10342 Z= 0.466 Chirality : 0.182 1.706 1250 Planarity : 0.006 0.077 1236 Dihedral : 6.799 82.806 1060 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.79 % Favored : 94.00 % Rotamer: Outliers : 2.00 % Allowed : 23.94 % Favored : 74.06 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.65 (0.30), residues: 916 helix: 1.91 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -1.40 (0.47), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 278 TYR 0.011 0.001 TYR A 517 PHE 0.014 0.001 PHE A 314 TRP 0.009 0.001 TRP A 547 HIS 0.003 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 7576) covalent geometry : angle 1.05576 / 0.47 (10336) hydrogen bonds : bond 0.03711 / 2.35 ( 486) hydrogen bonds : angle 4.16707 / 2.97 ( 1440) link_NAG-ASN : bond 0.00700 / 0.35 ( 2) link_NAG-ASN : angle 2.78469 / 1.25 ( 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 120 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8898 (tppt) cc_final: 0.8666 (mmpt) REVERT: B 224 LEU cc_start: 0.9003 (tp) cc_final: 0.8760 (tm) REVERT: B 296 LYS cc_start: 0.8857 (tppt) cc_final: 0.8630 (mmpt) REVERT: B 304 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7637 (tm-30) outliers start: 16 outliers final: 13 residues processed: 119 average time/residue: 0.7917 time to fit residues: 103.6322 Evaluate side-chains 112 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 39 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.086735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.072254 restraints weight = 49902.463| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.90 r_work: 0.3027 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7578 Z= 0.204 Angle : 1.066 26.433 10342 Z= 0.470 Chirality : 0.183 1.702 1250 Planarity : 0.006 0.056 1236 Dihedral : 7.125 89.338 1060 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.00 % Favored : 93.78 % Rotamer: Outliers : 3.12 % Allowed : 23.07 % Favored : 73.82 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.61 (0.30), residues: 916 helix: 1.86 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -1.52 (0.49), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 307 TYR 0.015 0.001 TYR A 276 PHE 0.015 0.001 PHE A 314 TRP 0.011 0.001 TRP B 49 HIS 0.003 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 ( 7576) covalent geometry : angle 1.06468 / 0.47 (10336) hydrogen bonds : bond 0.03821 / 2.42 ( 486) hydrogen bonds : angle 4.19843 / 2.99 ( 1440) link_NAG-ASN : bond 0.00636 / 0.32 ( 2) link_NAG-ASN : angle 2.71451 / 1.22 ( 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 124 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8930 (tppt) cc_final: 0.8555 (mmmt) REVERT: A 304 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7916 (mm-30) REVERT: B 224 LEU cc_start: 0.9026 (tp) cc_final: 0.8770 (tm) REVERT: B 236 GLN cc_start: 0.9334 (OUTLIER) cc_final: 0.8989 (mp10) REVERT: B 296 LYS cc_start: 0.8880 (tppt) cc_final: 0.8652 (mmpt) outliers start: 25 outliers final: 16 residues processed: 120 average time/residue: 0.7929 time to fit residues: 104.6156 Evaluate side-chains 113 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 36 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 87 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 80 optimal weight: 0.4980 chunk 55 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.088343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.073944 restraints weight = 49353.763| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.90 r_work: 0.3065 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7578 Z= 0.136 Angle : 1.049 26.581 10342 Z= 0.457 Chirality : 0.182 1.701 1250 Planarity : 0.006 0.056 1236 Dihedral : 6.998 88.747 1058 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.00 % Favored : 93.78 % Rotamer: Outliers : 2.87 % Allowed : 23.07 % Favored : 74.06 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.65 (0.30), residues: 916 helix: 1.85 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -1.46 (0.50), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 307 TYR 0.010 0.001 TYR A 517 PHE 0.014 0.001 PHE B 18 TRP 0.011 0.001 TRP A 399 HIS 0.003 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 7576) covalent geometry : angle 1.04767 / 0.46 (10336) hydrogen bonds : bond 0.03531 / 2.22 ( 486) hydrogen bonds : angle 4.10089 / 2.92 ( 1440) link_NAG-ASN : bond 0.00752 / 0.38 ( 2) link_NAG-ASN : angle 2.75635 / 1.24 ( 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 124 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8935 (tppt) cc_final: 0.8563 (mmmt) REVERT: B 224 LEU cc_start: 0.9005 (tp) cc_final: 0.8773 (tm) REVERT: B 296 LYS cc_start: 0.8888 (tppt) cc_final: 0.8661 (mmpt) REVERT: B 304 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7740 (tm-30) outliers start: 23 outliers final: 18 residues processed: 120 average time/residue: 0.7676 time to fit residues: 101.4865 Evaluate side-chains 113 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 249 ASN 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 413 LEU Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.088128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.073710 restraints weight = 49352.555| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.88 r_work: 0.3045 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7578 Z= 0.142 Angle : 1.048 26.504 10342 Z= 0.456 Chirality : 0.182 1.709 1250 Planarity : 0.006 0.066 1236 Dihedral : 6.971 88.794 1058 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.00 % Allowed : 24.19 % Favored : 73.82 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.75 (0.30), residues: 916 helix: 1.93 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -1.36 (0.50), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 307 TYR 0.011 0.001 TYR A 517 PHE 0.011 0.001 PHE A 314 TRP 0.011 0.001 TRP B 49 HIS 0.002 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 ( 7576) covalent geometry : angle 1.04637 / 0.46 (10336) hydrogen bonds : bond 0.03490 / 2.21 ( 486) hydrogen bonds : angle 4.08006 / 2.90 ( 1440) link_NAG-ASN : bond 0.00752 / 0.38 ( 2) link_NAG-ASN : angle 2.74056 / 1.24 ( 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 113 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.440 Fit side-chains REVERT: A 296 LYS cc_start: 0.8943 (tppt) cc_final: 0.8577 (mmmt) REVERT: A 304 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7889 (mm-30) REVERT: B 224 LEU cc_start: 0.9004 (tp) cc_final: 0.8785 (tm) REVERT: B 296 LYS cc_start: 0.8926 (tppt) cc_final: 0.8609 (mmmt) REVERT: B 304 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7647 (tm-30) outliers start: 16 outliers final: 11 residues processed: 112 average time/residue: 0.7839 time to fit residues: 96.6941 Evaluate side-chains 104 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.087856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.073428 restraints weight = 49262.675| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.88 r_work: 0.3058 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7578 Z= 0.144 Angle : 1.056 26.512 10342 Z= 0.458 Chirality : 0.183 1.705 1250 Planarity : 0.006 0.050 1236 Dihedral : 6.886 88.456 1056 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.11 % Favored : 93.67 % Rotamer: Outliers : 1.87 % Allowed : 24.81 % Favored : 73.32 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 (0.31), residues: 916 helix: 1.96 (0.21), residues: 694 sheet: None (None), residues: 0 loop : -1.27 (0.50), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 307 TYR 0.009 0.001 TYR B 353 PHE 0.016 0.001 PHE B 18 TRP 0.009 0.001 TRP B 49 HIS 0.003 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 ( 7576) covalent geometry : angle 1.05459 / 0.46 (10336) hydrogen bonds : bond 0.03452 / 2.17 ( 486) hydrogen bonds : angle 4.07172 / 2.89 ( 1440) link_NAG-ASN : bond 0.00743 / 0.37 ( 2) link_NAG-ASN : angle 2.71942 / 1.23 ( 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 111 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8965 (tppt) cc_final: 0.8593 (mmmt) REVERT: B 224 LEU cc_start: 0.8995 (tp) cc_final: 0.8789 (tm) REVERT: B 296 LYS cc_start: 0.8934 (tppt) cc_final: 0.8622 (mmmt) REVERT: B 304 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7633 (tm-30) outliers start: 15 outliers final: 13 residues processed: 110 average time/residue: 0.7817 time to fit residues: 94.6724 Evaluate side-chains 106 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.086893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.072514 restraints weight = 49359.635| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.85 r_work: 0.3036 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7578 Z= 0.158 Angle : 1.058 26.515 10342 Z= 0.460 Chirality : 0.183 1.705 1250 Planarity : 0.006 0.080 1236 Dihedral : 6.911 87.891 1056 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.22 % Favored : 93.56 % Rotamer: Outliers : 1.75 % Allowed : 24.94 % Favored : 73.32 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.69 (0.30), residues: 916 helix: 1.91 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -1.54 (0.49), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 307 TYR 0.011 0.001 TYR B 517 PHE 0.013 0.001 PHE A 314 TRP 0.009 0.001 TRP B 547 HIS 0.003 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 7576) covalent geometry : angle 1.05670 / 0.46 (10336) hydrogen bonds : bond 0.03518 / 2.21 ( 486) hydrogen bonds : angle 4.08479 / 2.90 ( 1440) link_NAG-ASN : bond 0.00712 / 0.36 ( 2) link_NAG-ASN : angle 2.67845 / 1.20 ( 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 109 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 236 GLN cc_start: 0.9428 (OUTLIER) cc_final: 0.8401 (mp10) REVERT: A 296 LYS cc_start: 0.8979 (tppt) cc_final: 0.8695 (mmpt) REVERT: B 224 LEU cc_start: 0.8990 (tp) cc_final: 0.8789 (tm) REVERT: B 296 LYS cc_start: 0.8940 (tppt) cc_final: 0.8632 (mmmt) REVERT: B 304 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7682 (tm-30) outliers start: 14 outliers final: 12 residues processed: 109 average time/residue: 0.8123 time to fit residues: 97.1755 Evaluate side-chains 105 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 19 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 76 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.087893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.073531 restraints weight = 49488.258| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.88 r_work: 0.3062 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7578 Z= 0.140 Angle : 1.058 26.567 10342 Z= 0.457 Chirality : 0.182 1.707 1250 Planarity : 0.006 0.049 1236 Dihedral : 6.906 85.792 1056 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.62 % Allowed : 24.81 % Favored : 73.57 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.74 (0.31), residues: 916 helix: 1.91 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.48 (0.51), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 307 TYR 0.010 0.001 TYR B 517 PHE 0.018 0.001 PHE A 18 TRP 0.009 0.001 TRP B 399 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 7576) covalent geometry : angle 1.05589 / 0.46 (10336) hydrogen bonds : bond 0.03415 / 2.14 ( 486) hydrogen bonds : angle 4.04510 / 2.87 ( 1440) link_NAG-ASN : bond 0.00754 / 0.38 ( 2) link_NAG-ASN : angle 2.68791 / 1.21 ( 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 110 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 236 GLN cc_start: 0.9406 (OUTLIER) cc_final: 0.8394 (mp10) REVERT: A 296 LYS cc_start: 0.8976 (tppt) cc_final: 0.8690 (mmpt) REVERT: B 296 LYS cc_start: 0.8939 (tppt) cc_final: 0.8631 (mmmt) REVERT: B 304 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7681 (tm-30) outliers start: 13 outliers final: 12 residues processed: 110 average time/residue: 0.7773 time to fit residues: 94.0070 Evaluate side-chains 104 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 61 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.086249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.071972 restraints weight = 48437.826| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.78 r_work: 0.2967 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7578 Z= 0.142 Angle : 1.059 26.495 10342 Z= 0.457 Chirality : 0.183 1.706 1250 Planarity : 0.006 0.067 1236 Dihedral : 6.895 86.123 1056 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.87 % Allowed : 24.56 % Favored : 73.57 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.73 (0.30), residues: 916 helix: 1.92 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.55 (0.50), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 307 TYR 0.011 0.001 TYR B 517 PHE 0.011 0.001 PHE A 314 TRP 0.009 0.001 TRP A 547 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 ( 7576) covalent geometry : angle 1.05735 / 0.46 (10336) hydrogen bonds : bond 0.03402 / 2.13 ( 486) hydrogen bonds : angle 4.03765 / 2.86 ( 1440) link_NAG-ASN : bond 0.00756 / 0.38 ( 2) link_NAG-ASN : angle 2.68052 / 1.21 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4784.00 seconds wall clock time: 81 minutes 49.81 seconds (4909.81 seconds total)