Starting phenix.real_space_refine on Wed Mar 4 05:39:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsg_32757/03_2026/7wsg_32757.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsg_32757/03_2026/7wsg_32757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wsg_32757/03_2026/7wsg_32757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsg_32757/03_2026/7wsg_32757.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wsg_32757/03_2026/7wsg_32757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsg_32757/03_2026/7wsg_32757.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5903 atoms to isotropic. 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 Zn 1 6.06 5 S 37 5.16 5 C 4102 2.51 5 N 1067 2.21 5 O 1206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6413 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4885 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 567} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1527 Classifications: {'peptide': 190} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 177} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.50, per 1000 atoms: 0.23 Number of scatterers: 6413 At special positions: 0 Unit cell: (80.949, 83.625, 120.42, 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) Zn 1 29.99 S 37 16.00 O 1206 8.00 N 1067 7.00 C 4102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 280.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1486 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 4 sheets defined 53.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 20 through 27 Processing helix chain 'A' and resid 27 through 53 removed outlier: 4.091A pdb=" N ASN A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 82 removed outlier: 3.611A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.647A pdb=" N LYS A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.777A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.653A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 154 removed outlier: 4.081A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 171 removed outlier: 3.585A pdb=" N TRP A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 194 Proline residue: A 178 - end of helix removed outlier: 3.620A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 218 through 252 removed outlier: 4.097A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.935A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 304 through 318 removed outlier: 3.806A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.838A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.866A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.628A pdb=" N ASN A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 450 removed outlier: 3.532A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 464 removed outlier: 4.478A pdb=" N GLU A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 474 removed outlier: 3.530A pdb=" N TRP A 473 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET A 474 " --> pdb=" O GLU A 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 470 through 474' Processing helix chain 'A' and resid 475 through 485 removed outlier: 3.523A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 531 removed outlier: 4.600A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 removed outlier: 3.694A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 560 " --> pdb=" O GLN A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.711A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.573A pdb=" N LEU B 374 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 371 through 375' Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 488 through 491 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.401A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'B' and resid 341 through 343 removed outlier: 3.539A pdb=" N ALA B 384 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 495 " --> pdb=" O TRP B 423 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP B 423 " --> pdb=" O ARG B 495 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 439 through 441 263 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2060 1.34 - 1.46: 1669 1.46 - 1.58: 2813 1.58 - 1.70: 0 1.70 - 1.81: 59 Bond restraints: 6601 Sorted by residual: bond pdb=" CA VAL B 507 " pdb=" CB VAL B 507 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 9.20e-01 bond pdb=" CB THR A 453 " pdb=" CG2 THR A 453 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.20e-01 bond pdb=" CG1 ILE A 379 " pdb=" CD1 ILE A 379 " ideal model delta sigma weight residual 1.513 1.488 0.025 3.90e-02 6.57e+02 4.06e-01 bond pdb=" CB PRO B 470 " pdb=" CG PRO B 470 " ideal model delta sigma weight residual 1.506 1.482 0.024 3.90e-02 6.57e+02 3.64e-01 bond pdb=" N THR B 468 " pdb=" CA THR B 468 " ideal model delta sigma weight residual 1.460 1.453 0.007 1.29e-02 6.01e+03 3.15e-01 ... (remaining 6596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 8820 1.64 - 3.28: 125 3.28 - 4.92: 22 4.92 - 6.56: 3 6.56 - 8.19: 2 Bond angle restraints: 8972 Sorted by residual: angle pdb=" N ALA A 304 " pdb=" CA ALA A 304 " pdb=" C ALA A 304 " ideal model delta sigma weight residual 114.62 110.96 3.66 1.14e+00 7.69e-01 1.03e+01 angle pdb=" CA ALA A 304 " pdb=" C ALA A 304 " pdb=" N ARG A 305 " ideal model delta sigma weight residual 119.71 116.33 3.38 1.17e+00 7.31e-01 8.34e+00 angle pdb=" CA LEU A 266 " pdb=" CB LEU A 266 " pdb=" CG LEU A 266 " ideal model delta sigma weight residual 116.30 124.49 -8.19 3.50e+00 8.16e-02 5.48e+00 angle pdb=" CA LEU B 421 " pdb=" CB LEU B 421 " pdb=" CG LEU B 421 " ideal model delta sigma weight residual 116.30 124.30 -8.00 3.50e+00 8.16e-02 5.23e+00 angle pdb=" CA TYR A 385 " pdb=" CB TYR A 385 " pdb=" CG TYR A 385 " ideal model delta sigma weight residual 113.90 117.91 -4.01 1.80e+00 3.09e-01 4.95e+00 ... (remaining 8967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 3563 16.40 - 32.80: 252 32.80 - 49.20: 54 49.20 - 65.60: 24 65.60 - 82.00: 5 Dihedral angle restraints: 3898 sinusoidal: 1582 harmonic: 2316 Sorted by residual: dihedral pdb=" CA ALA A 396 " pdb=" C ALA A 396 " pdb=" N ASN A 397 " pdb=" CA ASN A 397 " ideal model delta harmonic sigma weight residual 180.00 162.19 17.81 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA LYS A 475 " pdb=" C LYS A 475 " pdb=" N LYS A 476 " pdb=" CA LYS A 476 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASP A 499 " pdb=" CB ASP A 499 " pdb=" CG ASP A 499 " pdb=" OD1 ASP A 499 " ideal model delta sinusoidal sigma weight residual -30.00 -85.77 55.77 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 3895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 485 0.026 - 0.052: 283 0.052 - 0.078: 100 0.078 - 0.103: 47 0.103 - 0.129: 11 Chirality restraints: 926 Sorted by residual: chirality pdb=" CG LEU A 266 " pdb=" CB LEU A 266 " pdb=" CD1 LEU A 266 " pdb=" CD2 LEU A 266 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA VAL B 420 " pdb=" N VAL B 420 " pdb=" C VAL B 420 " pdb=" CB VAL B 420 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.18e-01 chirality pdb=" CA PRO B 477 " pdb=" N PRO B 477 " pdb=" C PRO B 477 " pdb=" CB PRO B 477 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.04e-01 ... (remaining 923 not shown) Planarity restraints: 1163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 146 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 489 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO A 490 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 490 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 490 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 291 " -0.006 2.00e-02 2.50e+03 1.25e-02 1.57e+00 pdb=" C ILE A 291 " 0.022 2.00e-02 2.50e+03 pdb=" O ILE A 291 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP A 292 " -0.007 2.00e-02 2.50e+03 ... (remaining 1160 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 81 2.63 - 3.19: 5785 3.19 - 3.76: 10416 3.76 - 4.33: 14655 4.33 - 4.90: 23875 Nonbonded interactions: 54812 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.058 2.230 nonbonded pdb=" O THR A 125 " pdb=" OG1 THR A 129 " model vdw 2.207 3.040 nonbonded pdb=" O THR A 449 " pdb=" OG1 THR A 453 " model vdw 2.226 3.040 nonbonded pdb=" NH1 ARG A 245 " pdb=" O PRO A 258 " model vdw 2.235 3.120 nonbonded pdb=" OG1 THR A 276 " pdb=" OG1 THR A 445 " model vdw 2.245 3.040 ... (remaining 54807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.850 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6609 Z= 0.117 Angle : 0.524 8.195 8984 Z= 0.275 Chirality : 0.039 0.129 926 Planarity : 0.003 0.039 1163 Dihedral : 12.816 81.998 2394 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.60 % Allowed : 11.08 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -1.05 (0.29), residues: 783 helix: -0.44 (0.27), residues: 344 sheet: -1.89 (1.09), residues: 23 loop : -0.76 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 161 TYR 0.020 0.001 TYR A 385 PHE 0.009 0.001 PHE A 369 TRP 0.010 0.001 TRP A 328 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6601) covalent geometry : angle 0.52388 ( 8972) SS BOND : bond 0.00228 ( 6) SS BOND : angle 0.60592 ( 12) hydrogen bonds : bond 0.28332 ( 263) hydrogen bonds : angle 9.52979 ( 759) metal coordination : bond 0.00144 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6271 (mp) REVERT: A 480 MET cc_start: 0.6049 (OUTLIER) cc_final: 0.5717 (mtp) REVERT: A 552 GLN cc_start: 0.7338 (mt0) cc_final: 0.7028 (pt0) REVERT: A 597 GLU cc_start: 0.8382 (tt0) cc_final: 0.7916 (tm-30) REVERT: B 365 LYS cc_start: 0.7484 (ttmt) cc_final: 0.7111 (mtpp) REVERT: B 396 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6632 (mt0) REVERT: B 498 VAL cc_start: 0.7580 (t) cc_final: 0.7342 (m) outliers start: 32 outliers final: 14 residues processed: 159 average time/residue: 0.0868 time to fit residues: 18.0088 Evaluate side-chains 121 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.184172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.161700 restraints weight = 9360.413| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 2.20 r_work: 0.3993 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3871 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6609 Z= 0.148 Angle : 0.605 7.995 8984 Z= 0.313 Chirality : 0.043 0.199 926 Planarity : 0.004 0.041 1163 Dihedral : 7.570 63.380 891 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.45 % Allowed : 15.11 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -1.08 (0.28), residues: 783 helix: -0.35 (0.26), residues: 357 sheet: -1.51 (1.17), residues: 23 loop : -0.92 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 600 TYR 0.023 0.002 TYR A 385 PHE 0.021 0.002 PHE A 369 TRP 0.011 0.001 TRP A 594 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6601) covalent geometry : angle 0.60472 ( 8972) SS BOND : bond 0.00192 ( 6) SS BOND : angle 0.48808 ( 12) hydrogen bonds : bond 0.05584 ( 263) hydrogen bonds : angle 6.05659 ( 759) metal coordination : bond 0.00211 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.5931 (t70) REVERT: A 485 VAL cc_start: 0.7127 (OUTLIER) cc_final: 0.6847 (t) REVERT: A 552 GLN cc_start: 0.7227 (mt0) cc_final: 0.7023 (pt0) REVERT: A 597 GLU cc_start: 0.8168 (tt0) cc_final: 0.7819 (tm-30) REVERT: B 328 VAL cc_start: 0.5046 (OUTLIER) cc_final: 0.4811 (p) REVERT: B 396 GLN cc_start: 0.6819 (OUTLIER) cc_final: 0.6495 (mt0) outliers start: 24 outliers final: 17 residues processed: 130 average time/residue: 0.0653 time to fit residues: 11.6859 Evaluate side-chains 116 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 373 HIS ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.183891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.162068 restraints weight = 9273.889| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 2.15 r_work: 0.4001 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6609 Z= 0.134 Angle : 0.553 7.716 8984 Z= 0.286 Chirality : 0.041 0.134 926 Planarity : 0.004 0.038 1163 Dihedral : 7.063 58.644 884 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.74 % Allowed : 15.97 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.85 (0.28), residues: 783 helix: -0.14 (0.26), residues: 356 sheet: -1.46 (1.25), residues: 23 loop : -0.82 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 495 TYR 0.025 0.001 TYR A 237 PHE 0.018 0.002 PHE B 364 TRP 0.029 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6601) covalent geometry : angle 0.55305 ( 8972) SS BOND : bond 0.00207 ( 6) SS BOND : angle 0.40420 ( 12) hydrogen bonds : bond 0.04900 ( 263) hydrogen bonds : angle 5.63409 ( 759) metal coordination : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 VAL cc_start: 0.7186 (OUTLIER) cc_final: 0.6911 (t) REVERT: A 597 GLU cc_start: 0.8196 (tt0) cc_final: 0.7858 (tm-30) REVERT: B 328 VAL cc_start: 0.5050 (OUTLIER) cc_final: 0.4820 (p) REVERT: B 367 TYR cc_start: 0.7025 (m-80) cc_final: 0.6591 (m-80) REVERT: B 396 GLN cc_start: 0.6822 (OUTLIER) cc_final: 0.6523 (mt0) outliers start: 26 outliers final: 18 residues processed: 121 average time/residue: 0.0679 time to fit residues: 11.3267 Evaluate side-chains 113 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.183456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.161452 restraints weight = 9259.152| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.16 r_work: 0.3997 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3873 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6609 Z= 0.139 Angle : 0.561 9.299 8984 Z= 0.285 Chirality : 0.042 0.229 926 Planarity : 0.004 0.041 1163 Dihedral : 6.944 54.443 883 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.32 % Allowed : 16.98 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.72 (0.29), residues: 783 helix: -0.02 (0.27), residues: 354 sheet: -1.21 (1.26), residues: 23 loop : -0.78 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 495 TYR 0.024 0.002 TYR A 237 PHE 0.016 0.002 PHE A 523 TRP 0.019 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6601) covalent geometry : angle 0.56141 ( 8972) SS BOND : bond 0.00220 ( 6) SS BOND : angle 0.39760 ( 12) hydrogen bonds : bond 0.04519 ( 263) hydrogen bonds : angle 5.48337 ( 759) metal coordination : bond 0.00121 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 485 VAL cc_start: 0.7239 (OUTLIER) cc_final: 0.6996 (t) REVERT: A 597 GLU cc_start: 0.8182 (tt0) cc_final: 0.7886 (tm-30) REVERT: B 328 VAL cc_start: 0.5058 (OUTLIER) cc_final: 0.4812 (p) outliers start: 30 outliers final: 22 residues processed: 121 average time/residue: 0.0727 time to fit residues: 12.0976 Evaluate side-chains 115 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 60 optimal weight: 0.0970 chunk 67 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.184920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.163299 restraints weight = 9429.299| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 2.15 r_work: 0.4019 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3895 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6609 Z= 0.115 Angle : 0.529 7.406 8984 Z= 0.271 Chirality : 0.041 0.178 926 Planarity : 0.004 0.041 1163 Dihedral : 6.189 53.976 879 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.17 % Allowed : 17.41 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.65 (0.29), residues: 783 helix: 0.07 (0.27), residues: 362 sheet: -0.97 (1.28), residues: 23 loop : -0.80 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 495 TYR 0.021 0.001 TYR A 385 PHE 0.015 0.001 PHE A 523 TRP 0.026 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6601) covalent geometry : angle 0.52916 ( 8972) SS BOND : bond 0.00224 ( 6) SS BOND : angle 0.47457 ( 12) hydrogen bonds : bond 0.04187 ( 263) hydrogen bonds : angle 5.41015 ( 759) metal coordination : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 485 VAL cc_start: 0.7237 (OUTLIER) cc_final: 0.6990 (t) REVERT: A 597 GLU cc_start: 0.8156 (tt0) cc_final: 0.7875 (tm-30) outliers start: 29 outliers final: 22 residues processed: 123 average time/residue: 0.0647 time to fit residues: 11.2347 Evaluate side-chains 116 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 0.0020 chunk 38 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 70 optimal weight: 0.0670 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 58 optimal weight: 0.0020 chunk 36 optimal weight: 0.0060 overall best weight: 0.1350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.188158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.166579 restraints weight = 9349.707| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 2.17 r_work: 0.4061 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3938 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6609 Z= 0.097 Angle : 0.508 7.027 8984 Z= 0.261 Chirality : 0.039 0.145 926 Planarity : 0.004 0.039 1163 Dihedral : 5.943 59.105 879 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.60 % Allowed : 17.84 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.40 (0.29), residues: 783 helix: 0.30 (0.27), residues: 363 sheet: -0.57 (1.32), residues: 23 loop : -0.72 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 495 TYR 0.024 0.001 TYR A 41 PHE 0.013 0.001 PHE A 523 TRP 0.029 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 6601) covalent geometry : angle 0.50785 ( 8972) SS BOND : bond 0.00108 ( 6) SS BOND : angle 0.40888 ( 12) hydrogen bonds : bond 0.03814 ( 263) hydrogen bonds : angle 5.18132 ( 759) metal coordination : bond 0.00089 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 485 VAL cc_start: 0.7114 (OUTLIER) cc_final: 0.6788 (t) REVERT: A 573 VAL cc_start: 0.8164 (OUTLIER) cc_final: 0.7866 (p) REVERT: A 597 GLU cc_start: 0.8046 (tt0) cc_final: 0.7806 (tm-30) outliers start: 25 outliers final: 17 residues processed: 121 average time/residue: 0.0600 time to fit residues: 10.3119 Evaluate side-chains 111 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 232 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.184741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.162854 restraints weight = 9336.882| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 2.17 r_work: 0.4012 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6609 Z= 0.131 Angle : 0.544 6.024 8984 Z= 0.281 Chirality : 0.042 0.251 926 Planarity : 0.004 0.038 1163 Dihedral : 5.277 59.331 871 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.02 % Allowed : 19.28 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.45 (0.29), residues: 783 helix: 0.20 (0.27), residues: 362 sheet: -0.84 (1.27), residues: 23 loop : -0.65 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 495 TYR 0.022 0.001 TYR A 385 PHE 0.015 0.001 PHE A 523 TRP 0.030 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6601) covalent geometry : angle 0.54464 ( 8972) SS BOND : bond 0.00210 ( 6) SS BOND : angle 0.41362 ( 12) hydrogen bonds : bond 0.04091 ( 263) hydrogen bonds : angle 5.27627 ( 759) metal coordination : bond 0.00141 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TRP cc_start: 0.7186 (OUTLIER) cc_final: 0.6608 (t60) REVERT: A 485 VAL cc_start: 0.7232 (OUTLIER) cc_final: 0.6958 (t) REVERT: A 597 GLU cc_start: 0.8117 (tt0) cc_final: 0.7876 (tm-30) outliers start: 21 outliers final: 17 residues processed: 107 average time/residue: 0.0630 time to fit residues: 9.6574 Evaluate side-chains 111 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 378 HIS ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.183709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.161717 restraints weight = 9327.042| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.15 r_work: 0.3999 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3878 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.767 6609 Z= 0.344 Angle : 0.555 6.789 8984 Z= 0.285 Chirality : 0.042 0.253 926 Planarity : 0.004 0.040 1163 Dihedral : 5.369 58.881 871 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.02 % Allowed : 19.86 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.49 (0.29), residues: 783 helix: 0.15 (0.27), residues: 361 sheet: -0.94 (1.25), residues: 23 loop : -0.64 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 495 TYR 0.022 0.002 TYR A 385 PHE 0.017 0.001 PHE A 523 TRP 0.024 0.001 TRP A 163 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6601) covalent geometry : angle 0.55489 ( 8972) SS BOND : bond 0.00240 ( 6) SS BOND : angle 0.44380 ( 12) hydrogen bonds : bond 0.04152 ( 263) hydrogen bonds : angle 5.28136 ( 759) metal coordination : bond 0.54249 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 597 GLU cc_start: 0.8128 (tt0) cc_final: 0.7876 (tm-30) outliers start: 21 outliers final: 16 residues processed: 109 average time/residue: 0.0594 time to fit residues: 9.4364 Evaluate side-chains 107 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 chunk 2 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.185631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.163630 restraints weight = 9580.120| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.22 r_work: 0.4024 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3901 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6609 Z= 0.114 Angle : 0.535 7.094 8984 Z= 0.275 Chirality : 0.041 0.237 926 Planarity : 0.004 0.039 1163 Dihedral : 5.166 54.451 871 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.73 % Allowed : 20.29 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.41 (0.29), residues: 783 helix: 0.22 (0.27), residues: 370 sheet: -0.83 (1.27), residues: 23 loop : -0.62 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 495 TYR 0.020 0.001 TYR A 385 PHE 0.014 0.001 PHE A 523 TRP 0.037 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6601) covalent geometry : angle 0.53528 ( 8972) SS BOND : bond 0.00185 ( 6) SS BOND : angle 0.39833 ( 12) hydrogen bonds : bond 0.03904 ( 263) hydrogen bonds : angle 5.16709 ( 759) metal coordination : bond 0.00420 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TRP cc_start: 0.6992 (OUTLIER) cc_final: 0.6543 (t60) REVERT: A 597 GLU cc_start: 0.8095 (tt0) cc_final: 0.7842 (tm-30) REVERT: B 508 LEU cc_start: 0.2861 (OUTLIER) cc_final: 0.2523 (tm) outliers start: 19 outliers final: 16 residues processed: 106 average time/residue: 0.0646 time to fit residues: 9.7199 Evaluate side-chains 108 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 34 optimal weight: 0.0020 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.184793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.162869 restraints weight = 9275.109| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.20 r_work: 0.4022 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6609 Z= 0.118 Angle : 0.537 6.865 8984 Z= 0.275 Chirality : 0.041 0.235 926 Planarity : 0.004 0.039 1163 Dihedral : 5.107 50.786 871 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.59 % Allowed : 20.29 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.29 (0.30), residues: 783 helix: 0.31 (0.27), residues: 365 sheet: -0.91 (1.27), residues: 23 loop : -0.54 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 495 TYR 0.020 0.001 TYR A 385 PHE 0.015 0.001 PHE A 523 TRP 0.032 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6601) covalent geometry : angle 0.53665 ( 8972) SS BOND : bond 0.00195 ( 6) SS BOND : angle 0.43989 ( 12) hydrogen bonds : bond 0.03913 ( 263) hydrogen bonds : angle 5.12091 ( 759) metal coordination : bond 0.00117 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TRP cc_start: 0.6989 (OUTLIER) cc_final: 0.6515 (t60) REVERT: A 266 LEU cc_start: 0.7251 (mt) cc_final: 0.7010 (mt) REVERT: A 473 TRP cc_start: 0.5438 (OUTLIER) cc_final: 0.4797 (t60) REVERT: A 597 GLU cc_start: 0.8121 (tt0) cc_final: 0.7861 (tm-30) REVERT: B 508 LEU cc_start: 0.2832 (OUTLIER) cc_final: 0.2497 (tm) outliers start: 18 outliers final: 13 residues processed: 105 average time/residue: 0.0623 time to fit residues: 9.6013 Evaluate side-chains 106 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0980 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 48 optimal weight: 0.0970 chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.186168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.163613 restraints weight = 9495.938| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 2.29 r_work: 0.4030 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6609 Z= 0.110 Angle : 0.529 7.069 8984 Z= 0.272 Chirality : 0.041 0.227 926 Planarity : 0.004 0.038 1163 Dihedral : 4.824 44.324 869 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.45 % Allowed : 20.72 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.17 (0.30), residues: 783 helix: 0.46 (0.28), residues: 361 sheet: -0.85 (1.27), residues: 23 loop : -0.53 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 495 TYR 0.020 0.001 TYR A 385 PHE 0.014 0.001 PHE A 523 TRP 0.032 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 6601) covalent geometry : angle 0.52889 ( 8972) SS BOND : bond 0.00170 ( 6) SS BOND : angle 0.44458 ( 12) hydrogen bonds : bond 0.03830 ( 263) hydrogen bonds : angle 5.05674 ( 759) metal coordination : bond 0.00122 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1932.13 seconds wall clock time: 33 minutes 39.46 seconds (2019.46 seconds total)