Starting phenix.real_space_refine on Tue Mar 3 15:46:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q3v_72208/03_2026/9q3v_72208.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q3v_72208/03_2026/9q3v_72208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q3v_72208/03_2026/9q3v_72208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q3v_72208/03_2026/9q3v_72208.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q3v_72208/03_2026/9q3v_72208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q3v_72208/03_2026/9q3v_72208.map" } resolution = 3.3 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= -0.001 sd= 0.037 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: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 4148 2.51 5 N 1066 2.21 5 O 1230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 6482 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1540 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 13, 'TRANS': 180} Chain: "A" Number of atoms: 4886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4886 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 24, 'TRANS': 570} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.12, per 1000 atoms: 0.17 Number of scatterers: 6482 At special positions: 0 Unit cell: (72.384, 99.008, 122.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1230 8.00 N 1066 7.00 C 4148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 529 " - pdb=" SG CYS A 541 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 431 " " NAG A 704 " - " ASN A 545 " Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 135.1 milliseconds 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 3 sheets defined 50.1% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.643A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.842A pdb=" N HIS A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.681A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.864A pdb=" N LYS A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ARG A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 146 through 151 removed outlier: 3.861A pdb=" N MET A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 156 through 172 Processing helix chain 'A' and resid 175 through 193 removed outlier: 3.618A pdb=" N TYR A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 203 Processing helix chain 'A' and resid 219 through 251 removed outlier: 3.661A pdb=" N LYS A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A 231 " --> pdb=" O HIS A 227 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) Proline residue: A 234 - end of helix removed outlier: 3.863A pdb=" N ASP A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 292 through 299 removed outlier: 3.883A pdb=" N MET A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 317 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 364 through 382 Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 400 through 410 removed outlier: 3.885A pdb=" N GLY A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 430 through 446 removed outlier: 4.315A pdb=" N ASN A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 471 through 484 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 512 through 532 removed outlier: 4.407A pdb=" N THR A 518 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'A' and resid 559 through 563 removed outlier: 3.564A pdb=" N SER A 562 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU A 563 " --> pdb=" O GLY A 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 559 through 563' Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 587 through 598 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.747A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 348 removed outlier: 3.766A pdb=" N THR A 346 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A 358 " --> pdb=" O THR A 346 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 786 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: 0.89 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2055 1.34 - 1.46: 1700 1.46 - 1.58: 2851 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 6666 Sorted by residual: bond pdb=" C5 NAG A 704 " pdb=" O5 NAG A 704 " ideal model delta sigma weight residual 1.413 1.442 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C5 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.413 1.439 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C ALA B 372 " pdb=" N PRO B 373 " ideal model delta sigma weight residual 1.328 1.344 -0.016 1.26e-02 6.30e+03 1.65e+00 bond pdb=" CD2 HIS A 227 " pdb=" NE2 HIS A 227 " ideal model delta sigma weight residual 1.374 1.361 0.013 1.10e-02 8.26e+03 1.47e+00 bond pdb=" C5 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.39e+00 ... (remaining 6661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 8936 2.65 - 5.30: 99 5.30 - 7.95: 11 7.95 - 10.60: 1 10.60 - 13.24: 2 Bond angle restraints: 9049 Sorted by residual: angle pdb=" N PHE B 375 " pdb=" CA PHE B 375 " pdb=" C PHE B 375 " ideal model delta sigma weight residual 114.75 108.62 6.13 1.26e+00 6.30e-01 2.37e+01 angle pdb=" C2 NAG A 703 " pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 110.06 123.30 -13.24 3.00e+00 1.11e-01 1.95e+01 angle pdb=" CA LYS B 378 " pdb=" CB LYS B 378 " pdb=" CG LYS B 378 " ideal model delta sigma weight residual 114.10 122.31 -8.21 2.00e+00 2.50e-01 1.69e+01 angle pdb=" C ALA A 263 " pdb=" N HIS A 264 " pdb=" CA HIS A 264 " ideal model delta sigma weight residual 121.54 128.77 -7.23 1.91e+00 2.74e-01 1.43e+01 angle pdb=" N PHE B 374 " pdb=" CA PHE B 374 " pdb=" C PHE B 374 " ideal model delta sigma weight residual 107.32 112.99 -5.67 1.65e+00 3.67e-01 1.18e+01 ... (remaining 9044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 3267 17.78 - 35.56: 512 35.56 - 53.34: 159 53.34 - 71.12: 45 71.12 - 88.90: 10 Dihedral angle restraints: 3993 sinusoidal: 1667 harmonic: 2326 Sorted by residual: dihedral pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " pdb=" SG CYS A 360 " pdb=" CB CYS A 360 " ideal model delta sinusoidal sigma weight residual 93.00 -179.06 -87.94 1 1.00e+01 1.00e-02 9.25e+01 dihedral pdb=" CA PHE B 374 " pdb=" C PHE B 374 " pdb=" N PHE B 375 " pdb=" CA PHE B 375 " ideal model delta harmonic sigma weight residual 180.00 152.92 27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA PRO A 262 " pdb=" C PRO A 262 " pdb=" N ALA A 263 " pdb=" CA ALA A 263 " ideal model delta harmonic sigma weight residual -180.00 -153.58 -26.42 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 3990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.220: 950 0.220 - 0.440: 1 0.440 - 0.659: 0 0.659 - 0.879: 0 0.879 - 1.099: 1 Chirality restraints: 952 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 431 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.30 -1.10 2.00e-01 2.50e+01 3.02e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CA ASP A 508 " pdb=" N ASP A 508 " pdb=" C ASP A 508 " pdb=" CB ASP A 508 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.34e-01 ... (remaining 949 not shown) Planarity restraints: 1164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 702 " 0.302 2.00e-02 2.50e+03 2.57e-01 8.28e+02 pdb=" C7 NAG A 702 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG A 702 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG A 702 " -0.451 2.00e-02 2.50e+03 pdb=" O7 NAG A 702 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 703 " 0.257 2.00e-02 2.50e+03 2.18e-01 5.95e+02 pdb=" C7 NAG A 703 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG A 703 " 0.166 2.00e-02 2.50e+03 pdb=" N2 NAG A 703 " -0.375 2.00e-02 2.50e+03 pdb=" O7 NAG A 703 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 704 " 0.142 2.00e-02 2.50e+03 1.16e-01 1.69e+02 pdb=" C7 NAG A 704 " -0.044 2.00e-02 2.50e+03 pdb=" C8 NAG A 704 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG A 704 " -0.183 2.00e-02 2.50e+03 pdb=" O7 NAG A 704 " -0.021 2.00e-02 2.50e+03 ... (remaining 1161 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 94 2.69 - 3.24: 6640 3.24 - 3.80: 10583 3.80 - 4.35: 13142 4.35 - 4.90: 21620 Nonbonded interactions: 52079 Sorted by model distance: nonbonded pdb=" O LYS A 223 " pdb=" ND1 HIS A 227 " model vdw 2.142 3.120 nonbonded pdb=" O ASP B 428 " pdb=" OD1 ASP B 428 " model vdw 2.399 3.040 nonbonded pdb=" O4 NAG A 703 " pdb=" O6 NAG A 703 " model vdw 2.435 3.040 nonbonded pdb=" O VAL A 59 " pdb=" OD1 ASN A 63 " model vdw 2.460 3.040 nonbonded pdb=" O4 NAG A 701 " pdb=" O6 NAG A 701 " model vdw 2.501 3.040 ... (remaining 52074 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: 18.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.880 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 0.038 6675 Z= 0.150 Angle : 0.698 13.245 9071 Z= 0.362 Chirality : 0.057 1.099 952 Planarity : 0.011 0.257 1160 Dihedral : 19.468 88.896 2486 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.13 % Favored : 92.74 % Rotamer: Outliers : 5.48 % Allowed : 33.77 % Favored : 60.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.30), residues: 785 helix: 0.97 (0.28), residues: 360 sheet: 0.55 (0.88), residues: 40 loop : -1.98 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 509 TYR 0.020 0.001 TYR A 157 PHE 0.012 0.001 PHE A 522 TRP 0.012 0.001 TRP A 565 HIS 0.010 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6666) covalent geometry : angle 0.68112 ( 9049) SS BOND : bond 0.00292 ( 5) SS BOND : angle 0.69523 ( 10) hydrogen bonds : bond 0.15298 ( 272) hydrogen bonds : angle 6.01452 ( 786) link_NAG-ASN : bond 0.00174 ( 4) link_NAG-ASN : angle 4.20339 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 69 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 441 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7664 (mp) REVERT: B 467 ASP cc_start: 0.8014 (t0) cc_final: 0.7779 (t0) REVERT: B 519 HIS cc_start: 0.7674 (p90) cc_final: 0.7246 (p90) REVERT: A 83 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.5385 (p90) REVERT: A 202 TRP cc_start: 0.8658 (OUTLIER) cc_final: 0.8129 (m-10) REVERT: A 214 TYR cc_start: 0.6585 (OUTLIER) cc_final: 0.6052 (m-10) REVERT: A 231 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8330 (mt-10) REVERT: A 246 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7328 (tppt) REVERT: A 254 TYR cc_start: 0.6435 (m-80) cc_final: 0.5956 (m-10) REVERT: A 331 MET cc_start: 0.7905 (ttt) cc_final: 0.7566 (ttt) REVERT: A 339 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.8000 (ptp-170) REVERT: A 348 TRP cc_start: 0.8519 (OUTLIER) cc_final: 0.7119 (m-90) REVERT: A 432 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6952 (pm20) REVERT: A 517 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7713 (ppt-90) outliers start: 38 outliers final: 23 residues processed: 102 average time/residue: 0.0696 time to fit residues: 9.8704 Evaluate side-chains 98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 214 TYR Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 348 TRP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 554 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.0060 overall best weight: 0.9378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** 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 = 0.3908 r_free = 0.3908 target = 0.115750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.096404 restraints weight = 18209.045| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.11 r_work: 0.3459 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6675 Z= 0.148 Angle : 0.615 8.615 9071 Z= 0.311 Chirality : 0.043 0.183 952 Planarity : 0.004 0.051 1160 Dihedral : 9.878 74.933 1018 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.41 % Favored : 91.46 % Rotamer: Outliers : 6.35 % Allowed : 32.90 % Favored : 60.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.57 (0.31), residues: 785 helix: 1.10 (0.28), residues: 359 sheet: -0.12 (0.94), residues: 40 loop : -1.93 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 392 TYR 0.014 0.001 TYR A 515 PHE 0.015 0.001 PHE A 326 TRP 0.010 0.001 TRP A 565 HIS 0.010 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 6666) covalent geometry : angle 0.60411 ( 9049) SS BOND : bond 0.00415 ( 5) SS BOND : angle 0.69175 ( 10) hydrogen bonds : bond 0.04768 ( 272) hydrogen bonds : angle 5.08562 ( 786) link_NAG-ASN : bond 0.00096 ( 4) link_NAG-ASN : angle 3.23720 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 75 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 335 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8097 (tt) REVERT: B 441 LEU cc_start: 0.8309 (pp) cc_final: 0.7829 (mp) REVERT: A 45 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8507 (tt) REVERT: A 83 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.5158 (p90) REVERT: A 202 TRP cc_start: 0.8785 (OUTLIER) cc_final: 0.8268 (m-10) REVERT: A 214 TYR cc_start: 0.6721 (OUTLIER) cc_final: 0.5899 (m-10) REVERT: A 254 TYR cc_start: 0.6537 (m-80) cc_final: 0.6009 (m-10) REVERT: A 432 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7057 (pm20) REVERT: A 513 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8208 (mtp180) outliers start: 44 outliers final: 22 residues processed: 109 average time/residue: 0.0743 time to fit residues: 10.9929 Evaluate side-chains 96 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 214 TYR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 0.0770 chunk 59 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** 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 = 0.3905 r_free = 0.3905 target = 0.115697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.096298 restraints weight = 18230.551| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.11 r_work: 0.3457 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6675 Z= 0.140 Angle : 0.606 7.369 9071 Z= 0.306 Chirality : 0.042 0.174 952 Planarity : 0.004 0.052 1160 Dihedral : 8.492 58.270 983 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.41 % Favored : 91.46 % Rotamer: Outliers : 5.92 % Allowed : 32.47 % Favored : 61.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 (0.31), residues: 785 helix: 1.11 (0.28), residues: 363 sheet: -0.35 (0.76), residues: 55 loop : -1.88 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 392 TYR 0.013 0.001 TYR A 515 PHE 0.015 0.001 PHE A 522 TRP 0.011 0.001 TRP A 565 HIS 0.010 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6666) covalent geometry : angle 0.59897 ( 9049) SS BOND : bond 0.00399 ( 5) SS BOND : angle 0.54835 ( 10) hydrogen bonds : bond 0.04398 ( 272) hydrogen bonds : angle 4.92314 ( 786) link_NAG-ASN : bond 0.00117 ( 4) link_NAG-ASN : angle 2.62078 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 70 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8112 (tt) REVERT: B 441 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7833 (mp) REVERT: B 462 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8333 (mmtm) REVERT: B 467 ASP cc_start: 0.8008 (t0) cc_final: 0.7757 (t0) REVERT: A 45 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8533 (tt) REVERT: A 83 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.5289 (p90) REVERT: A 202 TRP cc_start: 0.8784 (OUTLIER) cc_final: 0.8214 (m-10) REVERT: A 254 TYR cc_start: 0.6454 (m-80) cc_final: 0.6005 (m-10) REVERT: A 502 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8494 (tt) outliers start: 41 outliers final: 26 residues processed: 102 average time/residue: 0.0588 time to fit residues: 8.5922 Evaluate side-chains 99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 66 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.115082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.095743 restraints weight = 18382.270| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.12 r_work: 0.3446 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6675 Z= 0.148 Angle : 0.594 7.190 9071 Z= 0.302 Chirality : 0.043 0.165 952 Planarity : 0.004 0.052 1160 Dihedral : 7.981 58.780 976 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.04 % Favored : 90.83 % Rotamer: Outliers : 8.37 % Allowed : 30.59 % Favored : 61.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.42 (0.31), residues: 785 helix: 1.20 (0.28), residues: 354 sheet: -0.39 (0.75), residues: 55 loop : -1.79 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 509 TYR 0.014 0.001 TYR A 515 PHE 0.016 0.001 PHE A 522 TRP 0.011 0.001 TRP A 565 HIS 0.010 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6666) covalent geometry : angle 0.58855 ( 9049) SS BOND : bond 0.00434 ( 5) SS BOND : angle 0.51120 ( 10) hydrogen bonds : bond 0.04341 ( 272) hydrogen bonds : angle 4.90369 ( 786) link_NAG-ASN : bond 0.00126 ( 4) link_NAG-ASN : angle 2.37965 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 73 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 335 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8114 (tt) REVERT: B 441 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7777 (mp) REVERT: B 462 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8329 (mmtm) REVERT: B 467 ASP cc_start: 0.8057 (t0) cc_final: 0.7808 (t0) REVERT: A 45 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8619 (tt) REVERT: A 79 MET cc_start: 0.7940 (mpp) cc_final: 0.7640 (mpp) REVERT: A 83 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.5317 (p90) REVERT: A 202 TRP cc_start: 0.8798 (OUTLIER) cc_final: 0.8238 (m-10) REVERT: A 254 TYR cc_start: 0.6551 (m-80) cc_final: 0.6019 (m-10) REVERT: A 432 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7096 (pm20) REVERT: A 502 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8544 (tt) REVERT: A 513 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8203 (mtp180) REVERT: A 517 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7869 (ppt-90) outliers start: 58 outliers final: 34 residues processed: 121 average time/residue: 0.0588 time to fit residues: 10.1130 Evaluate side-chains 111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 67 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** 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 = 0.3898 r_free = 0.3898 target = 0.115384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.097293 restraints weight = 18434.445| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.88 r_work: 0.3471 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6675 Z= 0.141 Angle : 0.603 11.220 9071 Z= 0.305 Chirality : 0.043 0.165 952 Planarity : 0.004 0.052 1160 Dihedral : 7.879 57.289 974 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.17 % Favored : 90.70 % Rotamer: Outliers : 7.36 % Allowed : 32.32 % Favored : 60.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.38 (0.31), residues: 785 helix: 1.25 (0.28), residues: 354 sheet: -0.38 (0.75), residues: 55 loop : -1.77 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 509 TYR 0.013 0.001 TYR A 515 PHE 0.015 0.001 PHE A 522 TRP 0.011 0.001 TRP A 565 HIS 0.010 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6666) covalent geometry : angle 0.59753 ( 9049) SS BOND : bond 0.00451 ( 5) SS BOND : angle 0.84397 ( 10) hydrogen bonds : bond 0.04268 ( 272) hydrogen bonds : angle 4.81480 ( 786) link_NAG-ASN : bond 0.00163 ( 4) link_NAG-ASN : angle 2.22581 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 67 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 335 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8112 (tt) REVERT: B 441 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7763 (mp) REVERT: B 462 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8341 (mmtm) REVERT: B 467 ASP cc_start: 0.8070 (t0) cc_final: 0.7837 (t0) REVERT: A 45 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8629 (tt) REVERT: A 83 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.5446 (p90) REVERT: A 133 LEU cc_start: 0.6262 (pp) cc_final: 0.5929 (mt) REVERT: A 202 TRP cc_start: 0.8817 (OUTLIER) cc_final: 0.8256 (m-10) REVERT: A 254 TYR cc_start: 0.6474 (m-80) cc_final: 0.6015 (m-10) REVERT: A 348 TRP cc_start: 0.8580 (OUTLIER) cc_final: 0.6830 (m-90) REVERT: A 432 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7104 (pm20) REVERT: A 513 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8255 (mtp180) REVERT: A 517 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7832 (ppt-90) outliers start: 51 outliers final: 33 residues processed: 111 average time/residue: 0.0655 time to fit residues: 10.2498 Evaluate side-chains 106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 63 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 348 TRP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** 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 = 0.3877 r_free = 0.3877 target = 0.114112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.094942 restraints weight = 18300.407| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.07 r_work: 0.3444 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6675 Z= 0.176 Angle : 0.640 9.411 9071 Z= 0.326 Chirality : 0.044 0.171 952 Planarity : 0.004 0.051 1160 Dihedral : 8.031 56.794 974 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.06 % Favored : 89.81 % Rotamer: Outliers : 8.51 % Allowed : 31.60 % Favored : 59.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.57 (0.31), residues: 785 helix: 1.04 (0.28), residues: 361 sheet: -0.40 (0.75), residues: 55 loop : -1.90 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.020 0.001 TYR A 157 PHE 0.019 0.002 PHE A 522 TRP 0.011 0.002 TRP A 565 HIS 0.010 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 6666) covalent geometry : angle 0.63545 ( 9049) SS BOND : bond 0.00484 ( 5) SS BOND : angle 0.81908 ( 10) hydrogen bonds : bond 0.04592 ( 272) hydrogen bonds : angle 4.93995 ( 786) link_NAG-ASN : bond 0.00133 ( 4) link_NAG-ASN : angle 2.21104 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 68 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8054 (tt) REVERT: B 462 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8314 (mmtm) REVERT: B 467 ASP cc_start: 0.8113 (t0) cc_final: 0.7902 (t0) REVERT: A 45 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8690 (tt) REVERT: A 83 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.5753 (p90) REVERT: A 133 LEU cc_start: 0.6391 (pp) cc_final: 0.6009 (mt) REVERT: A 202 TRP cc_start: 0.8834 (OUTLIER) cc_final: 0.8275 (m-10) REVERT: A 348 TRP cc_start: 0.8581 (OUTLIER) cc_final: 0.6913 (m-90) REVERT: A 432 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7138 (pm20) REVERT: A 513 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8252 (mtp180) REVERT: A 517 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7926 (ppt-90) outliers start: 59 outliers final: 35 residues processed: 117 average time/residue: 0.0649 time to fit residues: 10.7028 Evaluate side-chains 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 63 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 348 TRP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B 506 GLN ** 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 = 0.3897 r_free = 0.3897 target = 0.115292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.096252 restraints weight = 18079.328| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.04 r_work: 0.3467 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6675 Z= 0.139 Angle : 0.616 8.935 9071 Z= 0.311 Chirality : 0.043 0.157 952 Planarity : 0.004 0.051 1160 Dihedral : 7.862 56.294 972 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.79 % Favored : 91.08 % Rotamer: Outliers : 8.08 % Allowed : 31.89 % Favored : 60.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.44 (0.31), residues: 785 helix: 1.25 (0.28), residues: 356 sheet: -0.06 (0.85), residues: 45 loop : -1.91 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 509 TYR 0.020 0.001 TYR A 157 PHE 0.016 0.001 PHE A 326 TRP 0.012 0.001 TRP A 565 HIS 0.010 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6666) covalent geometry : angle 0.61153 ( 9049) SS BOND : bond 0.00487 ( 5) SS BOND : angle 0.65990 ( 10) hydrogen bonds : bond 0.04246 ( 272) hydrogen bonds : angle 4.81501 ( 786) link_NAG-ASN : bond 0.00215 ( 4) link_NAG-ASN : angle 2.06969 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 71 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 335 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8051 (tt) REVERT: B 441 LEU cc_start: 0.8333 (pp) cc_final: 0.7836 (mp) REVERT: B 462 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8297 (mmtm) REVERT: B 467 ASP cc_start: 0.8128 (t0) cc_final: 0.7918 (t0) REVERT: A 45 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8640 (tt) REVERT: A 83 TYR cc_start: 0.7292 (OUTLIER) cc_final: 0.5852 (p90) REVERT: A 131 LYS cc_start: 0.5515 (OUTLIER) cc_final: 0.5206 (tptt) REVERT: A 133 LEU cc_start: 0.6418 (pp) cc_final: 0.6069 (mt) REVERT: A 202 TRP cc_start: 0.8831 (OUTLIER) cc_final: 0.8220 (m-10) REVERT: A 348 TRP cc_start: 0.8588 (OUTLIER) cc_final: 0.6867 (m-90) REVERT: A 432 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7130 (pm20) REVERT: A 513 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8249 (mtp180) REVERT: A 517 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7819 (ppt-90) outliers start: 56 outliers final: 33 residues processed: 118 average time/residue: 0.0701 time to fit residues: 11.4543 Evaluate side-chains 110 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 67 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 348 TRP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.1980 chunk 76 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 66 optimal weight: 0.0770 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** 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 = 0.3921 r_free = 0.3921 target = 0.116773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.097568 restraints weight = 18079.834| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.07 r_work: 0.3491 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6675 Z= 0.120 Angle : 0.607 8.633 9071 Z= 0.307 Chirality : 0.042 0.160 952 Planarity : 0.004 0.053 1160 Dihedral : 7.691 56.277 971 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.66 % Favored : 91.21 % Rotamer: Outliers : 6.20 % Allowed : 33.62 % Favored : 60.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.34 (0.31), residues: 785 helix: 1.25 (0.28), residues: 364 sheet: -0.75 (0.74), residues: 60 loop : -1.73 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 305 TYR 0.020 0.001 TYR A 157 PHE 0.013 0.001 PHE A 503 TRP 0.011 0.001 TRP A 565 HIS 0.010 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6666) covalent geometry : angle 0.60339 ( 9049) SS BOND : bond 0.00296 ( 5) SS BOND : angle 0.73479 ( 10) hydrogen bonds : bond 0.03954 ( 272) hydrogen bonds : angle 4.71542 ( 786) link_NAG-ASN : bond 0.00303 ( 4) link_NAG-ASN : angle 1.88452 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 73 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: B 441 LEU cc_start: 0.8221 (pp) cc_final: 0.7719 (mp) REVERT: B 462 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8314 (mmtm) REVERT: B 467 ASP cc_start: 0.8118 (t0) cc_final: 0.7900 (t0) REVERT: A 45 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8552 (tt) REVERT: A 83 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.5789 (p90) REVERT: A 131 LYS cc_start: 0.5320 (OUTLIER) cc_final: 0.5034 (tptt) REVERT: A 133 LEU cc_start: 0.6509 (pp) cc_final: 0.6191 (mt) REVERT: A 202 TRP cc_start: 0.8769 (OUTLIER) cc_final: 0.8149 (m-10) REVERT: A 254 TYR cc_start: 0.6653 (m-80) cc_final: 0.6113 (m-10) REVERT: A 339 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7979 (ptp-170) REVERT: A 348 TRP cc_start: 0.8560 (OUTLIER) cc_final: 0.6859 (m-90) REVERT: A 432 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6963 (pm20) REVERT: A 517 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7717 (ppt-90) outliers start: 43 outliers final: 28 residues processed: 110 average time/residue: 0.0721 time to fit residues: 10.9029 Evaluate side-chains 103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 348 TRP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 0.0870 chunk 64 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** 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 = 0.3918 r_free = 0.3918 target = 0.116499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.097211 restraints weight = 18303.865| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.09 r_work: 0.3485 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6675 Z= 0.127 Angle : 0.637 10.993 9071 Z= 0.319 Chirality : 0.043 0.176 952 Planarity : 0.004 0.053 1160 Dihedral : 7.424 56.028 968 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.28 % Favored : 91.59 % Rotamer: Outliers : 5.34 % Allowed : 35.06 % Favored : 59.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.27 (0.31), residues: 785 helix: 1.31 (0.28), residues: 360 sheet: -0.82 (0.73), residues: 60 loop : -1.66 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 509 TYR 0.020 0.001 TYR A 157 PHE 0.013 0.001 PHE A 522 TRP 0.011 0.001 TRP A 565 HIS 0.009 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6666) covalent geometry : angle 0.63400 ( 9049) SS BOND : bond 0.00307 ( 5) SS BOND : angle 0.64630 ( 10) hydrogen bonds : bond 0.03992 ( 272) hydrogen bonds : angle 4.76993 ( 786) link_NAG-ASN : bond 0.00224 ( 4) link_NAG-ASN : angle 1.85980 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 69 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 441 LEU cc_start: 0.8249 (pp) cc_final: 0.7729 (mp) REVERT: B 462 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8325 (mmtm) REVERT: B 467 ASP cc_start: 0.8110 (t0) cc_final: 0.7897 (t0) REVERT: A 45 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8621 (tt) REVERT: A 83 TYR cc_start: 0.7270 (OUTLIER) cc_final: 0.5798 (p90) REVERT: A 131 LYS cc_start: 0.5300 (OUTLIER) cc_final: 0.5015 (tptt) REVERT: A 133 LEU cc_start: 0.6449 (pp) cc_final: 0.6124 (mt) REVERT: A 202 TRP cc_start: 0.8796 (OUTLIER) cc_final: 0.8188 (m-10) REVERT: A 231 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8411 (mt-10) REVERT: A 254 TYR cc_start: 0.6661 (m-80) cc_final: 0.6114 (m-10) REVERT: A 339 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7977 (ptp-170) REVERT: A 348 TRP cc_start: 0.8565 (OUTLIER) cc_final: 0.6868 (m-90) REVERT: A 432 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6914 (pm20) REVERT: A 517 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7726 (ppt-90) outliers start: 37 outliers final: 26 residues processed: 102 average time/residue: 0.0689 time to fit residues: 9.8657 Evaluate side-chains 101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 65 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 348 TRP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 40 optimal weight: 0.4980 chunk 19 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** 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 = 0.3921 r_free = 0.3921 target = 0.116691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.097713 restraints weight = 18157.164| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.97 r_work: 0.3499 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6675 Z= 0.127 Angle : 0.641 11.074 9071 Z= 0.321 Chirality : 0.043 0.182 952 Planarity : 0.004 0.053 1160 Dihedral : 7.339 56.044 968 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.54 % Favored : 91.34 % Rotamer: Outliers : 5.34 % Allowed : 35.50 % Favored : 59.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.23 (0.31), residues: 785 helix: 1.32 (0.28), residues: 359 sheet: 0.09 (0.79), residues: 50 loop : -1.74 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 509 TYR 0.020 0.001 TYR A 157 PHE 0.014 0.001 PHE A 522 TRP 0.011 0.001 TRP A 565 HIS 0.009 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6666) covalent geometry : angle 0.63856 ( 9049) SS BOND : bond 0.00311 ( 5) SS BOND : angle 0.60297 ( 10) hydrogen bonds : bond 0.03971 ( 272) hydrogen bonds : angle 4.73101 ( 786) link_NAG-ASN : bond 0.00243 ( 4) link_NAG-ASN : angle 1.75950 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 68 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 441 LEU cc_start: 0.8239 (pp) cc_final: 0.7711 (mp) REVERT: B 462 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8314 (mmtm) REVERT: B 467 ASP cc_start: 0.8122 (t0) cc_final: 0.7907 (t0) REVERT: A 45 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8608 (tt) REVERT: A 83 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.5903 (p90) REVERT: A 131 LYS cc_start: 0.5216 (OUTLIER) cc_final: 0.4902 (tptt) REVERT: A 133 LEU cc_start: 0.6444 (pp) cc_final: 0.6158 (tp) REVERT: A 202 TRP cc_start: 0.8761 (OUTLIER) cc_final: 0.8147 (m-10) REVERT: A 254 TYR cc_start: 0.6669 (m-80) cc_final: 0.6134 (m-10) REVERT: A 339 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7955 (ptp-170) REVERT: A 348 TRP cc_start: 0.8553 (OUTLIER) cc_final: 0.6808 (m-90) REVERT: A 432 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: A 517 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7730 (ppt-90) outliers start: 37 outliers final: 23 residues processed: 102 average time/residue: 0.0631 time to fit residues: 9.1018 Evaluate side-chains 98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 66 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 348 TRP Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 19 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** 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 = 0.3896 r_free = 0.3896 target = 0.115269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.096346 restraints weight = 18321.660| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.94 r_work: 0.3468 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6675 Z= 0.154 Angle : 0.661 11.470 9071 Z= 0.332 Chirality : 0.043 0.176 952 Planarity : 0.004 0.052 1160 Dihedral : 7.373 55.915 966 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.55 % Favored : 90.32 % Rotamer: Outliers : 5.48 % Allowed : 35.06 % Favored : 59.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.36 (0.31), residues: 785 helix: 1.21 (0.28), residues: 359 sheet: -0.80 (0.73), residues: 60 loop : -1.68 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 509 TYR 0.020 0.001 TYR A 157 PHE 0.040 0.002 PHE A 451 TRP 0.010 0.001 TRP A 565 HIS 0.009 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6666) covalent geometry : angle 0.65728 ( 9049) SS BOND : bond 0.00401 ( 5) SS BOND : angle 0.61030 ( 10) hydrogen bonds : bond 0.04222 ( 272) hydrogen bonds : angle 4.81939 ( 786) link_NAG-ASN : bond 0.00118 ( 4) link_NAG-ASN : angle 2.10726 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1807.91 seconds wall clock time: 31 minutes 49.12 seconds (1909.12 seconds total)