Starting phenix.real_space_refine on Fri Sep 11 16:37:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6j5v_0682/09_2026/6j5v_0682.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j5v_0682/09_2026/6j5v_0682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6j5v_0682/09_2026/6j5v_0682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j5v_0682/09_2026/6j5v_0682.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6j5v_0682/09_2026/6j5v_0682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j5v_0682/09_2026/6j5v_0682.map" } resolution = 4.25 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 63 5.16 5 C 6678 2.51 5 N 1810 2.21 5 O 1976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10529 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6507 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 27, 'TRANS': 788} Chain breaks: 1 Chain: "C" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1340 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain breaks: 4 Chain: "B" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2629 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N BQL C 501 " occ=0.00 ... (24 atoms not shown) pdb=" P BQL C 501 " occ=0.00 Time building chain proxies: 2.62, per 1000 atoms: 0.25 Number of scatterers: 10529 At special positions: 0 Unit cell: (87.28, 100.372, 133.102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 2 15.00 O 1976 8.00 N 1810 7.00 C 6678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of additional links: simple=2, symmetry=0 Simple link: pdb=" C VAL C 252 " - pdb=" N BQL C 501 " Simple link: pdb=" N LYS C 255 " - pdb=" C BQO C 502 " Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 373.6 milliseconds 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 40.6% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 1 through 17 removed outlier: 3.941A pdb=" N VAL A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 20 No H-bonds generated for 'chain 'A' and resid 18 through 20' Processing helix chain 'A' and resid 26 through 31 Processing helix chain 'A' and resid 31 through 42 removed outlier: 5.403A pdb=" N GLU A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 removed outlier: 3.798A pdb=" N ARG A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 removed outlier: 4.439A pdb=" N ARG A 59 " --> pdb=" O ASN A 55 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 60' Processing helix chain 'A' and resid 61 through 79 Processing helix chain 'A' and resid 89 through 105 removed outlier: 3.896A pdb=" N HIS A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Proline residue: A 102 - end of helix Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 194 through 198 removed outlier: 4.220A pdb=" N THR A 197 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.806A pdb=" N GLU A 209 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N HIS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 210' Processing helix chain 'A' and resid 246 through 254 removed outlier: 4.256A pdb=" N GLN A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'A' and resid 343 through 355 removed outlier: 4.228A pdb=" N VAL A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'A' and resid 375 through 390 removed outlier: 3.798A pdb=" N TRP A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 389 " --> pdb=" O HIS A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 410 removed outlier: 3.740A pdb=" N MET A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A 405 " --> pdb=" O MET A 401 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 422 removed outlier: 3.664A pdb=" N THR A 421 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 422 " --> pdb=" O ILE A 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 418 through 422' Processing helix chain 'A' and resid 433 through 444 removed outlier: 4.802A pdb=" N HIS A 438 " --> pdb=" O GLN A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 468 removed outlier: 4.139A pdb=" N ASP A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 501 removed outlier: 4.841A pdb=" N LEU A 494 " --> pdb=" O MET A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 557 removed outlier: 3.654A pdb=" N THR A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 627 through 633 removed outlier: 3.775A pdb=" N ILE A 630 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE A 633 " --> pdb=" O ILE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 657 removed outlier: 3.944A pdb=" N LEU A 657 " --> pdb=" O ILE A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 683 removed outlier: 3.574A pdb=" N VAL A 680 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN A 682 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.744A pdb=" N LEU A 704 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 733 removed outlier: 4.004A pdb=" N THR A 730 " --> pdb=" O ASP A 726 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A 733 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 807 through 815 Processing helix chain 'C' and resid 193 through 210 removed outlier: 4.075A pdb=" N PHE C 207 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 264 through 270 removed outlier: 3.551A pdb=" N ALA C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 292 removed outlier: 3.792A pdb=" N ASP C 278 " --> pdb=" O THR C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'B' and resid 18 through 39 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.710A pdb=" N ILE B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 95' Processing helix chain 'B' and resid 97 through 114 removed outlier: 3.533A pdb=" N ASN B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 162 through 182 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 247 through 254 removed outlier: 4.278A pdb=" N VAL B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER B 253 " --> pdb=" O THR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 4.220A pdb=" N VAL B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 290 removed outlier: 3.941A pdb=" N GLU B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 307 through 322 removed outlier: 3.575A pdb=" N GLN B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 330 Processing helix chain 'B' and resid 332 through 343 Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 186 Processing sheet with id=AA2, first strand: chain 'A' and resid 431 through 432 Processing sheet with id=AA3, first strand: chain 'A' and resid 515 through 517 removed outlier: 3.650A pdb=" N LEU A 591 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP A 616 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 690 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 746 " --> pdb=" O SER A 770 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 796 " --> pdb=" O THR A 820 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 47 removed outlier: 3.624A pdb=" N CYS B 126 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY B 125 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET B 85 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ARG B 76 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N PHE B 65 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 189 Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 199 343 hydrogen bonds defined for protein. 963 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1770 1.31 - 1.44: 2741 1.44 - 1.57: 6122 1.57 - 1.70: 5 1.70 - 1.82: 94 Bond restraints: 10732 Sorted by residual: bond pdb=" OP3 BQO C 502 " pdb=" P BQO C 502 " ideal model delta sigma weight residual 1.494 1.643 -0.149 2.00e-02 2.50e+03 5.56e+01 bond pdb=" C VAL A 105 " pdb=" N PRO A 106 " ideal model delta sigma weight residual 1.335 1.397 -0.062 9.40e-03 1.13e+04 4.39e+01 bond pdb=" C1' BQO C 502 " pdb=" O4' BQO C 502 " ideal model delta sigma weight residual 1.390 1.473 -0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C4 BQO C 502 " pdb=" C5 BQO C 502 " ideal model delta sigma weight residual 1.439 1.358 0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C1' BQO C 502 " pdb=" N1 BQO C 502 " ideal model delta sigma weight residual 1.483 1.410 0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 10727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 14151 3.36 - 6.72: 293 6.72 - 10.07: 45 10.07 - 13.43: 11 13.43 - 16.79: 1 Bond angle restraints: 14501 Sorted by residual: angle pdb=" N CYS A 649 " pdb=" CA CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sigma weight residual 114.17 108.33 5.84 1.14e+00 7.69e-01 2.63e+01 angle pdb=" CA LEU A 612 " pdb=" CB LEU A 612 " pdb=" CG LEU A 612 " ideal model delta sigma weight residual 116.30 133.09 -16.79 3.50e+00 8.16e-02 2.30e+01 angle pdb=" CA THR A 541 " pdb=" CB THR A 541 " pdb=" CG2 THR A 541 " ideal model delta sigma weight residual 110.50 118.44 -7.94 1.70e+00 3.46e-01 2.18e+01 angle pdb=" C ASN A 611 " pdb=" N LEU A 612 " pdb=" CA LEU A 612 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C GLU B 80 " pdb=" N ASP B 81 " pdb=" CA ASP B 81 " ideal model delta sigma weight residual 122.61 129.34 -6.73 1.56e+00 4.11e-01 1.86e+01 ... (remaining 14496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5597 17.65 - 35.30: 772 35.30 - 52.95: 156 52.95 - 70.60: 19 70.60 - 88.25: 9 Dihedral angle restraints: 6553 sinusoidal: 2736 harmonic: 3817 Sorted by residual: dihedral pdb=" CA ASP A 33 " pdb=" C ASP A 33 " pdb=" N LEU A 34 " pdb=" CA LEU A 34 " ideal model delta harmonic sigma weight residual 180.00 141.18 38.82 0 5.00e+00 4.00e-02 6.03e+01 dihedral pdb=" CA CYS A 649 " pdb=" C CYS A 649 " pdb=" N PHE A 650 " pdb=" CA PHE A 650 " ideal model delta harmonic sigma weight residual 180.00 143.13 36.87 0 5.00e+00 4.00e-02 5.44e+01 dihedral pdb=" CA GLU A 648 " pdb=" C GLU A 648 " pdb=" N CYS A 649 " pdb=" CA CYS A 649 " ideal model delta harmonic sigma weight residual 180.00 145.49 34.51 0 5.00e+00 4.00e-02 4.76e+01 ... (remaining 6550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1095 0.057 - 0.114: 392 0.114 - 0.171: 114 0.171 - 0.227: 27 0.227 - 0.284: 6 Chirality restraints: 1634 Sorted by residual: chirality pdb=" CB VAL B 251 " pdb=" CA VAL B 251 " pdb=" CG1 VAL B 251 " pdb=" CG2 VAL B 251 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C2' BQO C 502 " pdb=" C1' BQO C 502 " pdb=" C3' BQO C 502 " pdb=" O1 BQO C 502 " both_signs ideal model delta sigma weight residual False -2.75 -2.47 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA THR A 541 " pdb=" N THR A 541 " pdb=" C THR A 541 " pdb=" CB THR A 541 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1631 not shown) Planarity restraints: 1840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 43 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO B 44 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 781 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO A 782 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 782 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 782 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 312 " -0.047 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO C 313 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 313 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 313 " -0.040 5.00e-02 4.00e+02 ... (remaining 1837 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2730 2.79 - 3.32: 10244 3.32 - 3.85: 18189 3.85 - 4.37: 20153 4.37 - 4.90: 32283 Nonbonded interactions: 83599 Sorted by model distance: nonbonded pdb=" O GLN A 621 " pdb=" OG SER A 646 " model vdw 2.263 3.040 nonbonded pdb=" O GLY A 785 " pdb=" OG1 THR A 789 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR A 749 " pdb=" O SER A 753 " model vdw 2.314 3.040 nonbonded pdb=" OG SER A 576 " pdb=" O GLN A 601 " model vdw 2.316 3.040 nonbonded pdb=" O LEU C 205 " pdb=" ND1 HIS C 209 " model vdw 2.325 3.120 ... (remaining 83594 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.390 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.840 Find NCS groups from input model: 0.060 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.007 0.149 10734 Z= 0.346 Angle : 1.217 16.788 14507 Z= 0.635 Chirality : 0.066 0.284 1634 Planarity : 0.008 0.102 1838 Dihedral : 16.422 88.247 4075 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.19 % Favored : 85.81 % Rotamer: Outliers : 0.94 % Allowed : 15.83 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.32 % 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: -4.88 (0.19), residues: 1297 helix: -3.12 (0.16), residues: 469 sheet: -2.90 (0.48), residues: 89 loop : -3.50 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 468 TYR 0.042 0.003 TYR A 721 PHE 0.023 0.003 PHE B 244 TRP 0.032 0.003 TRP A 844 HIS 0.010 0.002 HIS B 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.35 (10732) covalent geometry : angle 1.21726 / 0.64 (14501) hydrogen bonds : bond 0.12792 / 8.65 ( 343) hydrogen bonds : angle 7.13596 / 4.86 ( 963) link_TRANS : bond 0.00302 / 0.15 ( 2) link_TRANS : angle 0.70664 / 0.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 228 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LYS cc_start: 0.7990 (ttpt) cc_final: 0.7565 (tttt) REVERT: A 401 MET cc_start: 0.8911 (tpp) cc_final: 0.8706 (tpp) REVERT: A 714 MET cc_start: 0.8312 (tpp) cc_final: 0.7822 (mmm) REVERT: A 829 LEU cc_start: 0.9030 (mt) cc_final: 0.8554 (mt) REVERT: C 217 TYR cc_start: 0.7998 (t80) cc_final: 0.7189 (t80) REVERT: C 219 ASP cc_start: 0.8089 (m-30) cc_final: 0.7827 (m-30) REVERT: C 224 ASN cc_start: 0.8904 (m-40) cc_final: 0.8608 (t0) REVERT: C 231 PHE cc_start: 0.8522 (m-80) cc_final: 0.8268 (m-10) REVERT: C 293 ARG cc_start: 0.6152 (mpp-170) cc_final: 0.5541 (mtm-85) REVERT: C 294 ARG cc_start: 0.8273 (ptp90) cc_final: 0.7961 (ptm160) REVERT: C 359 MET cc_start: 0.7366 (tpp) cc_final: 0.6926 (tmm) REVERT: B 68 GLN cc_start: 0.8918 (tt0) cc_final: 0.8558 (tm-30) REVERT: B 138 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7763 (tm-30) REVERT: B 171 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8479 (mm-30) REVERT: B 244 PHE cc_start: 0.8224 (p90) cc_final: 0.7631 (p90) REVERT: B 247 GLU cc_start: 0.8711 (tp30) cc_final: 0.8346 (tp30) REVERT: B 313 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8451 (tm-30) REVERT: B 335 GLN cc_start: 0.9226 (mp10) cc_final: 0.8972 (mp10) outliers start: 11 outliers final: 5 residues processed: 237 average time/residue: 0.1058 time to fit residues: 35.1464 Evaluate side-chains 171 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 166 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN A 178 ASN A 204 ASN A 273 ASN A 335 ASN A 377 HIS A 393 ASN A 434 GLN A 435 GLN A 520 ASN A 611 ASN A 643 ASN A 673 ASN A 742 HIS A 788 ASN A 812 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN B 68 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS B 311 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.118685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.086373 restraints weight = 28953.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.089060 restraints weight = 16945.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.090836 restraints weight = 11556.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091958 restraints weight = 8806.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.092851 restraints weight = 7332.144| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10734 Z= 0.150 Angle : 0.779 12.600 14507 Z= 0.396 Chirality : 0.048 0.208 1634 Planarity : 0.006 0.094 1838 Dihedral : 8.204 75.165 1485 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % Rotamer: Outliers : 0.26 % Allowed : 6.16 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.79 (0.21), residues: 1297 helix: -1.52 (0.22), residues: 443 sheet: -2.71 (0.50), residues: 86 loop : -3.28 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 468 TYR 0.026 0.002 TYR B 252 PHE 0.017 0.001 PHE B 244 TRP 0.027 0.002 TRP A 757 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (10732) covalent geometry : angle 0.77893 / 0.40 (14501) hydrogen bonds : bond 0.04137 / 2.71 ( 343) hydrogen bonds : angle 5.73568 / 3.91 ( 963) link_TRANS : bond 0.00152 / 0.07 ( 2) link_TRANS : angle 0.54675 / 0.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 219 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8890 (mmt) cc_final: 0.8672 (mmm) REVERT: A 362 ILE cc_start: 0.9380 (pt) cc_final: 0.9090 (mt) REVERT: A 469 CYS cc_start: 0.8700 (t) cc_final: 0.8490 (t) REVERT: A 714 MET cc_start: 0.8276 (tpp) cc_final: 0.7662 (mmm) REVERT: A 731 LYS cc_start: 0.8464 (pttm) cc_final: 0.7803 (pttp) REVERT: C 219 ASP cc_start: 0.7885 (m-30) cc_final: 0.7590 (m-30) REVERT: C 294 ARG cc_start: 0.8317 (ptp90) cc_final: 0.7940 (ptm160) REVERT: C 296 MET cc_start: 0.6386 (tmm) cc_final: 0.6029 (tmm) REVERT: C 356 ARG cc_start: 0.8771 (ttm170) cc_final: 0.8305 (ttm170) REVERT: C 361 GLU cc_start: 0.8955 (pt0) cc_final: 0.8526 (pp20) REVERT: B 52 GLN cc_start: 0.9123 (mt0) cc_final: 0.8807 (mt0) REVERT: B 68 GLN cc_start: 0.8977 (tt0) cc_final: 0.8647 (tm-30) REVERT: B 103 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7705 (tm-30) REVERT: B 121 LEU cc_start: 0.9278 (tp) cc_final: 0.9028 (tp) REVERT: B 138 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7837 (tm-30) REVERT: B 199 LEU cc_start: 0.8644 (tt) cc_final: 0.8362 (tp) REVERT: B 200 ASP cc_start: 0.8128 (p0) cc_final: 0.7844 (p0) REVERT: B 313 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8178 (tm-30) outliers start: 3 outliers final: 1 residues processed: 221 average time/residue: 0.1019 time to fit residues: 32.0527 Evaluate side-chains 165 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 99 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 126 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 ASN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS B 311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.119259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.087245 restraints weight = 29349.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.089849 restraints weight = 17290.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.091590 restraints weight = 11885.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.092656 restraints weight = 9099.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.093500 restraints weight = 7620.882| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10734 Z= 0.147 Angle : 0.753 12.716 14507 Z= 0.381 Chirality : 0.048 0.181 1634 Planarity : 0.005 0.087 1838 Dihedral : 7.730 70.798 1485 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.26 % Favored : 87.74 % Rotamer: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.37 (0.22), residues: 1297 helix: -1.06 (0.23), residues: 449 sheet: -2.26 (0.53), residues: 85 loop : -3.15 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 323 TYR 0.020 0.002 TYR B 252 PHE 0.018 0.002 PHE A 748 TRP 0.021 0.002 TRP A 757 HIS 0.006 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (10732) covalent geometry : angle 0.75270 / 0.38 (14501) hydrogen bonds : bond 0.03880 / 2.54 ( 343) hydrogen bonds : angle 5.48045 / 3.75 ( 963) link_TRANS : bond 0.00147 / 0.07 ( 2) link_TRANS : angle 0.49294 / 0.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 ILE cc_start: 0.9247 (pt) cc_final: 0.8896 (mt) REVERT: A 459 GLU cc_start: 0.8324 (mp0) cc_final: 0.7885 (mp0) REVERT: A 482 ILE cc_start: 0.9513 (mm) cc_final: 0.9300 (mm) REVERT: A 599 LEU cc_start: 0.9279 (tp) cc_final: 0.9050 (tp) REVERT: A 648 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7413 (tp30) REVERT: A 714 MET cc_start: 0.8149 (tpp) cc_final: 0.7753 (mmm) REVERT: A 731 LYS cc_start: 0.8451 (pttm) cc_final: 0.7916 (pttp) REVERT: A 741 LEU cc_start: 0.8803 (tp) cc_final: 0.7978 (tp) REVERT: C 178 GLU cc_start: 0.7801 (mp0) cc_final: 0.7599 (mp0) REVERT: C 184 ARG cc_start: 0.8812 (mmm160) cc_final: 0.8506 (mmm160) REVERT: C 217 TYR cc_start: 0.7751 (t80) cc_final: 0.7501 (t80) REVERT: C 219 ASP cc_start: 0.7816 (m-30) cc_final: 0.7571 (m-30) REVERT: C 293 ARG cc_start: 0.5702 (mpp-170) cc_final: 0.5397 (mtm-85) REVERT: C 294 ARG cc_start: 0.8271 (ptp90) cc_final: 0.7854 (ptm160) REVERT: C 361 GLU cc_start: 0.8946 (pt0) cc_final: 0.8496 (pp20) REVERT: B 52 GLN cc_start: 0.9101 (mt0) cc_final: 0.8829 (mt0) REVERT: B 68 GLN cc_start: 0.9028 (tt0) cc_final: 0.8743 (tm-30) REVERT: B 71 TYR cc_start: 0.7958 (m-80) cc_final: 0.7505 (m-80) REVERT: B 121 LEU cc_start: 0.9310 (tp) cc_final: 0.9002 (tp) REVERT: B 138 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7806 (tm-30) REVERT: B 195 MET cc_start: 0.7854 (mmt) cc_final: 0.7620 (mmt) REVERT: B 199 LEU cc_start: 0.8636 (tt) cc_final: 0.8392 (tp) REVERT: B 222 ARG cc_start: 0.8680 (ttt-90) cc_final: 0.8458 (ttt90) REVERT: B 313 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8235 (tm-30) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1070 time to fit residues: 31.6002 Evaluate side-chains 161 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 12 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 57 optimal weight: 0.0020 chunk 2 optimal weight: 30.0000 chunk 120 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 587 HIS ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN B 122 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.116526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.083941 restraints weight = 30282.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.086436 restraints weight = 17913.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.088102 restraints weight = 12391.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.089174 restraints weight = 9557.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.089948 restraints weight = 8021.794| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10734 Z= 0.198 Angle : 0.781 12.207 14507 Z= 0.397 Chirality : 0.049 0.175 1634 Planarity : 0.006 0.087 1838 Dihedral : 7.812 69.983 1485 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.34 % Favored : 86.66 % Rotamer: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.22 (0.22), residues: 1297 helix: -0.91 (0.24), residues: 458 sheet: -2.00 (0.57), residues: 74 loop : -3.12 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 308 TYR 0.020 0.002 TYR B 252 PHE 0.029 0.002 PHE A 175 TRP 0.020 0.002 TRP A 757 HIS 0.007 0.002 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (10732) covalent geometry : angle 0.78101 / 0.40 (14501) hydrogen bonds : bond 0.03914 / 2.56 ( 343) hydrogen bonds : angle 5.60723 / 3.86 ( 963) link_TRANS : bond 0.00240 / 0.12 ( 2) link_TRANS : angle 0.57952 / 0.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.9033 (mmt) cc_final: 0.8498 (mmm) REVERT: A 185 MET cc_start: 0.0288 (tpp) cc_final: -0.0122 (tpt) REVERT: A 266 MET cc_start: 0.8693 (mmp) cc_final: 0.8183 (mmp) REVERT: A 362 ILE cc_start: 0.9274 (pt) cc_final: 0.8839 (mt) REVERT: A 459 GLU cc_start: 0.8404 (mp0) cc_final: 0.8204 (mp0) REVERT: A 599 LEU cc_start: 0.9187 (tp) cc_final: 0.8968 (tp) REVERT: A 604 ARG cc_start: 0.8976 (tmt170) cc_final: 0.8691 (ttp80) REVERT: A 714 MET cc_start: 0.8133 (tpp) cc_final: 0.7757 (mmm) REVERT: A 731 LYS cc_start: 0.8399 (pttm) cc_final: 0.7834 (pttp) REVERT: A 741 LEU cc_start: 0.8822 (tp) cc_final: 0.8558 (tp) REVERT: C 178 GLU cc_start: 0.7724 (mp0) cc_final: 0.7503 (mp0) REVERT: C 208 LEU cc_start: 0.8846 (mt) cc_final: 0.8628 (mt) REVERT: C 217 TYR cc_start: 0.7679 (t80) cc_final: 0.7333 (t80) REVERT: C 219 ASP cc_start: 0.8138 (m-30) cc_final: 0.7822 (m-30) REVERT: C 272 ARG cc_start: 0.8158 (mmm-85) cc_final: 0.7950 (mmm-85) REVERT: C 294 ARG cc_start: 0.8304 (ptp90) cc_final: 0.7802 (ptm160) REVERT: C 296 MET cc_start: 0.6792 (tmm) cc_final: 0.6474 (tmm) REVERT: C 359 MET cc_start: 0.6549 (tpt) cc_final: 0.6236 (tpt) REVERT: C 361 GLU cc_start: 0.8949 (pt0) cc_final: 0.8558 (pp20) REVERT: B 52 GLN cc_start: 0.9109 (mt0) cc_final: 0.8830 (mt0) REVERT: B 68 GLN cc_start: 0.9010 (tt0) cc_final: 0.8734 (tm-30) REVERT: B 121 LEU cc_start: 0.9276 (tp) cc_final: 0.8933 (tp) REVERT: B 122 GLN cc_start: 0.8813 (mt0) cc_final: 0.8446 (tt0) REVERT: B 138 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7836 (tm-30) REVERT: B 313 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8233 (tm-30) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1034 time to fit residues: 28.7980 Evaluate side-chains 155 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 HIS ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.118307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.086148 restraints weight = 29807.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.088709 restraints weight = 17565.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.090382 restraints weight = 12048.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.091476 restraints weight = 9283.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.092268 restraints weight = 7771.070| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10734 Z= 0.159 Angle : 0.757 10.928 14507 Z= 0.382 Chirality : 0.048 0.184 1634 Planarity : 0.005 0.087 1838 Dihedral : 7.547 66.864 1485 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer: Outliers : 0.09 % Allowed : 5.47 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.23 (0.22), residues: 1297 helix: -1.04 (0.23), residues: 483 sheet: -1.89 (0.58), residues: 69 loop : -3.09 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 222 TYR 0.018 0.002 TYR B 252 PHE 0.028 0.002 PHE A 748 TRP 0.026 0.002 TRP A 757 HIS 0.007 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (10732) covalent geometry : angle 0.75738 / 0.38 (14501) hydrogen bonds : bond 0.03788 / 2.50 ( 343) hydrogen bonds : angle 5.49925 / 3.79 ( 963) link_TRANS : bond 0.00157 / 0.08 ( 2) link_TRANS : angle 0.49752 / 0.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.9019 (mmt) cc_final: 0.8482 (mmm) REVERT: A 362 ILE cc_start: 0.9269 (pt) cc_final: 0.8812 (mt) REVERT: A 459 GLU cc_start: 0.8552 (mp0) cc_final: 0.8287 (mp0) REVERT: A 599 LEU cc_start: 0.9296 (tp) cc_final: 0.9076 (tp) REVERT: A 604 ARG cc_start: 0.9039 (tmt170) cc_final: 0.8640 (ttp80) REVERT: A 686 LEU cc_start: 0.8788 (mm) cc_final: 0.8588 (mm) REVERT: A 714 MET cc_start: 0.8087 (tpp) cc_final: 0.7552 (mmm) REVERT: A 731 LYS cc_start: 0.8503 (pttm) cc_final: 0.7810 (pttp) REVERT: A 828 GLU cc_start: 0.8611 (tp30) cc_final: 0.8140 (tp30) REVERT: C 208 LEU cc_start: 0.8837 (mt) cc_final: 0.8604 (mt) REVERT: C 217 TYR cc_start: 0.7748 (t80) cc_final: 0.7362 (t80) REVERT: C 219 ASP cc_start: 0.8057 (m-30) cc_final: 0.7599 (m-30) REVERT: C 272 ARG cc_start: 0.8101 (mmm-85) cc_final: 0.7846 (mmm-85) REVERT: C 294 ARG cc_start: 0.8232 (ptp90) cc_final: 0.7999 (ptp90) REVERT: C 359 MET cc_start: 0.6630 (tpt) cc_final: 0.6229 (tpt) REVERT: C 361 GLU cc_start: 0.8957 (pt0) cc_final: 0.8581 (pp20) REVERT: B 52 GLN cc_start: 0.9117 (mt0) cc_final: 0.8844 (mt0) REVERT: B 68 GLN cc_start: 0.9034 (tt0) cc_final: 0.8686 (tm-30) REVERT: B 121 LEU cc_start: 0.9293 (tp) cc_final: 0.8937 (tp) REVERT: B 138 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7855 (tm-30) REVERT: B 235 ILE cc_start: 0.8096 (mm) cc_final: 0.7893 (mm) REVERT: B 313 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8278 (tm-30) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.1014 time to fit residues: 29.8047 Evaluate side-chains 164 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 21 optimal weight: 40.0000 chunk 90 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 HIS A 587 HIS A 742 HIS ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.118131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.086011 restraints weight = 29737.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.088610 restraints weight = 17335.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.090326 restraints weight = 11829.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.091448 restraints weight = 9050.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.092239 restraints weight = 7534.450| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10734 Z= 0.163 Angle : 0.762 13.413 14507 Z= 0.384 Chirality : 0.048 0.186 1634 Planarity : 0.005 0.085 1838 Dihedral : 7.479 64.666 1485 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.26 % Favored : 86.74 % Rotamer: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.14 (0.22), residues: 1297 helix: -0.97 (0.23), residues: 481 sheet: -2.02 (0.57), residues: 74 loop : -3.00 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 222 TYR 0.017 0.002 TYR B 71 PHE 0.017 0.002 PHE A 521 TRP 0.025 0.002 TRP A 757 HIS 0.007 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (10732) covalent geometry : angle 0.76238 / 0.38 (14501) hydrogen bonds : bond 0.03789 / 2.52 ( 343) hydrogen bonds : angle 5.51062 / 3.79 ( 963) link_TRANS : bond 0.00162 / 0.08 ( 2) link_TRANS : angle 0.50637 / 0.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.9002 (mmt) cc_final: 0.8530 (mmm) REVERT: A 459 GLU cc_start: 0.8547 (mp0) cc_final: 0.8251 (mp0) REVERT: A 599 LEU cc_start: 0.9208 (tp) cc_final: 0.8971 (tp) REVERT: A 604 ARG cc_start: 0.9051 (tmt170) cc_final: 0.8637 (ttp80) REVERT: A 686 LEU cc_start: 0.8810 (mm) cc_final: 0.8591 (mm) REVERT: A 731 LYS cc_start: 0.8428 (pttm) cc_final: 0.7887 (pttp) REVERT: A 828 GLU cc_start: 0.8601 (tp30) cc_final: 0.8095 (tp30) REVERT: C 208 LEU cc_start: 0.8900 (mt) cc_final: 0.8667 (mt) REVERT: C 217 TYR cc_start: 0.7808 (t80) cc_final: 0.7489 (t80) REVERT: C 219 ASP cc_start: 0.8032 (m-30) cc_final: 0.7565 (m-30) REVERT: C 272 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7870 (mmm-85) REVERT: C 294 ARG cc_start: 0.8221 (ptp90) cc_final: 0.7964 (ptp90) REVERT: C 359 MET cc_start: 0.6706 (tpt) cc_final: 0.6285 (tpt) REVERT: C 361 GLU cc_start: 0.8941 (pt0) cc_final: 0.8583 (pp20) REVERT: B 52 GLN cc_start: 0.9085 (mt0) cc_final: 0.8832 (mt0) REVERT: B 68 GLN cc_start: 0.9012 (tt0) cc_final: 0.8679 (tm-30) REVERT: B 121 LEU cc_start: 0.9299 (tp) cc_final: 0.8936 (tp) REVERT: B 138 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7855 (tm-30) REVERT: B 313 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8293 (tm-30) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1072 time to fit residues: 31.1590 Evaluate side-chains 159 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 129 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 87 optimal weight: 30.0000 chunk 127 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 HIS ** C 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.120822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088329 restraints weight = 29605.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.090952 restraints weight = 17464.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.092650 restraints weight = 11940.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.093882 restraints weight = 9126.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.094698 restraints weight = 7589.264| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10734 Z= 0.136 Angle : 0.770 12.999 14507 Z= 0.379 Chirality : 0.049 0.191 1634 Planarity : 0.005 0.086 1838 Dihedral : 7.262 60.814 1485 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.49 % Favored : 87.51 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.22), residues: 1297 helix: -0.88 (0.23), residues: 479 sheet: -1.78 (0.58), residues: 72 loop : -2.87 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 53 TYR 0.015 0.001 TYR B 105 PHE 0.019 0.002 PHE A 650 TRP 0.032 0.002 TRP A 173 HIS 0.007 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (10732) covalent geometry : angle 0.77018 / 0.38 (14501) hydrogen bonds : bond 0.03631 / 2.42 ( 343) hydrogen bonds : angle 5.42578 / 3.72 ( 963) link_TRANS : bond 0.00096 / 0.05 ( 2) link_TRANS : angle 0.46634 / 0.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8987 (mmt) cc_final: 0.8526 (mmm) REVERT: A 187 PHE cc_start: 0.6825 (m-80) cc_final: 0.6437 (m-80) REVERT: A 217 TRP cc_start: 0.7795 (t-100) cc_final: 0.7575 (t-100) REVERT: A 362 ILE cc_start: 0.9396 (pt) cc_final: 0.9069 (mt) REVERT: A 368 LEU cc_start: 0.9245 (tp) cc_final: 0.9022 (tp) REVERT: A 459 GLU cc_start: 0.8508 (mp0) cc_final: 0.8197 (mp0) REVERT: A 599 LEU cc_start: 0.9273 (tp) cc_final: 0.9023 (tp) REVERT: A 604 ARG cc_start: 0.8830 (tmt170) cc_final: 0.8422 (ttp80) REVERT: A 639 LEU cc_start: 0.8975 (tp) cc_final: 0.8738 (tp) REVERT: A 686 LEU cc_start: 0.8801 (mm) cc_final: 0.8583 (mm) REVERT: A 714 MET cc_start: 0.7842 (mmm) cc_final: 0.7505 (mmm) REVERT: A 828 GLU cc_start: 0.8570 (tp30) cc_final: 0.8026 (tp30) REVERT: C 208 LEU cc_start: 0.8896 (mt) cc_final: 0.8680 (mt) REVERT: C 217 TYR cc_start: 0.7765 (t80) cc_final: 0.7480 (t80) REVERT: C 219 ASP cc_start: 0.8020 (m-30) cc_final: 0.7473 (m-30) REVERT: C 266 GLU cc_start: 0.8243 (pm20) cc_final: 0.7964 (pm20) REVERT: C 272 ARG cc_start: 0.7981 (mmm-85) cc_final: 0.7728 (mmm-85) REVERT: C 294 ARG cc_start: 0.8299 (ptp90) cc_final: 0.8043 (ptp90) REVERT: C 359 MET cc_start: 0.6683 (tpt) cc_final: 0.6290 (tpt) REVERT: C 361 GLU cc_start: 0.8913 (pt0) cc_final: 0.8571 (pp20) REVERT: B 68 GLN cc_start: 0.9016 (tt0) cc_final: 0.8798 (tm-30) REVERT: B 121 LEU cc_start: 0.9262 (tp) cc_final: 0.8905 (tp) REVERT: B 138 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7855 (tm-30) REVERT: B 313 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8345 (tm-30) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1009 time to fit residues: 31.7916 Evaluate side-chains 162 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 126 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 15 optimal weight: 50.0000 chunk 91 optimal weight: 0.7980 chunk 54 optimal weight: 0.0570 chunk 107 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 405 GLN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 HIS C 332 GLN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.120645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.088704 restraints weight = 29168.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.091339 restraints weight = 17031.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.093129 restraints weight = 11555.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.094310 restraints weight = 8771.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.095097 restraints weight = 7255.067| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10734 Z= 0.135 Angle : 0.764 12.469 14507 Z= 0.376 Chirality : 0.048 0.174 1634 Planarity : 0.005 0.083 1838 Dihedral : 7.164 59.966 1485 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.22), residues: 1297 helix: -0.78 (0.23), residues: 472 sheet: -1.69 (0.59), residues: 69 loop : -2.88 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 222 TYR 0.015 0.002 TYR B 105 PHE 0.018 0.002 PHE A 666 TRP 0.022 0.002 TRP A 757 HIS 0.007 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (10732) covalent geometry : angle 0.76433 / 0.38 (14501) hydrogen bonds : bond 0.03588 / 2.37 ( 343) hydrogen bonds : angle 5.38306 / 3.69 ( 963) link_TRANS : bond 0.00105 / 0.05 ( 2) link_TRANS : angle 0.47573 / 0.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8908 (mmt) cc_final: 0.8684 (mmm) REVERT: A 187 PHE cc_start: 0.6817 (m-80) cc_final: 0.6348 (m-80) REVERT: A 362 ILE cc_start: 0.9390 (pt) cc_final: 0.9034 (mt) REVERT: A 459 GLU cc_start: 0.8512 (mp0) cc_final: 0.8203 (mp0) REVERT: A 599 LEU cc_start: 0.9238 (tp) cc_final: 0.9010 (tp) REVERT: A 604 ARG cc_start: 0.8864 (tmt170) cc_final: 0.8459 (ttp80) REVERT: A 639 LEU cc_start: 0.8860 (tp) cc_final: 0.8625 (tp) REVERT: A 686 LEU cc_start: 0.8850 (mm) cc_final: 0.8621 (mm) REVERT: A 714 MET cc_start: 0.7921 (mmm) cc_final: 0.7504 (mmm) REVERT: A 731 LYS cc_start: 0.8361 (pttm) cc_final: 0.7779 (pttp) REVERT: A 828 GLU cc_start: 0.8506 (tp30) cc_final: 0.8162 (tm-30) REVERT: A 829 LEU cc_start: 0.9190 (mt) cc_final: 0.8972 (mt) REVERT: C 208 LEU cc_start: 0.8909 (mt) cc_final: 0.8678 (mt) REVERT: C 217 TYR cc_start: 0.7747 (t80) cc_final: 0.7337 (t80) REVERT: C 219 ASP cc_start: 0.7971 (m-30) cc_final: 0.7007 (m-30) REVERT: C 266 GLU cc_start: 0.8208 (pm20) cc_final: 0.7959 (pm20) REVERT: C 272 ARG cc_start: 0.7940 (mmm-85) cc_final: 0.7719 (mmm-85) REVERT: C 356 ARG cc_start: 0.8792 (ptp-170) cc_final: 0.8296 (ttm170) REVERT: C 359 MET cc_start: 0.6636 (tpt) cc_final: 0.6238 (tpt) REVERT: C 361 GLU cc_start: 0.8894 (pt0) cc_final: 0.8544 (pp20) REVERT: B 121 LEU cc_start: 0.9282 (tp) cc_final: 0.8922 (tp) REVERT: B 138 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7870 (tm-30) REVERT: B 251 VAL cc_start: 0.9567 (m) cc_final: 0.9302 (m) REVERT: B 313 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8243 (tm-30) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1000 time to fit residues: 31.4431 Evaluate side-chains 158 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 123 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 62 optimal weight: 0.3980 chunk 94 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.122088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.089806 restraints weight = 29054.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.092462 restraints weight = 17041.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.094240 restraints weight = 11660.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.095444 restraints weight = 8903.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.096181 restraints weight = 7364.932| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10734 Z= 0.125 Angle : 0.767 12.092 14507 Z= 0.373 Chirality : 0.048 0.184 1634 Planarity : 0.005 0.084 1838 Dihedral : 6.881 54.526 1485 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.22), residues: 1297 helix: -0.77 (0.23), residues: 477 sheet: -1.51 (0.62), residues: 57 loop : -2.82 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 222 TYR 0.015 0.001 TYR A 281 PHE 0.016 0.002 PHE A 650 TRP 0.020 0.002 TRP A 173 HIS 0.007 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (10732) covalent geometry : angle 0.76704 / 0.37 (14501) hydrogen bonds : bond 0.03516 / 2.32 ( 343) hydrogen bonds : angle 5.29240 / 3.64 ( 963) link_TRANS : bond 0.00076 / 0.04 ( 2) link_TRANS : angle 0.45759 / 0.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8895 (mmt) cc_final: 0.8524 (mmm) REVERT: A 187 PHE cc_start: 0.6925 (m-80) cc_final: 0.6345 (m-10) REVERT: A 362 ILE cc_start: 0.9373 (pt) cc_final: 0.9062 (mt) REVERT: A 459 GLU cc_start: 0.8530 (mp0) cc_final: 0.8229 (mp0) REVERT: A 599 LEU cc_start: 0.9287 (tp) cc_final: 0.9013 (tp) REVERT: A 604 ARG cc_start: 0.8829 (tmt170) cc_final: 0.8543 (ttp80) REVERT: A 639 LEU cc_start: 0.8820 (tp) cc_final: 0.8544 (tp) REVERT: A 714 MET cc_start: 0.7844 (mmm) cc_final: 0.7598 (mmm) REVERT: A 731 LYS cc_start: 0.8200 (pttm) cc_final: 0.7554 (pttp) REVERT: A 828 GLU cc_start: 0.8535 (tp30) cc_final: 0.8140 (tm-30) REVERT: C 208 LEU cc_start: 0.8900 (mt) cc_final: 0.8671 (mt) REVERT: C 217 TYR cc_start: 0.7704 (t80) cc_final: 0.6860 (t80) REVERT: C 219 ASP cc_start: 0.7930 (m-30) cc_final: 0.6552 (m-30) REVERT: C 224 ASN cc_start: 0.9048 (m-40) cc_final: 0.8266 (t0) REVERT: C 266 GLU cc_start: 0.8180 (pm20) cc_final: 0.7933 (pm20) REVERT: C 272 ARG cc_start: 0.7904 (mmm-85) cc_final: 0.7672 (mmm-85) REVERT: C 350 ASN cc_start: 0.7837 (m110) cc_final: 0.7431 (m-40) REVERT: C 356 ARG cc_start: 0.8779 (ptp-170) cc_final: 0.8292 (ttm170) REVERT: C 359 MET cc_start: 0.6641 (tpt) cc_final: 0.6211 (tpt) REVERT: C 361 GLU cc_start: 0.8899 (pt0) cc_final: 0.8593 (pp20) REVERT: B 71 TYR cc_start: 0.7902 (m-80) cc_final: 0.7677 (m-80) REVERT: B 121 LEU cc_start: 0.9271 (tp) cc_final: 0.8939 (tp) REVERT: B 138 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7852 (tm-30) REVERT: B 313 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8299 (tm-30) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.0916 time to fit residues: 28.7527 Evaluate side-chains 166 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 88 optimal weight: 0.0980 chunk 67 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 0.0030 chunk 22 optimal weight: 0.3980 chunk 84 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 HIS ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.123541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.090868 restraints weight = 29271.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.093617 restraints weight = 17081.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.095471 restraints weight = 11631.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.096682 restraints weight = 8858.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.097429 restraints weight = 7347.461| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10734 Z= 0.119 Angle : 0.761 14.551 14507 Z= 0.367 Chirality : 0.047 0.164 1634 Planarity : 0.005 0.084 1838 Dihedral : 6.582 49.017 1485 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.87 % Favored : 88.13 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.22), residues: 1297 helix: -0.61 (0.24), residues: 465 sheet: -1.30 (0.66), residues: 57 loop : -2.76 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 222 TYR 0.016 0.001 TYR A 281 PHE 0.022 0.002 PHE A 650 TRP 0.022 0.002 TRP A 173 HIS 0.010 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (10732) covalent geometry : angle 0.76130 / 0.37 (14501) hydrogen bonds : bond 0.03351 / 2.20 ( 343) hydrogen bonds : angle 5.19027 / 3.55 ( 963) link_TRANS : bond 0.00049 / 0.03 ( 2) link_TRANS : angle 0.45332 / 0.25 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8888 (mmt) cc_final: 0.8565 (mmm) REVERT: A 187 PHE cc_start: 0.6907 (m-80) cc_final: 0.6439 (m-10) REVERT: A 362 ILE cc_start: 0.9360 (pt) cc_final: 0.9055 (mt) REVERT: A 459 GLU cc_start: 0.8627 (mp0) cc_final: 0.8323 (mp0) REVERT: A 599 LEU cc_start: 0.9323 (tp) cc_final: 0.9044 (tp) REVERT: A 604 ARG cc_start: 0.8870 (tmt170) cc_final: 0.8503 (ttp80) REVERT: A 828 GLU cc_start: 0.8543 (tp30) cc_final: 0.8214 (tm-30) REVERT: C 208 LEU cc_start: 0.8895 (mt) cc_final: 0.8675 (mt) REVERT: C 219 ASP cc_start: 0.7876 (m-30) cc_final: 0.7251 (m-30) REVERT: C 266 GLU cc_start: 0.8130 (pm20) cc_final: 0.7913 (pm20) REVERT: C 272 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7645 (mmm-85) REVERT: C 350 ASN cc_start: 0.7621 (m110) cc_final: 0.7219 (m-40) REVERT: C 354 LYS cc_start: 0.8810 (tppt) cc_final: 0.8504 (mmmt) REVERT: C 359 MET cc_start: 0.6684 (tpt) cc_final: 0.6269 (tpt) REVERT: C 361 GLU cc_start: 0.8882 (pt0) cc_final: 0.8586 (pp20) REVERT: B 71 TYR cc_start: 0.7761 (m-80) cc_final: 0.7494 (m-10) REVERT: B 121 LEU cc_start: 0.9243 (tp) cc_final: 0.8907 (tp) REVERT: B 138 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7867 (tm-30) REVERT: B 251 VAL cc_start: 0.9480 (m) cc_final: 0.9156 (m) REVERT: B 252 TYR cc_start: 0.8824 (t80) cc_final: 0.8378 (t80) REVERT: B 313 GLU cc_start: 0.8487 (tm-30) cc_final: 0.7951 (tm-30) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.0976 time to fit residues: 31.4937 Evaluate side-chains 162 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 117 optimal weight: 0.0570 chunk 55 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 374 HIS ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 GLN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS B 311 GLN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.121576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.089304 restraints weight = 29323.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.091902 restraints weight = 17192.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.093646 restraints weight = 11783.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.094804 restraints weight = 9052.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.095494 restraints weight = 7537.768| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10734 Z= 0.141 Angle : 0.765 13.926 14507 Z= 0.376 Chirality : 0.048 0.195 1634 Planarity : 0.005 0.083 1838 Dihedral : 6.639 49.707 1485 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.10 % Favored : 87.90 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.22), residues: 1297 helix: -0.62 (0.24), residues: 458 sheet: -1.70 (0.62), residues: 62 loop : -2.77 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 222 TYR 0.015 0.001 TYR A 281 PHE 0.016 0.002 PHE A 650 TRP 0.031 0.002 TRP A 173 HIS 0.011 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (10732) covalent geometry : angle 0.76489 / 0.38 (14501) hydrogen bonds : bond 0.03525 / 2.32 ( 343) hydrogen bonds : angle 5.30617 / 3.65 ( 963) link_TRANS : bond 0.00113 / 0.06 ( 2) link_TRANS : angle 0.49604 / 0.26 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1869.15 seconds wall clock time: 33 minutes 20.06 seconds (2000.06 seconds total)