Starting phenix.real_space_refine on Thu Jul 2 17:11:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vxc_43616/07_2026/8vxc_43616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vxc_43616/07_2026/8vxc_43616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vxc_43616/07_2026/8vxc_43616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vxc_43616/07_2026/8vxc_43616.map" model { file = "/net/cci-nas-00/data/ceres_data/8vxc_43616/07_2026/8vxc_43616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vxc_43616/07_2026/8vxc_43616.cif" } resolution = 2.93 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= 0.020 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 22 5.49 5 S 27 5.16 5 C 5857 2.51 5 N 1678 2.21 5 O 1806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9390 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 8946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1139, 8946 Classifications: {'peptide': 1139} Modifications used: {'COO': 1} Link IDs: {'PCIS': 5, 'PTRANS': 44, 'TRANS': 1089} Chain breaks: 1 Chain: "B" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 1.57, per 1000 atoms: 0.17 Number of scatterers: 9390 At special positions: 0 Unit cell: (85.855, 99.235, 112.615, 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 27 16.00 P 22 15.00 O 1806 8.00 N 1678 7.00 C 5857 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 custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 235.1 milliseconds 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 3 sheets defined 58.6% alpha, 7.6% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 11 through 16 Processing helix chain 'A' and resid 23 through 33 removed outlier: 3.759A pdb=" N VAL A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 72 removed outlier: 3.796A pdb=" N ALA A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 95 removed outlier: 3.532A pdb=" N ALA A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 118 removed outlier: 3.622A pdb=" N PHE A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N PHE A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 129 Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 151 through 166 removed outlier: 3.636A pdb=" N ASP A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 224 Processing helix chain 'A' and resid 225 through 247 removed outlier: 4.073A pdb=" N LEU A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 268 removed outlier: 3.964A pdb=" N HIS A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 285 through 299 removed outlier: 3.682A pdb=" N GLU A 291 " --> pdb=" O PRO A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 318 Processing helix chain 'A' and resid 330 through 333 Processing helix chain 'A' and resid 334 through 349 removed outlier: 4.279A pdb=" N ILE A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 375 removed outlier: 3.648A pdb=" N THR A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 400 removed outlier: 3.671A pdb=" N ALA A 397 " --> pdb=" O MET A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 418 removed outlier: 3.683A pdb=" N PHE A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 removed outlier: 3.611A pdb=" N ILE A 422 " --> pdb=" O PRO A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 453 removed outlier: 3.513A pdb=" N ARG A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 461 removed outlier: 6.180A pdb=" N ASP A 457 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP A 459 " --> pdb=" O GLN A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 485 Processing helix chain 'A' and resid 553 through 568 Processing helix chain 'A' and resid 578 through 596 removed outlier: 3.908A pdb=" N VAL A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Proline residue: A 584 - end of helix removed outlier: 3.992A pdb=" N GLU A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 removed outlier: 3.536A pdb=" N LEU A 609 " --> pdb=" O PRO A 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 606 through 609' Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 624 through 633 Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.644A pdb=" N ARG A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 734 Processing helix chain 'A' and resid 742 through 760 Processing helix chain 'A' and resid 762 through 773 Processing helix chain 'A' and resid 788 through 813 removed outlier: 4.166A pdb=" N ILE A 792 " --> pdb=" O GLN A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 830 Processing helix chain 'A' and resid 833 through 840 Processing helix chain 'A' and resid 844 through 865 removed outlier: 3.562A pdb=" N ARG A 848 " --> pdb=" O ASP A 844 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 865 " --> pdb=" O TYR A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 878 Processing helix chain 'A' and resid 880 through 907 removed outlier: 3.606A pdb=" N ALA A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA A 892 " --> pdb=" O ASP A 888 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LYS A 893 " --> pdb=" O ALA A 889 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLN A 896 " --> pdb=" O ALA A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 925 Processing helix chain 'A' and resid 938 through 948 Processing helix chain 'A' and resid 961 through 970 Processing helix chain 'A' and resid 973 through 990 Processing helix chain 'A' and resid 999 through 1003 Processing helix chain 'A' and resid 1007 through 1015 Processing helix chain 'A' and resid 1018 through 1028 removed outlier: 3.702A pdb=" N GLY A1028 " --> pdb=" O LEU A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1042 removed outlier: 4.053A pdb=" N ILE A1036 " --> pdb=" O ARG A1032 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A1037 " --> pdb=" O LEU A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1056 Processing helix chain 'A' and resid 1058 through 1063 removed outlier: 3.528A pdb=" N ILE A1062 " --> pdb=" O SER A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1079 removed outlier: 4.201A pdb=" N VAL A1077 " --> pdb=" O PRO A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1085 Processing sheet with id=AA1, first strand: chain 'A' and resid 381 through 382 removed outlier: 6.357A pdb=" N SER A 382 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A 353 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA A 406 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N PHE A 355 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ARG A 352 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N ILE A 429 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 354 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASP A 431 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE A 356 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY A 426 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL A 464 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE A 428 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU A 466 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N PHE A 430 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 526 through 531 removed outlier: 6.204A pdb=" N SER A 527 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LEU A 515 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY A 513 " --> pdb=" O PHE A 529 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 715 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL A 572 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N SER A 663 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE A 574 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1095 through 1100 removed outlier: 8.507A pdb=" N LEU A1150 " --> pdb=" O LEU A1118 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A1118 " --> pdb=" O LEU A1150 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A1152 " --> pdb=" O LEU A1116 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2737 1.33 - 1.45: 1545 1.45 - 1.57: 5247 1.57 - 1.69: 42 1.69 - 1.81: 46 Bond restraints: 9617 Sorted by residual: bond pdb=" C1' DC B 12 " pdb=" N1 DC B 12 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.30e+01 bond pdb=" C3' DA C 8 " pdb=" C2' DA C 8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.46e+00 bond pdb=" C5' DT B 10 " pdb=" C4' DT B 10 " ideal model delta sigma weight residual 1.512 1.532 -0.020 7.00e-03 2.04e+04 8.40e+00 bond pdb=" C3' DC C 2 " pdb=" C2' DC C 2 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.92e+00 bond pdb=" C5' DT B 9 " pdb=" C4' DT B 9 " ideal model delta sigma weight residual 1.512 1.527 -0.015 7.00e-03 2.04e+04 4.46e+00 ... (remaining 9612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 12777 1.38 - 2.76: 309 2.76 - 4.15: 53 4.15 - 5.53: 7 5.53 - 6.91: 2 Bond angle restraints: 13148 Sorted by residual: angle pdb=" N SER A 664 " pdb=" CA SER A 664 " pdb=" C SER A 664 " ideal model delta sigma weight residual 110.07 103.16 6.91 1.46e+00 4.69e-01 2.24e+01 angle pdb=" N3 DT B 4 " pdb=" C4 DT B 4 " pdb=" O4 DT B 4 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT C 5 " pdb=" C4 DT C 5 " pdb=" O4 DT C 5 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT B 10 " pdb=" C4 DT B 10 " pdb=" O4 DT B 10 " ideal model delta sigma weight residual 119.90 122.26 -2.36 6.00e-01 2.78e+00 1.55e+01 angle pdb=" N3 DT B 9 " pdb=" C4 DT B 9 " pdb=" O4 DT B 9 " ideal model delta sigma weight residual 119.90 122.19 -2.29 6.00e-01 2.78e+00 1.45e+01 ... (remaining 13143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5194 17.97 - 35.95: 385 35.95 - 53.92: 110 53.92 - 71.90: 40 71.90 - 89.87: 5 Dihedral angle restraints: 5734 sinusoidal: 2453 harmonic: 3281 Sorted by residual: dihedral pdb=" CA PRO A 665 " pdb=" C PRO A 665 " pdb=" N THR A 666 " pdb=" CA THR A 666 " ideal model delta harmonic sigma weight residual 180.00 161.87 18.13 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA PRO A 541 " pdb=" C PRO A 541 " pdb=" N ASN A 542 " pdb=" CA ASN A 542 " ideal model delta harmonic sigma weight residual -180.00 -162.91 -17.09 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ALA A 5 " pdb=" C ALA A 5 " pdb=" N ASP A 6 " pdb=" CA ASP A 6 " ideal model delta harmonic sigma weight residual -180.00 -164.84 -15.16 0 5.00e+00 4.00e-02 9.19e+00 ... (remaining 5731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 926 0.030 - 0.060: 376 0.060 - 0.090: 114 0.090 - 0.120: 63 0.120 - 0.150: 14 Chirality restraints: 1493 Sorted by residual: chirality pdb=" CA VAL A 955 " pdb=" N VAL A 955 " pdb=" C VAL A 955 " pdb=" CB VAL A 955 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA TRP A 563 " pdb=" N TRP A 563 " pdb=" C TRP A 563 " pdb=" CB TRP A 563 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA ILE A1138 " pdb=" N ILE A1138 " pdb=" C ILE A1138 " pdb=" CB ILE A1138 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1490 not shown) Planarity restraints: 1636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 535 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO A 536 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 536 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 536 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 534 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A 535 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 375 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO A 376 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 376 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 376 " -0.024 5.00e-02 4.00e+02 ... (remaining 1633 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 910 2.74 - 3.28: 9555 3.28 - 3.82: 16371 3.82 - 4.36: 19477 4.36 - 4.90: 32531 Nonbonded interactions: 78844 Sorted by model distance: nonbonded pdb=" NH1 ARG A 454 " pdb=" O ASP A 828 " model vdw 2.206 3.120 nonbonded pdb=" NH2 ARG A 595 " pdb=" OP1 DT B 4 " model vdw 2.215 3.120 nonbonded pdb=" O PHE A 413 " pdb=" ND2 ASN A 417 " model vdw 2.255 3.120 nonbonded pdb=" OG1 THR A1014 " pdb=" OG SER A1022 " model vdw 2.271 3.040 nonbonded pdb=" O ARG A 360 " pdb=" OG SER A 363 " model vdw 2.276 3.040 ... (remaining 78839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.650 Find NCS groups from input model: 0.020 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:8.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9617 Z= 0.195 Angle : 0.531 6.909 13148 Z= 0.337 Chirality : 0.040 0.150 1493 Planarity : 0.004 0.054 1636 Dihedral : 14.757 89.872 3614 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.25), residues: 1135 helix: 0.86 (0.22), residues: 590 sheet: -0.28 (0.55), residues: 98 loop : -0.56 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 646 TYR 0.021 0.001 TYR A 645 PHE 0.015 0.001 PHE A 925 TRP 0.025 0.001 TRP A 35 HIS 0.009 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.20 ( 9617) covalent geometry : angle 0.53058 / 0.34 (13148) hydrogen bonds : bond 0.15000 / 12.73 ( 475) hydrogen bonds : angle 6.16359 / 5.27 ( 1376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7427 (tpp) cc_final: 0.7090 (mmt) REVERT: A 336 THR cc_start: 0.7888 (m) cc_final: 0.7516 (m) REVERT: A 394 ASP cc_start: 0.6899 (m-30) cc_final: 0.6627 (m-30) REVERT: A 448 GLN cc_start: 0.8273 (tt0) cc_final: 0.8045 (tt0) REVERT: A 637 HIS cc_start: 0.7948 (t-90) cc_final: 0.7737 (t-170) REVERT: A 692 VAL cc_start: 0.7445 (p) cc_final: 0.7071 (t) REVERT: A 863 TRP cc_start: 0.7714 (m100) cc_final: 0.6802 (m-10) REVERT: A 928 TYR cc_start: 0.8425 (t80) cc_final: 0.8172 (t80) REVERT: A 1048 SER cc_start: 0.7645 (t) cc_final: 0.7110 (p) REVERT: A 1051 GLU cc_start: 0.7144 (mp0) cc_final: 0.6653 (mp0) REVERT: A 1078 MET cc_start: 0.3555 (ttt) cc_final: 0.3306 (ttt) REVERT: A 1098 ARG cc_start: 0.6652 (ttt90) cc_final: 0.6342 (ttt90) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.5487 time to fit residues: 112.8840 Evaluate side-chains 150 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.0770 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.0770 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 365 GLN A 821 GLN A 989 ASN A1064 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.168151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.151858 restraints weight = 12514.570| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.81 r_work: 0.3898 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9617 Z= 0.166 Angle : 0.589 6.171 13148 Z= 0.313 Chirality : 0.043 0.158 1493 Planarity : 0.005 0.053 1636 Dihedral : 14.576 75.513 1498 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.00 % Allowed : 10.44 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.25), residues: 1135 helix: 0.75 (0.21), residues: 596 sheet: -0.11 (0.56), residues: 100 loop : -0.66 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 944 TYR 0.015 0.002 TYR A 445 PHE 0.027 0.002 PHE A 695 TRP 0.022 0.001 TRP A 266 HIS 0.008 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 ( 9617) covalent geometry : angle 0.58931 / 0.31 (13148) hydrogen bonds : bond 0.04662 / 4.13 ( 475) hydrogen bonds : angle 5.19992 / 4.31 ( 1376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7167 (tpp) cc_final: 0.6814 (mmt) REVERT: A 394 ASP cc_start: 0.7175 (m-30) cc_final: 0.6891 (m-30) REVERT: A 448 GLN cc_start: 0.8274 (tt0) cc_final: 0.7996 (tt0) REVERT: A 695 PHE cc_start: 0.7860 (t80) cc_final: 0.7514 (t80) REVERT: A 863 TRP cc_start: 0.7802 (m100) cc_final: 0.6838 (m-10) REVERT: A 1048 SER cc_start: 0.7494 (t) cc_final: 0.7117 (p) REVERT: A 1078 MET cc_start: 0.3672 (ttt) cc_final: 0.3384 (ttt) outliers start: 19 outliers final: 10 residues processed: 173 average time/residue: 0.5265 time to fit residues: 96.6236 Evaluate side-chains 161 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1020 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 29 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN A 53 GLN A 119 HIS A 365 GLN ** A 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1050 GLN ** 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 = 0.4183 r_free = 0.4183 target = 0.167872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.151496 restraints weight = 12439.154| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 1.81 r_work: 0.3880 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9617 Z= 0.190 Angle : 0.589 8.031 13148 Z= 0.311 Chirality : 0.043 0.213 1493 Planarity : 0.005 0.054 1636 Dihedral : 14.523 74.219 1498 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.32 % Allowed : 13.50 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.25), residues: 1135 helix: 0.76 (0.22), residues: 593 sheet: -0.06 (0.57), residues: 100 loop : -0.83 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 654 TYR 0.021 0.002 TYR A 928 PHE 0.016 0.002 PHE A 106 TRP 0.028 0.002 TRP A 266 HIS 0.007 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 ( 9617) covalent geometry : angle 0.58861 / 0.31 (13148) hydrogen bonds : bond 0.04437 / 3.87 ( 475) hydrogen bonds : angle 5.13086 / 4.17 ( 1376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.7158 (tpp) cc_final: 0.6832 (mmt) REVERT: A 264 ASP cc_start: 0.6882 (OUTLIER) cc_final: 0.6544 (t0) REVERT: A 448 GLN cc_start: 0.8249 (tt0) cc_final: 0.7962 (tt0) REVERT: A 768 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7472 (pt0) REVERT: A 851 LEU cc_start: 0.7157 (mt) cc_final: 0.6927 (mp) REVERT: A 863 TRP cc_start: 0.7831 (m100) cc_final: 0.6842 (m-10) REVERT: A 1048 SER cc_start: 0.7593 (t) cc_final: 0.7190 (p) REVERT: A 1078 MET cc_start: 0.3733 (ttt) cc_final: 0.3431 (ttt) REVERT: A 1162 MET cc_start: 0.7507 (tmm) cc_final: 0.6916 (ttm) outliers start: 22 outliers final: 9 residues processed: 160 average time/residue: 0.4851 time to fit residues: 82.8309 Evaluate side-chains 157 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 1020 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 71 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 79 optimal weight: 0.0470 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS ** A 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.168569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.152256 restraints weight = 12423.299| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 1.80 r_work: 0.3898 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9617 Z= 0.158 Angle : 0.568 6.957 13148 Z= 0.302 Chirality : 0.042 0.187 1493 Planarity : 0.005 0.053 1636 Dihedral : 14.466 74.668 1498 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.53 % Allowed : 15.40 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.25), residues: 1135 helix: 0.84 (0.22), residues: 588 sheet: -0.06 (0.57), residues: 98 loop : -0.76 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 944 TYR 0.016 0.002 TYR A 445 PHE 0.013 0.002 PHE A 106 TRP 0.026 0.002 TRP A 266 HIS 0.006 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 9617) covalent geometry : angle 0.56838 / 0.30 (13148) hydrogen bonds : bond 0.04128 / 3.60 ( 475) hydrogen bonds : angle 5.05353 / 4.10 ( 1376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7092 (tpp) cc_final: 0.6775 (mmt) REVERT: A 388 ILE cc_start: 0.7882 (mm) cc_final: 0.7343 (mm) REVERT: A 393 MET cc_start: 0.7000 (tpt) cc_final: 0.6783 (mmm) REVERT: A 448 GLN cc_start: 0.8235 (tt0) cc_final: 0.7953 (tt0) REVERT: A 654 ARG cc_start: 0.6643 (mtm110) cc_final: 0.6433 (mtm110) REVERT: A 768 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7577 (pt0) REVERT: A 851 LEU cc_start: 0.7127 (mt) cc_final: 0.6894 (mp) REVERT: A 863 TRP cc_start: 0.7838 (m100) cc_final: 0.6840 (m-10) REVERT: A 1016 THR cc_start: 0.7315 (p) cc_final: 0.7107 (p) REVERT: A 1048 SER cc_start: 0.7598 (t) cc_final: 0.7175 (p) REVERT: A 1078 MET cc_start: 0.3612 (ttt) cc_final: 0.3348 (ttt) REVERT: A 1162 MET cc_start: 0.7471 (tmm) cc_final: 0.6985 (ttm) REVERT: A 1165 TYR cc_start: 0.7315 (t80) cc_final: 0.7075 (t80) outliers start: 24 outliers final: 14 residues processed: 166 average time/residue: 0.4929 time to fit residues: 87.6784 Evaluate side-chains 158 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 1020 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 0.0970 chunk 76 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 62 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS A 502 GLN A 542 ASN ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.167756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.151540 restraints weight = 12508.090| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 1.81 r_work: 0.3876 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9617 Z= 0.179 Angle : 0.563 7.455 13148 Z= 0.300 Chirality : 0.042 0.194 1493 Planarity : 0.005 0.055 1636 Dihedral : 14.419 76.083 1498 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.43 % Allowed : 17.30 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.25), residues: 1135 helix: 0.94 (0.22), residues: 583 sheet: -0.10 (0.56), residues: 98 loop : -0.84 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 944 TYR 0.025 0.002 TYR A 928 PHE 0.014 0.002 PHE A 106 TRP 0.026 0.002 TRP A 266 HIS 0.005 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 9617) covalent geometry : angle 0.56347 / 0.30 (13148) hydrogen bonds : bond 0.04136 / 3.60 ( 475) hydrogen bonds : angle 5.03317 / 4.07 ( 1376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7090 (tpp) cc_final: 0.6766 (mmt) REVERT: A 264 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.6557 (t0) REVERT: A 367 GLU cc_start: 0.6868 (tm-30) cc_final: 0.6647 (tp30) REVERT: A 393 MET cc_start: 0.7030 (tpt) cc_final: 0.6826 (mmm) REVERT: A 448 GLN cc_start: 0.8263 (tt0) cc_final: 0.7982 (tt0) REVERT: A 863 TRP cc_start: 0.7855 (m100) cc_final: 0.6820 (m-10) REVERT: A 1016 THR cc_start: 0.7408 (p) cc_final: 0.7182 (p) REVERT: A 1048 SER cc_start: 0.7589 (t) cc_final: 0.7158 (p) REVERT: A 1078 MET cc_start: 0.3541 (ttt) cc_final: 0.3259 (ttt) REVERT: A 1162 MET cc_start: 0.7478 (tmm) cc_final: 0.7007 (ttm) outliers start: 23 outliers final: 14 residues processed: 162 average time/residue: 0.4608 time to fit residues: 79.8506 Evaluate side-chains 159 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 1020 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS ** A 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.166356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.150110 restraints weight = 12603.271| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.83 r_work: 0.3866 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9617 Z= 0.189 Angle : 0.579 7.800 13148 Z= 0.308 Chirality : 0.043 0.198 1493 Planarity : 0.005 0.056 1636 Dihedral : 14.363 77.287 1498 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.85 % Allowed : 17.09 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.25), residues: 1135 helix: 1.00 (0.22), residues: 584 sheet: -0.16 (0.57), residues: 98 loop : -0.87 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 696 TYR 0.030 0.002 TYR A 928 PHE 0.015 0.002 PHE A 695 TRP 0.033 0.002 TRP A 266 HIS 0.004 0.001 HIS A 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 ( 9617) covalent geometry : angle 0.57861 / 0.31 (13148) hydrogen bonds : bond 0.04122 / 3.59 ( 475) hydrogen bonds : angle 5.00793 / 4.04 ( 1376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.7046 (tpp) cc_final: 0.6750 (mmt) REVERT: A 411 LEU cc_start: 0.7416 (tp) cc_final: 0.7195 (tt) REVERT: A 448 GLN cc_start: 0.8261 (tt0) cc_final: 0.7939 (tt0) REVERT: A 699 ILE cc_start: 0.8371 (pt) cc_final: 0.8156 (pt) REVERT: A 768 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7613 (pt0) REVERT: A 800 GLN cc_start: 0.7747 (mt0) cc_final: 0.7509 (mt0) REVERT: A 851 LEU cc_start: 0.7115 (mt) cc_final: 0.6900 (mp) REVERT: A 863 TRP cc_start: 0.7868 (m100) cc_final: 0.6851 (m100) REVERT: A 1016 THR cc_start: 0.7440 (p) cc_final: 0.7209 (p) REVERT: A 1048 SER cc_start: 0.7604 (t) cc_final: 0.7181 (p) REVERT: A 1078 MET cc_start: 0.3528 (ttt) cc_final: 0.3242 (ttt) REVERT: A 1162 MET cc_start: 0.7477 (tmm) cc_final: 0.6688 (tmm) REVERT: A 1165 TYR cc_start: 0.7392 (t80) cc_final: 0.7184 (t80) outliers start: 27 outliers final: 16 residues processed: 174 average time/residue: 0.4983 time to fit residues: 92.8702 Evaluate side-chains 167 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1020 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 93 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 66 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS A 502 GLN A 542 ASN ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.166931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.151000 restraints weight = 12597.539| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 1.81 r_work: 0.3878 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9617 Z= 0.157 Angle : 0.579 7.827 13148 Z= 0.307 Chirality : 0.042 0.196 1493 Planarity : 0.005 0.054 1636 Dihedral : 14.303 77.104 1498 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.32 % Allowed : 18.04 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.26), residues: 1135 helix: 0.92 (0.22), residues: 592 sheet: -0.22 (0.57), residues: 98 loop : -0.78 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 944 TYR 0.021 0.002 TYR A1099 PHE 0.013 0.001 PHE A 293 TRP 0.032 0.002 TRP A 266 HIS 0.003 0.001 HIS A 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 9617) covalent geometry : angle 0.57925 / 0.31 (13148) hydrogen bonds : bond 0.04040 / 3.49 ( 475) hydrogen bonds : angle 4.94765 / 4.01 ( 1376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7056 (tpp) cc_final: 0.6768 (mmt) REVERT: A 264 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.6541 (OUTLIER) REVERT: A 367 GLU cc_start: 0.6833 (tm-30) cc_final: 0.6594 (tp30) REVERT: A 411 LEU cc_start: 0.7464 (tp) cc_final: 0.7240 (tt) REVERT: A 448 GLN cc_start: 0.8249 (tt0) cc_final: 0.7964 (tt0) REVERT: A 699 ILE cc_start: 0.8382 (pt) cc_final: 0.8158 (pt) REVERT: A 800 GLN cc_start: 0.7734 (mt0) cc_final: 0.7508 (mt0) REVERT: A 851 LEU cc_start: 0.7068 (mt) cc_final: 0.6846 (mp) REVERT: A 863 TRP cc_start: 0.7878 (m100) cc_final: 0.6870 (m-10) REVERT: A 924 VAL cc_start: 0.7348 (OUTLIER) cc_final: 0.7023 (t) REVERT: A 1016 THR cc_start: 0.7402 (p) cc_final: 0.7168 (p) REVERT: A 1048 SER cc_start: 0.7581 (t) cc_final: 0.7210 (p) REVERT: A 1076 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7797 (mmm160) REVERT: A 1078 MET cc_start: 0.3458 (ttt) cc_final: 0.3206 (ttt) outliers start: 22 outliers final: 15 residues processed: 162 average time/residue: 0.4517 time to fit residues: 78.5298 Evaluate side-chains 165 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 823 GLU Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1076 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 76 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.165747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.149688 restraints weight = 12584.622| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.82 r_work: 0.3862 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9617 Z= 0.199 Angle : 0.601 8.670 13148 Z= 0.318 Chirality : 0.044 0.201 1493 Planarity : 0.006 0.076 1636 Dihedral : 14.294 77.794 1498 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.43 % Allowed : 18.46 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.25), residues: 1135 helix: 0.90 (0.22), residues: 586 sheet: -0.37 (0.56), residues: 98 loop : -0.88 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 156 TYR 0.030 0.003 TYR A 928 PHE 0.014 0.002 PHE A 925 TRP 0.034 0.002 TRP A 266 HIS 0.004 0.001 HIS A 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 9617) covalent geometry : angle 0.60092 / 0.32 (13148) hydrogen bonds : bond 0.04138 / 3.59 ( 475) hydrogen bonds : angle 5.00064 / 4.03 ( 1376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 ASP cc_start: 0.6864 (OUTLIER) cc_final: 0.6554 (OUTLIER) REVERT: A 367 GLU cc_start: 0.6907 (tm-30) cc_final: 0.6659 (tp30) REVERT: A 411 LEU cc_start: 0.7443 (tp) cc_final: 0.7230 (tt) REVERT: A 448 GLN cc_start: 0.8240 (tt0) cc_final: 0.7912 (tt0) REVERT: A 699 ILE cc_start: 0.8377 (pt) cc_final: 0.8158 (pt) REVERT: A 800 GLN cc_start: 0.7740 (mt0) cc_final: 0.7514 (mt0) REVERT: A 851 LEU cc_start: 0.7144 (mt) cc_final: 0.6928 (mp) REVERT: A 863 TRP cc_start: 0.7896 (m100) cc_final: 0.6915 (m100) REVERT: A 924 VAL cc_start: 0.7374 (OUTLIER) cc_final: 0.7058 (t) REVERT: A 1016 THR cc_start: 0.7426 (p) cc_final: 0.7196 (p) REVERT: A 1048 SER cc_start: 0.7631 (t) cc_final: 0.7186 (p) REVERT: A 1076 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7755 (tpt90) REVERT: A 1078 MET cc_start: 0.3520 (ttt) cc_final: 0.3248 (ttt) outliers start: 23 outliers final: 13 residues processed: 169 average time/residue: 0.4835 time to fit residues: 87.7166 Evaluate side-chains 166 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain A residue 1076 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 82 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 86 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS A 542 ASN ** A1050 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 = 0.4166 r_free = 0.4166 target = 0.166130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.150035 restraints weight = 12495.147| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.81 r_work: 0.3874 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9617 Z= 0.184 Angle : 0.615 9.304 13148 Z= 0.324 Chirality : 0.044 0.215 1493 Planarity : 0.005 0.057 1636 Dihedral : 14.258 77.502 1498 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.64 % Allowed : 18.67 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.25), residues: 1135 helix: 0.83 (0.22), residues: 592 sheet: -0.43 (0.56), residues: 98 loop : -0.88 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 70 TYR 0.032 0.002 TYR A 928 PHE 0.035 0.002 PHE A 106 TRP 0.029 0.002 TRP A 266 HIS 0.004 0.001 HIS A 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 9617) covalent geometry : angle 0.61463 / 0.32 (13148) hydrogen bonds : bond 0.04090 / 3.53 ( 475) hydrogen bonds : angle 5.01193 / 4.03 ( 1376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 ARG cc_start: 0.7516 (mtt-85) cc_final: 0.7242 (mtt-85) REVERT: A 448 GLN cc_start: 0.8228 (tt0) cc_final: 0.7898 (tt0) REVERT: A 800 GLN cc_start: 0.7740 (mt0) cc_final: 0.7507 (mt0) REVERT: A 851 LEU cc_start: 0.7157 (mt) cc_final: 0.6909 (mp) REVERT: A 863 TRP cc_start: 0.7894 (m100) cc_final: 0.6899 (m100) REVERT: A 924 VAL cc_start: 0.7402 (OUTLIER) cc_final: 0.7088 (t) REVERT: A 968 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: A 1016 THR cc_start: 0.7401 (p) cc_final: 0.7181 (p) REVERT: A 1048 SER cc_start: 0.7649 (t) cc_final: 0.7216 (p) REVERT: A 1076 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7808 (tpt90) REVERT: A 1078 MET cc_start: 0.3437 (ttt) cc_final: 0.3192 (ttt) REVERT: A 1165 TYR cc_start: 0.7359 (t80) cc_final: 0.7137 (t80) outliers start: 25 outliers final: 13 residues processed: 167 average time/residue: 0.4867 time to fit residues: 87.2161 Evaluate side-chains 162 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain A residue 1076 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 96 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 86 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS A 400 GLN A 831 GLN ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.167080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.150974 restraints weight = 12471.935| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.82 r_work: 0.3886 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9617 Z= 0.156 Angle : 0.607 10.026 13148 Z= 0.321 Chirality : 0.043 0.200 1493 Planarity : 0.005 0.055 1636 Dihedral : 14.212 77.817 1498 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.90 % Allowed : 19.62 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.25), residues: 1135 helix: 0.86 (0.22), residues: 592 sheet: -0.43 (0.56), residues: 98 loop : -0.84 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 156 TYR 0.017 0.002 TYR A 445 PHE 0.032 0.002 PHE A 106 TRP 0.033 0.002 TRP A 266 HIS 0.004 0.001 HIS A1097 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 9617) covalent geometry : angle 0.60657 / 0.32 (13148) hydrogen bonds : bond 0.03939 / 3.39 ( 475) hydrogen bonds : angle 5.02406 / 4.04 ( 1376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.6874 (tpp) cc_final: 0.6636 (mmt) REVERT: A 123 ARG cc_start: 0.8120 (ttm170) cc_final: 0.7912 (ttm170) REVERT: A 264 ASP cc_start: 0.6752 (OUTLIER) cc_final: 0.6459 (t0) REVERT: A 448 GLN cc_start: 0.8235 (tt0) cc_final: 0.7953 (tt0) REVERT: A 800 GLN cc_start: 0.8151 (mt0) cc_final: 0.7901 (mt0) REVERT: A 851 LEU cc_start: 0.7117 (mt) cc_final: 0.6876 (mp) REVERT: A 863 TRP cc_start: 0.7873 (m100) cc_final: 0.6907 (m-10) REVERT: A 924 VAL cc_start: 0.7320 (OUTLIER) cc_final: 0.6995 (t) REVERT: A 1016 THR cc_start: 0.7381 (p) cc_final: 0.7154 (p) REVERT: A 1048 SER cc_start: 0.7663 (t) cc_final: 0.7217 (p) REVERT: A 1076 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7794 (tpt90) REVERT: A 1078 MET cc_start: 0.3372 (ttt) cc_final: 0.3144 (ttt) REVERT: A 1165 TYR cc_start: 0.7328 (t80) cc_final: 0.7100 (t80) outliers start: 18 outliers final: 11 residues processed: 165 average time/residue: 0.5248 time to fit residues: 92.4922 Evaluate side-chains 167 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1076 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 chunk 56 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 109 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS A 400 GLN ** A1050 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 = 0.4172 r_free = 0.4172 target = 0.166580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.150467 restraints weight = 12477.106| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.83 r_work: 0.3885 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9617 Z= 0.164 Angle : 0.626 12.285 13148 Z= 0.326 Chirality : 0.043 0.222 1493 Planarity : 0.005 0.055 1636 Dihedral : 14.196 78.874 1498 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.00 % Allowed : 19.94 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.25), residues: 1135 helix: 0.73 (0.22), residues: 600 sheet: -0.43 (0.56), residues: 98 loop : -0.80 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 484 TYR 0.033 0.002 TYR A 928 PHE 0.030 0.002 PHE A 106 TRP 0.038 0.002 TRP A 266 HIS 0.004 0.001 HIS A1097 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 9617) covalent geometry : angle 0.62563 / 0.33 (13148) hydrogen bonds : bond 0.04006 / 3.42 ( 475) hydrogen bonds : angle 5.06348 / 4.06 ( 1376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2863.06 seconds wall clock time: 49 minutes 27.19 seconds (2967.19 seconds total)