Starting phenix.real_space_refine on Wed Aug 5 10:22:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vxc_43616/08_2026/8vxc_43616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vxc_43616/08_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_43616/08_2026/8vxc_43616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vxc_43616/08_2026/8vxc_43616.map" model { file = "/net/cci-nas-00/data/ceres_data/8vxc_43616/08_2026/8vxc_43616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vxc_43616/08_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-2.2rc3-6140/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: 1.64, 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: 0.61 Conformation dependent library (CDL) restraints added in 326.2 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: 0.77 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: 1.17 Time building geometry restraints manager: 0.84 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: 12774 1.38 - 2.76: 312 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: 1.050 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.390 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.130 ------------------------------------------------------------------------------- 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= 0.338 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 0.53146 / 0.34 (13148) hydrogen bonds : bond 0.15000 / 12.81 ( 475) hydrogen bonds : angle 6.16359 / 5.28 ( 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 : 0.253 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: 0.4660 time to fit residues: 96.2770 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 : 0.206 ------------------------------------------------------------------------------- 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 = 0.168141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.151866 restraints weight = 12509.313| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.81 r_work: 0.3891 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1594 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= 0.166 Angle : 0.586 6.182 13148 Z= 0.311 Chirality : 0.043 0.155 1493 Planarity : 0.005 0.053 1636 Dihedral : 14.553 75.381 1498 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.00 % Allowed : 10.34 % Favored : 87.66 % 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: -0.12 (0.56), residues: 100 loop : -0.66 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1098 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 0.00362 / 0.17 ( 9617) covalent geometry : angle 0.58614 / 0.31 (13148) hydrogen bonds : bond 0.04827 / 4.27 ( 475) hydrogen bonds : angle 5.20689 / 4.32 ( 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 182 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7134 (tpp) cc_final: 0.6788 (mmt) REVERT: A 394 ASP cc_start: 0.7171 (m-30) cc_final: 0.6887 (m-30) REVERT: A 448 GLN cc_start: 0.8273 (tt0) cc_final: 0.7997 (tt0) REVERT: A 654 ARG cc_start: 0.6749 (mtm110) cc_final: 0.6532 (mtm110) REVERT: A 695 PHE cc_start: 0.7799 (t80) cc_final: 0.7439 (t80) REVERT: A 863 TRP cc_start: 0.7796 (m100) cc_final: 0.6907 (m-10) REVERT: A 1048 SER cc_start: 0.7500 (t) cc_final: 0.7121 (p) REVERT: A 1078 MET cc_start: 0.3728 (ttt) cc_final: 0.3426 (ttt) outliers start: 19 outliers final: 10 residues processed: 172 average time/residue: 0.5047 time to fit residues: 92.4428 Evaluate side-chains 156 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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: 0.9980 chunk 97 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN A 53 GLN A 365 GLN ** A 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1050 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.167749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.151395 restraints weight = 12415.942| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 1.80 r_work: 0.3877 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1980 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= 0.196 Angle : 0.590 7.417 13148 Z= 0.312 Chirality : 0.044 0.198 1493 Planarity : 0.005 0.055 1636 Dihedral : 14.507 73.971 1498 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.43 % Allowed : 12.97 % Favored : 84.60 % 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: 0.75 (0.22), residues: 593 sheet: -0.07 (0.56), residues: 100 loop : -0.86 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 944 TYR 0.022 0.002 TYR A 928 PHE 0.016 0.002 PHE A 106 TRP 0.031 0.002 TRP A 266 HIS 0.007 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 ( 9617) covalent geometry : angle 0.59000 / 0.31 (13148) hydrogen bonds : bond 0.04501 / 3.93 ( 475) hydrogen bonds : angle 5.14708 / 4.18 ( 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 174 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.7136 (tpp) cc_final: 0.6811 (mmt) REVERT: A 388 ILE cc_start: 0.7965 (mm) cc_final: 0.7708 (mm) REVERT: A 448 GLN cc_start: 0.8253 (tt0) cc_final: 0.7970 (tt0) REVERT: A 768 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7591 (pt0) REVERT: A 863 TRP cc_start: 0.7838 (m100) cc_final: 0.6859 (m-10) REVERT: A 1048 SER cc_start: 0.7603 (t) cc_final: 0.7201 (p) REVERT: A 1078 MET cc_start: 0.3732 (ttt) cc_final: 0.3434 (ttt) REVERT: A 1162 MET cc_start: 0.7509 (tmm) cc_final: 0.6956 (ttm) outliers start: 23 outliers final: 11 residues processed: 162 average time/residue: 0.5037 time to fit residues: 87.2568 Evaluate side-chains 157 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 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: 0.0270 chunk 103 optimal weight: 0.5980 chunk 79 optimal weight: 0.0970 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 75 optimal weight: 0.0980 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.2636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.169307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.152913 restraints weight = 12394.942| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.81 r_work: 0.3913 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9617 Z= 0.128 Angle : 0.554 7.164 13148 Z= 0.294 Chirality : 0.041 0.181 1493 Planarity : 0.005 0.050 1636 Dihedral : 14.389 74.010 1498 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.22 % Allowed : 15.72 % 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: 0.22 (0.25), residues: 1135 helix: 0.94 (0.22), residues: 584 sheet: -0.08 (0.56), residues: 98 loop : -0.78 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 944 TYR 0.014 0.002 TYR A 445 PHE 0.011 0.001 PHE A 293 TRP 0.026 0.001 TRP A 266 HIS 0.006 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 9617) covalent geometry : angle 0.55385 / 0.29 (13148) hydrogen bonds : bond 0.03939 / 3.41 ( 475) hydrogen bonds : angle 5.00304 / 4.07 ( 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 173 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.7106 (tpp) cc_final: 0.6778 (mmt) REVERT: A 410 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7304 (tmtt) REVERT: A 448 GLN cc_start: 0.8234 (tt0) cc_final: 0.7942 (tt0) REVERT: A 768 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7562 (pt0) REVERT: A 863 TRP cc_start: 0.7795 (m100) cc_final: 0.6832 (m-10) REVERT: A 1016 THR cc_start: 0.7304 (p) cc_final: 0.7073 (p) REVERT: A 1048 SER cc_start: 0.7579 (t) cc_final: 0.7162 (p) REVERT: A 1078 MET cc_start: 0.3412 (ttt) cc_final: 0.3164 (ttt) REVERT: A 1162 MET cc_start: 0.7441 (tmm) cc_final: 0.6996 (ttm) outliers start: 21 outliers final: 14 residues processed: 163 average time/residue: 0.4863 time to fit residues: 84.7156 Evaluate side-chains 160 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 410 LYS 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 796 ILE Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 1050 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 0.0040 chunk 76 optimal weight: 2.9990 chunk 113 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.169078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.152845 restraints weight = 12529.320| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 1.82 r_work: 0.3910 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9617 Z= 0.143 Angle : 0.554 8.755 13148 Z= 0.293 Chirality : 0.042 0.188 1493 Planarity : 0.005 0.051 1636 Dihedral : 14.335 75.419 1498 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.43 % Allowed : 16.77 % Favored : 80.80 % 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: 0.27 (0.25), residues: 1135 helix: 1.00 (0.22), residues: 586 sheet: -0.11 (0.56), residues: 98 loop : -0.78 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 944 TYR 0.030 0.002 TYR A 928 PHE 0.012 0.001 PHE A 293 TRP 0.025 0.001 TRP A 266 HIS 0.006 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9617) covalent geometry : angle 0.55413 / 0.29 (13148) hydrogen bonds : bond 0.03927 / 3.41 ( 475) hydrogen bonds : angle 4.93104 / 4.00 ( 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 173 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7131 (tpp) cc_final: 0.6832 (mmt) REVERT: A 367 GLU cc_start: 0.6875 (tm-30) cc_final: 0.6641 (tp30) REVERT: A 388 ILE cc_start: 0.7686 (mm) cc_final: 0.7439 (mt) REVERT: A 394 ASP cc_start: 0.7117 (m-30) cc_final: 0.6767 (m-30) REVERT: A 410 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7243 (tmtt) REVERT: A 440 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7316 (pt0) REVERT: A 448 GLN cc_start: 0.8259 (tt0) cc_final: 0.7931 (tt0) REVERT: A 502 GLN cc_start: 0.6627 (pm20) cc_final: 0.6347 (pm20) REVERT: A 699 ILE cc_start: 0.8294 (pt) cc_final: 0.8065 (pt) REVERT: A 768 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7576 (pt0) REVERT: A 863 TRP cc_start: 0.7836 (m100) cc_final: 0.6913 (m-10) REVERT: A 928 TYR cc_start: 0.8155 (t80) cc_final: 0.7902 (t80) REVERT: A 1016 THR cc_start: 0.7195 (p) cc_final: 0.6965 (p) REVERT: A 1048 SER cc_start: 0.7556 (t) cc_final: 0.7186 (p) REVERT: A 1078 MET cc_start: 0.3372 (ttt) cc_final: 0.3128 (ttt) REVERT: A 1162 MET cc_start: 0.7468 (tmm) cc_final: 0.7037 (ttm) outliers start: 23 outliers final: 15 residues processed: 164 average time/residue: 0.4431 time to fit residues: 77.8959 Evaluate side-chains 157 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 410 LYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 456 GLN 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 1050 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 77 optimal weight: 0.5980 chunk 81 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 46 optimal weight: 0.0270 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 HIS ** 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 = 0.4205 r_free = 0.4205 target = 0.169394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.153116 restraints weight = 12574.721| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.83 r_work: 0.3902 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9617 Z= 0.136 Angle : 0.555 8.065 13148 Z= 0.293 Chirality : 0.042 0.226 1493 Planarity : 0.005 0.050 1636 Dihedral : 14.268 76.118 1498 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.64 % Allowed : 16.67 % Favored : 80.70 % 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: 0.32 (0.26), residues: 1135 helix: 0.98 (0.22), residues: 592 sheet: -0.02 (0.57), residues: 98 loop : -0.70 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 944 TYR 0.024 0.002 TYR A 928 PHE 0.012 0.001 PHE A 293 TRP 0.031 0.001 TRP A 266 HIS 0.005 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 9617) covalent geometry : angle 0.55457 / 0.29 (13148) hydrogen bonds : bond 0.03869 / 3.35 ( 475) hydrogen bonds : angle 4.88394 / 3.96 ( 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 165 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7112 (tpp) cc_final: 0.6810 (mmt) REVERT: A 394 ASP cc_start: 0.7041 (m-30) cc_final: 0.6736 (m-30) REVERT: A 410 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7310 (tmtt) REVERT: A 448 GLN cc_start: 0.8283 (tt0) cc_final: 0.7944 (tt0) REVERT: A 502 GLN cc_start: 0.6658 (pm20) cc_final: 0.6269 (pm20) REVERT: A 699 ILE cc_start: 0.8306 (pt) cc_final: 0.8066 (pt) REVERT: A 768 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7581 (pt0) REVERT: A 863 TRP cc_start: 0.7844 (m100) cc_final: 0.6916 (m-10) REVERT: A 1016 THR cc_start: 0.7213 (p) cc_final: 0.6983 (p) REVERT: A 1048 SER cc_start: 0.7587 (t) cc_final: 0.7170 (p) REVERT: A 1078 MET cc_start: 0.3393 (ttt) cc_final: 0.3144 (ttt) REVERT: A 1162 MET cc_start: 0.7450 (tmm) cc_final: 0.7043 (tpp) REVERT: A 1165 TYR cc_start: 0.7276 (t80) cc_final: 0.7029 (t80) outliers start: 25 outliers final: 17 residues processed: 154 average time/residue: 0.5039 time to fit residues: 82.9963 Evaluate side-chains 154 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 410 LYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 456 GLN 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 925 PHE Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain A residue 1050 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 93 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 66 optimal weight: 0.0000 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.167328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.151068 restraints weight = 12603.577| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.82 r_work: 0.3881 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2490 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= 0.170 Angle : 0.573 8.963 13148 Z= 0.303 Chirality : 0.043 0.192 1493 Planarity : 0.005 0.072 1636 Dihedral : 14.250 77.333 1498 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.64 % Allowed : 16.67 % Favored : 80.70 % 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: 0.27 (0.26), residues: 1135 helix: 0.95 (0.22), residues: 592 sheet: -0.07 (0.57), residues: 98 loop : -0.73 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 156 TYR 0.016 0.002 TYR A 445 PHE 0.012 0.001 PHE A 106 TRP 0.033 0.002 TRP A 266 HIS 0.004 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 9617) covalent geometry : angle 0.57322 / 0.30 (13148) hydrogen bonds : bond 0.03978 / 3.47 ( 475) hydrogen bonds : angle 4.90825 / 3.97 ( 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 173 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.199 Fit side-chains REVERT: A 110 MET cc_start: 0.7074 (tpp) cc_final: 0.6770 (mmt) REVERT: A 130 MET cc_start: 0.7240 (ptp) cc_final: 0.6999 (ptp) REVERT: A 367 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6641 (tp30) REVERT: A 394 ASP cc_start: 0.7084 (m-30) cc_final: 0.6789 (m-30) REVERT: A 410 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7340 (tmtt) REVERT: A 448 GLN cc_start: 0.8252 (tt0) cc_final: 0.7955 (tt0) REVERT: A 502 GLN cc_start: 0.6746 (pm20) cc_final: 0.6353 (pm20) REVERT: A 699 ILE cc_start: 0.8350 (pt) cc_final: 0.8119 (pt) REVERT: A 863 TRP cc_start: 0.7892 (m100) cc_final: 0.6865 (m-10) REVERT: A 1016 THR cc_start: 0.7401 (p) cc_final: 0.7170 (p) REVERT: A 1048 SER cc_start: 0.7632 (t) cc_final: 0.7216 (p) REVERT: A 1078 MET cc_start: 0.3399 (ttt) cc_final: 0.3159 (ttt) REVERT: A 1162 MET cc_start: 0.7473 (tmm) cc_final: 0.7088 (tpp) outliers start: 25 outliers final: 16 residues processed: 164 average time/residue: 0.4800 time to fit residues: 84.1163 Evaluate side-chains 158 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 410 LYS 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 925 PHE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1020 SER 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: 0.9990 chunk 88 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 106 optimal weight: 0.0470 chunk 77 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.166230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.150001 restraints weight = 12648.007| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.83 r_work: 0.3867 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 9617 Z= 0.198 Angle : 0.605 10.622 13148 Z= 0.319 Chirality : 0.044 0.204 1493 Planarity : 0.005 0.053 1636 Dihedral : 14.222 77.423 1498 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.22 % Allowed : 17.62 % Favored : 80.17 % 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: 0.17 (0.25), residues: 1135 helix: 0.93 (0.22), residues: 586 sheet: -0.21 (0.56), residues: 98 loop : -0.82 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 156 TYR 0.032 0.003 TYR A 928 PHE 0.013 0.002 PHE A 106 TRP 0.037 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 0.60521 / 0.32 (13148) hydrogen bonds : bond 0.04151 / 3.61 ( 475) hydrogen bonds : angle 4.94870 / 3.99 ( 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 172 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7052 (tpp) cc_final: 0.6741 (mmt) REVERT: A 394 ASP cc_start: 0.7032 (m-30) cc_final: 0.6676 (m-30) REVERT: A 410 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7271 (tmtt) REVERT: A 448 GLN cc_start: 0.8248 (tt0) cc_final: 0.7921 (tt0) REVERT: A 502 GLN cc_start: 0.6773 (pm20) cc_final: 0.6360 (pm20) REVERT: A 699 ILE cc_start: 0.8340 (pt) cc_final: 0.8096 (pt) REVERT: A 768 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7600 (pt0) REVERT: A 863 TRP cc_start: 0.7904 (m100) cc_final: 0.6848 (m-10) REVERT: A 1016 THR cc_start: 0.7410 (p) cc_final: 0.7197 (p) REVERT: A 1048 SER cc_start: 0.7648 (t) cc_final: 0.7217 (p) REVERT: A 1076 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7769 (tpt90) REVERT: A 1078 MET cc_start: 0.3481 (ttt) cc_final: 0.3223 (ttt) outliers start: 21 outliers final: 18 residues processed: 165 average time/residue: 0.4489 time to fit residues: 79.7029 Evaluate side-chains 165 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 356 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 410 LYS 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 943 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain A residue 1046 PHE 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: 0.0670 chunk 102 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.166783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.150664 restraints weight = 12535.303| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 1.81 r_work: 0.3882 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9617 Z= 0.186 Angle : 0.612 10.121 13148 Z= 0.323 Chirality : 0.043 0.202 1493 Planarity : 0.006 0.085 1636 Dihedral : 14.196 76.849 1498 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.22 % Allowed : 17.62 % Favored : 80.17 % 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: 0.84 (0.22), residues: 590 sheet: -0.25 (0.56), residues: 98 loop : -0.83 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 696 TYR 0.034 0.002 TYR A 928 PHE 0.018 0.002 PHE A 925 TRP 0.036 0.002 TRP A 266 HIS 0.004 0.001 HIS A 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 ( 9617) covalent geometry : angle 0.61203 / 0.32 (13148) hydrogen bonds : bond 0.04124 / 3.57 ( 475) hydrogen bonds : angle 4.97418 / 4.00 ( 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 166 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 394 ASP cc_start: 0.7016 (m-30) cc_final: 0.6658 (m-30) REVERT: A 410 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7257 (tmtt) REVERT: A 411 LEU cc_start: 0.7486 (tp) cc_final: 0.7260 (tt) REVERT: A 448 GLN cc_start: 0.8239 (tt0) cc_final: 0.7906 (tt0) REVERT: A 502 GLN cc_start: 0.6684 (pm20) cc_final: 0.6260 (pm20) REVERT: A 699 ILE cc_start: 0.8353 (pt) cc_final: 0.8107 (pt) REVERT: A 768 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7645 (pt0) REVERT: A 863 TRP cc_start: 0.7887 (m100) cc_final: 0.6820 (m-10) REVERT: A 924 VAL cc_start: 0.7326 (OUTLIER) cc_final: 0.6996 (t) REVERT: A 1016 THR cc_start: 0.7398 (p) cc_final: 0.7178 (p) REVERT: A 1048 SER cc_start: 0.7701 (t) cc_final: 0.7307 (p) REVERT: A 1076 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7812 (tpt90) REVERT: A 1078 MET cc_start: 0.3394 (ttt) cc_final: 0.3164 (ttt) outliers start: 21 outliers final: 14 residues processed: 159 average time/residue: 0.4736 time to fit residues: 80.5368 Evaluate side-chains 157 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 356 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 474 GLU 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 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 96 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 72 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.166943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.150818 restraints weight = 12472.434| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.81 r_work: 0.3887 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9617 Z= 0.166 Angle : 0.622 10.292 13148 Z= 0.325 Chirality : 0.043 0.200 1493 Planarity : 0.005 0.054 1636 Dihedral : 14.154 76.498 1498 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.90 % Allowed : 18.67 % Favored : 79.43 % 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: 0.91 (0.22), residues: 587 sheet: -0.26 (0.57), residues: 98 loop : -0.84 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 696 TYR 0.035 0.002 TYR A 928 PHE 0.042 0.002 PHE A 106 TRP 0.039 0.002 TRP A 266 HIS 0.003 0.001 HIS A 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 9617) covalent geometry : angle 0.62240 / 0.32 (13148) hydrogen bonds : bond 0.03967 / 3.42 ( 475) hydrogen bonds : angle 5.00483 / 4.03 ( 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 164 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.217 Fit side-chains REVERT: A 110 MET cc_start: 0.6889 (tpp) cc_final: 0.6627 (mmt) REVERT: A 236 LEU cc_start: 0.6848 (tp) cc_final: 0.6522 (mt) REVERT: A 394 ASP cc_start: 0.6992 (m-30) cc_final: 0.6659 (m-30) REVERT: A 411 LEU cc_start: 0.7475 (tp) cc_final: 0.7251 (tt) REVERT: A 448 GLN cc_start: 0.8240 (tt0) cc_final: 0.7907 (tt0) REVERT: A 502 GLN cc_start: 0.6685 (pm20) cc_final: 0.6273 (pm20) REVERT: A 699 ILE cc_start: 0.8331 (pt) cc_final: 0.8106 (pt) REVERT: A 768 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7633 (pt0) REVERT: A 863 TRP cc_start: 0.7864 (m100) cc_final: 0.6886 (m-10) REVERT: A 924 VAL cc_start: 0.7305 (OUTLIER) cc_final: 0.6993 (t) REVERT: A 968 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: A 1016 THR cc_start: 0.7366 (p) cc_final: 0.7144 (p) REVERT: A 1048 SER cc_start: 0.7694 (t) cc_final: 0.7291 (p) REVERT: A 1060 GLU cc_start: 0.5741 (pm20) cc_final: 0.5442 (pm20) REVERT: A 1076 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7809 (tpt90) REVERT: A 1078 MET cc_start: 0.3398 (ttt) cc_final: 0.3155 (ttt) outliers start: 18 outliers final: 15 residues processed: 158 average time/residue: 0.4701 time to fit residues: 79.6866 Evaluate side-chains 157 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 474 GLU 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 1009 VAL Chi-restraints excluded: chain A residue 1076 ARG Chi-restraints excluded: chain A residue 1156 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 13 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 25 optimal weight: 0.0020 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 542 ASN ** A 637 HIS ** 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 = 0.4184 r_free = 0.4184 target = 0.167906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.151790 restraints weight = 12512.623| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.81 r_work: 0.3894 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9617 Z= 0.162 Angle : 0.623 9.864 13148 Z= 0.326 Chirality : 0.043 0.199 1493 Planarity : 0.005 0.061 1636 Dihedral : 14.139 76.568 1498 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.90 % Allowed : 18.25 % Favored : 79.85 % 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: 0.09 (0.25), residues: 1135 helix: 0.89 (0.22), residues: 586 sheet: -0.28 (0.57), residues: 98 loop : -0.89 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 123 TYR 0.017 0.002 TYR A 874 PHE 0.032 0.002 PHE A 106 TRP 0.040 0.002 TRP A 266 HIS 0.004 0.001 HIS A 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 9617) covalent geometry : angle 0.62262 / 0.33 (13148) hydrogen bonds : bond 0.03976 / 3.40 ( 475) hydrogen bonds : angle 5.02078 / 4.03 ( 1376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2631.29 seconds wall clock time: 45 minutes 28.71 seconds (2728.71 seconds total)