Starting phenix.real_space_refine on Sun Aug 4 02:22:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxc_43616/08_2024/8vxc_43616.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxc_43616/08_2024/8vxc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxc_43616/08_2024/8vxc_43616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxc_43616/08_2024/8vxc_43616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxc_43616/08_2024/8vxc_43616.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxc_43616/08_2024/8vxc_43616.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/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: 5.71, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 4.22 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 3.40 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: 3.98 Time building geometry restraints manager: 4.62 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=" C TYR A 575 " pdb=" N CYS A 576 " ideal model delta sigma weight residual 1.333 1.316 0.017 1.69e-02 3.50e+03 1.02e+00 bond pdb=" C1' DC B 12 " pdb=" N1 DC B 12 " ideal model delta sigma weight residual 1.490 1.518 -0.028 3.00e-02 1.11e+03 8.97e-01 bond pdb=" CA MET A 1 " pdb=" C MET A 1 " ideal model delta sigma weight residual 1.525 1.541 -0.016 2.10e-02 2.27e+03 6.10e-01 bond pdb=" C3' DA C 8 " pdb=" C2' DA C 8 " ideal model delta sigma weight residual 1.525 1.541 -0.016 2.00e-02 2.50e+03 6.09e-01 bond pdb=" CB TRP A 563 " pdb=" CG TRP A 563 " ideal model delta sigma weight residual 1.498 1.522 -0.024 3.10e-02 1.04e+03 5.96e-01 ... (remaining 9612 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.26: 365 106.26 - 113.26: 5234 113.26 - 120.26: 3535 120.26 - 127.26: 3874 127.26 - 134.26: 140 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=" C GLU A 923 " pdb=" N VAL A 924 " pdb=" CA VAL A 924 " ideal model delta sigma weight residual 122.35 119.41 2.94 1.18e+00 7.18e-01 6.22e+00 angle pdb=" N THR A 666 " pdb=" CA THR A 666 " pdb=" C THR A 666 " ideal model delta sigma weight residual 113.16 110.20 2.96 1.24e+00 6.50e-01 5.69e+00 angle pdb=" N SER A 664 " pdb=" CA SER A 664 " pdb=" CB SER A 664 " ideal model delta sigma weight residual 109.55 112.30 -2.75 1.30e+00 5.92e-01 4.47e+00 angle pdb=" N VAL A 955 " pdb=" CA VAL A 955 " pdb=" C VAL A 955 " ideal model delta sigma weight residual 109.34 104.99 4.35 2.08e+00 2.31e-01 4.36e+00 ... (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: 947 0.030 - 0.060: 375 0.060 - 0.090: 98 0.090 - 0.120: 60 0.120 - 0.150: 13 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.820 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 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 0.028 9617 Z= 0.164 Angle : 0.507 6.909 13148 Z= 0.284 Chirality : 0.039 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.025 0.001 TRP A 35 HIS 0.009 0.001 HIS A 756 PHE 0.015 0.001 PHE A 925 TYR 0.021 0.001 TYR A 645 ARG 0.003 0.000 ARG A 646 *********************** 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 fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.335 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: 0.7515 (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: 0.7715 (m100) cc_final: 0.6802 (m-10) REVERT: A 928 TYR cc_start: 0.8426 (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: 0.7145 (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: 1.3477 time to fit residues: 278.6218 Evaluate side-chains 150 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 365 GLN A 821 GLN A 989 ASN A1064 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9617 Z= 0.275 Angle : 0.577 6.268 13148 Z= 0.307 Chirality : 0.043 0.150 1493 Planarity : 0.005 0.055 1636 Dihedral : 14.487 74.827 1498 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.64 % Allowed : 11.08 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1135 helix: 0.78 (0.21), residues: 595 sheet: -0.16 (0.56), residues: 100 loop : -0.81 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 266 HIS 0.009 0.002 HIS A 756 PHE 0.016 0.002 PHE A 106 TYR 0.016 0.002 TYR A 445 ARG 0.005 0.001 ARG A 944 *********************** 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 190 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7406 (tpp) cc_final: 0.7053 (mmt) REVERT: A 394 ASP cc_start: 0.7092 (m-30) cc_final: 0.6830 (m-30) REVERT: A 448 GLN cc_start: 0.8263 (tt0) cc_final: 0.7993 (tt0) REVERT: A 491 PRO cc_start: 0.8729 (Cg_endo) cc_final: 0.8438 (Cg_exo) REVERT: A 637 HIS cc_start: 0.7982 (t-90) cc_final: 0.7734 (t-170) REVERT: A 863 TRP cc_start: 0.7841 (m100) cc_final: 0.6857 (m-10) REVERT: A 946 TRP cc_start: 0.7466 (t-100) cc_final: 0.6892 (t-100) REVERT: A 1048 SER cc_start: 0.7613 (t) cc_final: 0.7250 (p) REVERT: A 1078 MET cc_start: 0.3533 (ttt) cc_final: 0.3294 (ttt) outliers start: 25 outliers final: 11 residues processed: 177 average time/residue: 1.3309 time to fit residues: 250.8199 Evaluate side-chains 164 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 420 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 649 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.0970 chunk 104 optimal weight: 0.1980 chunk 113 optimal weight: 0.3980 chunk 93 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 83 optimal weight: 0.2980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN A 502 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9617 Z= 0.186 Angle : 0.535 7.027 13148 Z= 0.282 Chirality : 0.041 0.160 1493 Planarity : 0.005 0.051 1636 Dihedral : 14.268 76.053 1498 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.90 % Allowed : 14.66 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1135 helix: 1.03 (0.22), residues: 590 sheet: 0.11 (0.56), residues: 98 loop : -0.82 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 266 HIS 0.006 0.001 HIS A 756 PHE 0.012 0.001 PHE A 293 TYR 0.021 0.002 TYR A 928 ARG 0.005 0.000 ARG A1098 *********************** 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 167 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.7352 (tpp) cc_final: 0.7021 (mmt) REVERT: A 306 ASP cc_start: 0.7002 (p0) cc_final: 0.6778 (p0) REVERT: A 388 ILE cc_start: 0.7884 (mm) cc_final: 0.7673 (mm) REVERT: A 399 ARG cc_start: 0.7557 (mtt-85) cc_final: 0.7323 (mtt-85) REVERT: A 448 GLN cc_start: 0.8286 (tt0) cc_final: 0.7992 (tt0) REVERT: A 491 PRO cc_start: 0.8674 (Cg_endo) cc_final: 0.8452 (Cg_exo) REVERT: A 637 HIS cc_start: 0.7901 (t-90) cc_final: 0.7661 (t-170) REVERT: A 863 TRP cc_start: 0.7793 (m100) cc_final: 0.6845 (m-10) REVERT: A 963 THR cc_start: 0.7180 (t) cc_final: 0.6941 (m) REVERT: A 1048 SER cc_start: 0.7668 (t) cc_final: 0.7283 (p) REVERT: A 1078 MET cc_start: 0.3512 (ttt) cc_final: 0.3285 (ttt) outliers start: 18 outliers final: 10 residues processed: 158 average time/residue: 1.3620 time to fit residues: 229.6104 Evaluate side-chains 156 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 390 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 968 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.0030 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN A 821 GLN A1064 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2394 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= 0.261 Angle : 0.561 6.749 13148 Z= 0.298 Chirality : 0.042 0.150 1493 Planarity : 0.005 0.054 1636 Dihedral : 14.196 78.033 1498 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.64 % Allowed : 14.98 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1135 helix: 1.02 (0.22), residues: 589 sheet: -0.12 (0.54), residues: 100 loop : -0.74 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 266 HIS 0.005 0.001 HIS A 756 PHE 0.012 0.002 PHE A 106 TYR 0.017 0.002 TYR A 445 ARG 0.008 0.001 ARG A 156 *********************** 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 180 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 LEU cc_start: 0.6044 (tp) cc_final: 0.5665 (tt) REVERT: A 306 ASP cc_start: 0.7091 (p0) cc_final: 0.6811 (p0) REVERT: A 448 GLN cc_start: 0.8280 (tt0) cc_final: 0.7993 (tt0) REVERT: A 502 GLN cc_start: 0.6551 (OUTLIER) cc_final: 0.6280 (mt0) REVERT: A 637 HIS cc_start: 0.7939 (t-90) cc_final: 0.7700 (t-170) REVERT: A 699 ILE cc_start: 0.8311 (pt) cc_final: 0.8007 (pt) REVERT: A 796 ILE cc_start: 0.7989 (pt) cc_final: 0.7760 (OUTLIER) REVERT: A 863 TRP cc_start: 0.7868 (m100) cc_final: 0.6818 (m-10) REVERT: A 1016 THR cc_start: 0.7607 (p) cc_final: 0.7347 (p) REVERT: A 1048 SER cc_start: 0.7685 (t) cc_final: 0.7331 (p) REVERT: A 1078 MET cc_start: 0.3532 (ttt) cc_final: 0.3291 (ttt) outliers start: 25 outliers final: 13 residues processed: 169 average time/residue: 1.2100 time to fit residues: 219.3449 Evaluate side-chains 162 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 459 ASP Chi-restraints excluded: chain A residue 502 GLN Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 1020 SER 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 63 optimal weight: 0.3980 chunk 1 optimal weight: 0.0670 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 94 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN A 400 GLN A 800 GLN A 821 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9617 Z= 0.208 Angle : 0.547 7.981 13148 Z= 0.289 Chirality : 0.041 0.179 1493 Planarity : 0.005 0.052 1636 Dihedral : 14.067 78.026 1498 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.74 % Allowed : 16.03 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1135 helix: 1.11 (0.22), residues: 590 sheet: -0.14 (0.54), residues: 100 loop : -0.70 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 266 HIS 0.003 0.001 HIS A 116 PHE 0.030 0.002 PHE A 106 TYR 0.027 0.002 TYR A 928 ARG 0.008 0.000 ARG A 944 *********************** 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 182 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ASP cc_start: 0.7103 (p0) cc_final: 0.6829 (p0) REVERT: A 448 GLN cc_start: 0.8274 (tt0) cc_final: 0.7958 (tt0) REVERT: A 502 GLN cc_start: 0.6476 (pt0) cc_final: 0.6235 (mt0) REVERT: A 637 HIS cc_start: 0.7889 (t-90) cc_final: 0.7664 (t-170) REVERT: A 699 ILE cc_start: 0.8326 (pt) cc_final: 0.8054 (pt) REVERT: A 796 ILE cc_start: 0.8003 (pt) cc_final: 0.7798 (OUTLIER) REVERT: A 863 TRP cc_start: 0.7842 (m100) cc_final: 0.6778 (m-10) REVERT: A 963 THR cc_start: 0.7151 (t) cc_final: 0.6913 (m) REVERT: A 1016 THR cc_start: 0.7562 (p) cc_final: 0.7310 (p) REVERT: A 1048 SER cc_start: 0.7648 (t) cc_final: 0.7215 (p) REVERT: A 1078 MET cc_start: 0.3517 (ttt) cc_final: 0.3269 (ttt) outliers start: 26 outliers final: 19 residues processed: 172 average time/residue: 1.2585 time to fit residues: 231.3106 Evaluate side-chains 169 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 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 692 VAL Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 1009 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 111 optimal weight: 0.0040 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 0.0470 chunk 107 optimal weight: 0.0970 overall best weight: 0.3088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 GLN A 831 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9617 Z= 0.183 Angle : 0.541 8.189 13148 Z= 0.287 Chirality : 0.040 0.160 1493 Planarity : 0.005 0.051 1636 Dihedral : 13.944 79.182 1498 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.43 % Allowed : 17.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1135 helix: 1.21 (0.22), residues: 594 sheet: -0.18 (0.53), residues: 100 loop : -0.63 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 266 HIS 0.003 0.001 HIS A 116 PHE 0.022 0.001 PHE A 106 TYR 0.031 0.002 TYR A 928 ARG 0.008 0.000 ARG A1096 *********************** 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 177 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LEU cc_start: 0.5758 (OUTLIER) cc_final: 0.5529 (tt) REVERT: A 306 ASP cc_start: 0.7095 (p0) cc_final: 0.6839 (p0) REVERT: A 394 ASP cc_start: 0.6993 (m-30) cc_final: 0.6762 (m-30) REVERT: A 448 GLN cc_start: 0.8284 (tt0) cc_final: 0.7994 (tt0) REVERT: A 502 GLN cc_start: 0.6467 (OUTLIER) cc_final: 0.6242 (mt0) REVERT: A 637 HIS cc_start: 0.7840 (t-90) cc_final: 0.7200 (t-170) REVERT: A 699 ILE cc_start: 0.8297 (pt) cc_final: 0.8058 (pt) REVERT: A 863 TRP cc_start: 0.7813 (m100) cc_final: 0.6704 (m-10) REVERT: A 1016 THR cc_start: 0.7530 (p) cc_final: 0.7258 (p) REVERT: A 1048 SER cc_start: 0.7652 (t) cc_final: 0.7295 (p) REVERT: A 1076 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7764 (tpt90) REVERT: A 1078 MET cc_start: 0.3513 (ttt) cc_final: 0.3264 (ttt) outliers start: 23 outliers final: 18 residues processed: 169 average time/residue: 1.3217 time to fit residues: 238.7711 Evaluate side-chains 166 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 248 MET 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 356 ILE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 502 GLN 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 755 MET Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 821 GLN 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 1076 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 0.0870 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 110 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9617 Z= 0.214 Angle : 0.554 8.891 13148 Z= 0.292 Chirality : 0.040 0.150 1493 Planarity : 0.005 0.051 1636 Dihedral : 13.916 79.497 1498 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.32 % Allowed : 18.46 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1135 helix: 1.18 (0.22), residues: 595 sheet: -0.16 (0.54), residues: 100 loop : -0.67 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 266 HIS 0.003 0.001 HIS A 638 PHE 0.015 0.001 PHE A 106 TYR 0.016 0.002 TYR A 445 ARG 0.012 0.001 ARG A1098 *********************** 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 fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 ASP cc_start: 0.7115 (p0) cc_final: 0.6855 (p0) REVERT: A 367 GLU cc_start: 0.6864 (tm-30) cc_final: 0.6654 (tm-30) REVERT: A 448 GLN cc_start: 0.8285 (tt0) cc_final: 0.7993 (tt0) REVERT: A 699 ILE cc_start: 0.8313 (pt) cc_final: 0.8058 (pt) REVERT: A 796 ILE cc_start: 0.7985 (pt) cc_final: 0.7781 (OUTLIER) REVERT: A 863 TRP cc_start: 0.7848 (m100) cc_final: 0.6786 (m-10) REVERT: A 924 VAL cc_start: 0.7411 (OUTLIER) cc_final: 0.7104 (t) REVERT: A 944 ARG cc_start: 0.7844 (tpt-90) cc_final: 0.7640 (tpt-90) REVERT: A 1016 THR cc_start: 0.7522 (p) cc_final: 0.7267 (p) REVERT: A 1048 SER cc_start: 0.7631 (t) cc_final: 0.7248 (p) REVERT: A 1076 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7770 (tpt90) REVERT: A 1078 MET cc_start: 0.3506 (ttt) cc_final: 0.3257 (ttt) REVERT: A 1162 MET cc_start: 0.6443 (ttp) cc_final: 0.6094 (ttt) outliers start: 22 outliers final: 15 residues processed: 164 average time/residue: 1.2681 time to fit residues: 222.2539 Evaluate side-chains 165 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 390 VAL 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 755 MET Chi-restraints excluded: chain A residue 821 GLN 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 1076 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.2980 chunk 96 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1050 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9617 Z= 0.258 Angle : 0.587 9.482 13148 Z= 0.307 Chirality : 0.041 0.165 1493 Planarity : 0.005 0.052 1636 Dihedral : 13.928 79.007 1498 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.43 % Allowed : 18.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1135 helix: 1.14 (0.22), residues: 589 sheet: -0.28 (0.55), residues: 98 loop : -0.75 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 266 HIS 0.004 0.001 HIS A 638 PHE 0.015 0.002 PHE A 106 TYR 0.028 0.002 TYR A 928 ARG 0.012 0.001 ARG A1098 *********************** 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 173 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ASP cc_start: 0.7134 (p0) cc_final: 0.6868 (p0) REVERT: A 411 LEU cc_start: 0.7544 (tp) cc_final: 0.7326 (tt) REVERT: A 418 ASP cc_start: 0.7438 (t70) cc_final: 0.7226 (t0) REVERT: A 448 GLN cc_start: 0.8277 (tt0) cc_final: 0.7953 (tt0) REVERT: A 637 HIS cc_start: 0.7777 (t-90) cc_final: 0.7519 (t-90) REVERT: A 685 ARG cc_start: 0.8663 (ttm110) cc_final: 0.8440 (ttm110) REVERT: A 699 ILE cc_start: 0.8332 (pt) cc_final: 0.8102 (pt) REVERT: A 821 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: A 863 TRP cc_start: 0.7878 (m100) cc_final: 0.6767 (m-10) REVERT: A 924 VAL cc_start: 0.7425 (OUTLIER) cc_final: 0.7125 (t) REVERT: A 968 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6300 (mp0) REVERT: A 1016 THR cc_start: 0.7536 (p) cc_final: 0.7299 (p) REVERT: A 1048 SER cc_start: 0.7726 (t) cc_final: 0.7306 (p) REVERT: A 1076 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7849 (tpt90) REVERT: A 1078 MET cc_start: 0.3517 (ttt) cc_final: 0.3265 (ttt) outliers start: 23 outliers final: 14 residues processed: 166 average time/residue: 1.2425 time to fit residues: 221.1431 Evaluate side-chains 162 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 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 755 MET Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 821 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 81 optimal weight: 0.0870 chunk 31 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 102 optimal weight: 0.0270 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9617 Z= 0.210 Angle : 0.595 11.433 13148 Z= 0.309 Chirality : 0.041 0.218 1493 Planarity : 0.005 0.054 1636 Dihedral : 13.878 78.764 1498 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.90 % Allowed : 19.94 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1135 helix: 1.23 (0.22), residues: 588 sheet: -0.26 (0.55), residues: 100 loop : -0.77 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 266 HIS 0.003 0.001 HIS A 116 PHE 0.013 0.001 PHE A 106 TYR 0.031 0.002 TYR A 928 ARG 0.010 0.001 ARG A1098 *********************** 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 165 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.6997 (tpp) cc_final: 0.6741 (tpp) REVERT: A 306 ASP cc_start: 0.7094 (p0) cc_final: 0.6856 (p0) REVERT: A 411 LEU cc_start: 0.7522 (tp) cc_final: 0.7301 (tt) REVERT: A 448 GLN cc_start: 0.8278 (tt0) cc_final: 0.7949 (tt0) REVERT: A 637 HIS cc_start: 0.7746 (t-90) cc_final: 0.7528 (t-90) REVERT: A 699 ILE cc_start: 0.8278 (pt) cc_final: 0.8052 (pt) REVERT: A 796 ILE cc_start: 0.7987 (pt) cc_final: 0.7784 (pp) REVERT: A 863 TRP cc_start: 0.7860 (m100) cc_final: 0.6818 (m-10) REVERT: A 924 VAL cc_start: 0.7377 (OUTLIER) cc_final: 0.7079 (t) REVERT: A 1016 THR cc_start: 0.7495 (p) cc_final: 0.7220 (p) REVERT: A 1048 SER cc_start: 0.7697 (t) cc_final: 0.7338 (p) REVERT: A 1076 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7812 (tpt90) REVERT: A 1078 MET cc_start: 0.3509 (ttt) cc_final: 0.3254 (ttt) outliers start: 18 outliers final: 14 residues processed: 157 average time/residue: 1.2715 time to fit residues: 213.7774 Evaluate side-chains 157 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 390 VAL 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 755 MET Chi-restraints excluded: chain A residue 821 GLN 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 66 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 chunk 91 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 70 optimal weight: 0.0980 chunk 55 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 97 optimal weight: 0.2980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS A 821 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9617 Z= 0.199 Angle : 0.597 10.996 13148 Z= 0.310 Chirality : 0.041 0.220 1493 Planarity : 0.005 0.077 1636 Dihedral : 13.829 78.990 1498 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.90 % Allowed : 19.73 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.26), residues: 1135 helix: 1.17 (0.22), residues: 591 sheet: -0.14 (0.52), residues: 110 loop : -0.80 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 266 HIS 0.003 0.001 HIS A 638 PHE 0.013 0.001 PHE A 695 TYR 0.015 0.001 TYR A 445 ARG 0.008 0.000 ARG A1098 ********************** 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 161 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7079 (tpp) cc_final: 0.6702 (tpp) REVERT: A 264 ASP cc_start: 0.6924 (OUTLIER) cc_final: 0.6619 (t0) REVERT: A 306 ASP cc_start: 0.7087 (p0) cc_final: 0.6847 (p0) REVERT: A 411 LEU cc_start: 0.7538 (tp) cc_final: 0.7314 (tt) REVERT: A 448 GLN cc_start: 0.8276 (tt0) cc_final: 0.7979 (tt0) REVERT: A 502 GLN cc_start: 0.6778 (mp-120) cc_final: 0.6474 (mm-40) REVERT: A 863 TRP cc_start: 0.7871 (m100) cc_final: 0.6800 (m-10) REVERT: A 924 VAL cc_start: 0.7416 (OUTLIER) cc_final: 0.7077 (t) REVERT: A 1016 THR cc_start: 0.7472 (p) cc_final: 0.7210 (p) REVERT: A 1048 SER cc_start: 0.7666 (t) cc_final: 0.7262 (p) REVERT: A 1076 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7796 (tpt90) REVERT: A 1078 MET cc_start: 0.3502 (ttt) cc_final: 0.3261 (ttt) outliers start: 18 outliers final: 13 residues processed: 153 average time/residue: 1.2150 time to fit residues: 199.1607 Evaluate side-chains 157 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 390 VAL 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 755 MET Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 821 GLN 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 27 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.0270 chunk 91 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN A 821 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.166649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.150643 restraints weight = 12542.438| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.81 r_work: 0.3887 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9617 Z= 0.248 Angle : 0.616 10.755 13148 Z= 0.321 Chirality : 0.042 0.193 1493 Planarity : 0.005 0.052 1636 Dihedral : 13.837 78.544 1498 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.90 % Allowed : 20.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1135 helix: 1.04 (0.22), residues: 599 sheet: -0.27 (0.52), residues: 113 loop : -0.80 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 266 HIS 0.005 0.001 HIS A 637 PHE 0.014 0.002 PHE A 925 TYR 0.030 0.002 TYR A 928 ARG 0.008 0.000 ARG A 696 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4192.61 seconds wall clock time: 73 minutes 42.44 seconds (4422.44 seconds total)