Starting phenix.real_space_refine on Wed Aug 5 14:55:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sv8_40782/08_2026/8sv8_40782.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sv8_40782/08_2026/8sv8_40782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sv8_40782/08_2026/8sv8_40782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sv8_40782/08_2026/8sv8_40782.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8sv8_40782/08_2026/8sv8_40782.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sv8_40782/08_2026/8sv8_40782.cif" model { file = "/net/cci-nas-00/data/ceres_data/8sv8_40782/08_2026/8sv8_40782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sv8_40782/08_2026/8sv8_40782.cif" } resolution = 3.38 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= 0.004 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 1 5.49 5 S 37 5.16 5 C 6490 2.51 5 N 1792 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 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: 10208 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7712 Classifications: {'peptide': 992} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 926} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "C" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1243 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 133} Chain: "D" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLY%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 2.23, per 1000 atoms: 0.22 Number of scatterers: 10208 At special positions: 0 Unit cell: (90.8188, 104.15, 115.815, 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 37 16.00 P 1 15.00 O 1888 8.00 N 1792 7.00 C 6490 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 377.5 milliseconds 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2426 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 12 sheets defined 44.3% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 removed outlier: 3.581A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 55 Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.941A pdb=" N ALA A 73 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.572A pdb=" N LEU A 83 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 99 removed outlier: 4.178A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 119 removed outlier: 3.693A pdb=" N ASP A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 142 removed outlier: 3.715A pdb=" N HIS A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 203 removed outlier: 4.052A pdb=" N HIS A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 221 removed outlier: 3.523A pdb=" N ASN A 221 " --> pdb=" O VAL A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 281 through 305 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.540A pdb=" N ARG A 331 " --> pdb=" O PRO A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 357 through 378 Processing helix chain 'A' and resid 391 through 395 Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 415 through 423 removed outlier: 3.924A pdb=" N VAL A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 432 Processing helix chain 'A' and resid 442 through 455 Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.624A pdb=" N SER A 478 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG A 479 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 480 " --> pdb=" O LEU A 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 475 through 480' Processing helix chain 'A' and resid 491 through 504 Processing helix chain 'A' and resid 526 through 532 removed outlier: 4.192A pdb=" N ARG A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 555 removed outlier: 3.723A pdb=" N ARG A 545 " --> pdb=" O SER A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 593 removed outlier: 4.238A pdb=" N ASP A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 607 through 631 removed outlier: 4.353A pdb=" N LEU A 625 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 637 removed outlier: 3.521A pdb=" N HIS A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 651 removed outlier: 3.870A pdb=" N THR A 648 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 657 Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.947A pdb=" N GLY A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 721 through 740 removed outlier: 3.680A pdb=" N LEU A 725 " --> pdb=" O GLN A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 757 Processing helix chain 'A' and resid 761 through 765 removed outlier: 4.086A pdb=" N MET A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 800 removed outlier: 3.777A pdb=" N GLN A 786 " --> pdb=" O PHE A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 832 Processing helix chain 'A' and resid 838 through 845 removed outlier: 3.531A pdb=" N SER A 842 " --> pdb=" O ASN A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 874 removed outlier: 3.985A pdb=" N GLY A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 881 Processing helix chain 'A' and resid 927 through 939 Processing helix chain 'A' and resid 959 through 967 Processing helix chain 'A' and resid 970 through 980 Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'C' and resid 3 through 17 removed outlier: 3.734A pdb=" N LYS C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 114 Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 132 through 148 Processing helix chain 'D' and resid 103 through 116 removed outlier: 3.713A pdb=" N LEU D 107 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 122 Processing helix chain 'D' and resid 136 through 141 removed outlier: 4.256A pdb=" N TYR D 140 " --> pdb=" O PRO D 136 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.582A pdb=" N VAL A 35 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG A 34 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL A 123 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 36 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.617A pdb=" N VAL A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 178 through 179 Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 184 Processing sheet with id=AA6, first strand: chain 'A' and resid 214 through 216 Processing sheet with id=AA7, first strand: chain 'A' and resid 511 through 512 removed outlier: 6.059A pdb=" N VAL A 466 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU A 437 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 562 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 559 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 904 through 906 Processing sheet with id=AA9, first strand: chain 'A' and resid 917 through 920 removed outlier: 6.661A pdb=" N LEU A 917 " --> pdb=" O HIS A1009 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU A1011 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL A 919 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU A 946 " --> pdb=" O LEU A 953 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 92 through 99 removed outlier: 3.907A pdb=" N ARG B 92 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 129 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 22 through 27 removed outlier: 6.058A pdb=" N ASN C 24 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU C 38 " --> pdb=" O ASN C 24 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 124 through 126 432 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2488 1.33 - 1.45: 1984 1.45 - 1.57: 5930 1.57 - 1.69: 2 1.69 - 1.81: 56 Bond restraints: 10460 Sorted by residual: bond pdb=" N VAL A 728 " pdb=" CA VAL A 728 " ideal model delta sigma weight residual 1.461 1.492 -0.030 1.17e-02 7.31e+03 6.79e+00 bond pdb=" C CYS A 711 " pdb=" N PRO A 712 " ideal model delta sigma weight residual 1.331 1.363 -0.032 1.28e-02 6.10e+03 6.17e+00 bond pdb=" N ASP A 161 " pdb=" CA ASP A 161 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 6.08e+00 bond pdb=" C ASP C 42 " pdb=" N GLN C 43 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.36e-02 5.41e+03 5.91e+00 bond pdb=" N LEU A 715 " pdb=" CA LEU A 715 " ideal model delta sigma weight residual 1.455 1.485 -0.029 1.22e-02 6.72e+03 5.81e+00 ... (remaining 10455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 13414 1.33 - 2.65: 622 2.65 - 3.98: 152 3.98 - 5.31: 37 5.31 - 6.63: 17 Bond angle restraints: 14242 Sorted by residual: angle pdb=" C TYR A 603 " pdb=" N PHE A 604 " pdb=" CA PHE A 604 " ideal model delta sigma weight residual 122.28 116.78 5.50 8.80e-01 1.29e+00 3.91e+01 angle pdb=" CA PRO A 25 " pdb=" N PRO A 25 " pdb=" CD PRO A 25 " ideal model delta sigma weight residual 112.00 106.56 5.44 1.40e+00 5.10e-01 1.51e+01 angle pdb=" N GLU C 93 " pdb=" CA GLU C 93 " pdb=" C GLU C 93 " ideal model delta sigma weight residual 114.56 110.09 4.47 1.27e+00 6.20e-01 1.24e+01 angle pdb=" CA GLY A 922 " pdb=" C GLY A 922 " pdb=" O GLY A 922 " ideal model delta sigma weight residual 122.23 119.98 2.25 6.90e-01 2.10e+00 1.06e+01 angle pdb=" O CYS A 711 " pdb=" C CYS A 711 " pdb=" N PRO A 712 " ideal model delta sigma weight residual 121.19 118.84 2.35 7.30e-01 1.88e+00 1.04e+01 ... (remaining 14237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5459 17.92 - 35.83: 640 35.83 - 53.75: 162 53.75 - 71.66: 28 71.66 - 89.58: 10 Dihedral angle restraints: 6299 sinusoidal: 2548 harmonic: 3751 Sorted by residual: dihedral pdb=" CA GLY A 143 " pdb=" C GLY A 143 " pdb=" N VAL A 144 " pdb=" CA VAL A 144 " ideal model delta harmonic sigma weight residual -180.00 -157.39 -22.61 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA GLN A 923 " pdb=" C GLN A 923 " pdb=" N PRO A 924 " pdb=" CA PRO A 924 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLU A 215 " pdb=" C GLU A 215 " pdb=" N GLY A 216 " pdb=" CA GLY A 216 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 6296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1303 0.051 - 0.102: 254 0.102 - 0.152: 26 0.152 - 0.203: 5 0.203 - 0.254: 3 Chirality restraints: 1591 Sorted by residual: chirality pdb=" CA PHE A 159 " pdb=" N PHE A 159 " pdb=" C PHE A 159 " pdb=" CB PHE A 159 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE A 630 " pdb=" CA ILE A 630 " pdb=" CG1 ILE A 630 " pdb=" CG2 ILE A 630 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA LEU A 729 " pdb=" N LEU A 729 " pdb=" C LEU A 729 " pdb=" CB LEU A 729 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1588 not shown) Planarity restraints: 1867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 24 " 0.045 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO A 25 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 25 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 25 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 64 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO C 65 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 65 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 65 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 114 " -0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO C 115 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 115 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 115 " -0.027 5.00e-02 4.00e+02 ... (remaining 1864 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 847 2.74 - 3.28: 10258 3.28 - 3.82: 16947 3.82 - 4.36: 19703 4.36 - 4.90: 34016 Nonbonded interactions: 81771 Sorted by model distance: nonbonded pdb=" OD1 ASN B 88 " pdb=" N ASN B 89 " model vdw 2.199 3.120 nonbonded pdb=" OG SER A 266 " pdb=" OD1 ASP A 268 " model vdw 2.230 3.040 nonbonded pdb=" O ASN A 695 " pdb=" OG SER A 706 " model vdw 2.255 3.040 nonbonded pdb=" O PHE A 623 " pdb=" OG SER A 626 " model vdw 2.283 3.040 nonbonded pdb=" O ASP A 812 " pdb=" ND2 ASN A 815 " model vdw 2.287 3.120 ... (remaining 81766 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 82 through 157) selection = chain 'D' } 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: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.720 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 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 : 0.004 0.080 10461 Z= 0.185 Angle : 0.717 6.634 14242 Z= 0.416 Chirality : 0.041 0.254 1591 Planarity : 0.006 0.066 1867 Dihedral : 16.375 89.580 3873 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.50 % Favored : 94.42 % Rotamer: Outliers : 0.54 % Allowed : 23.16 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.43 (0.24), residues: 1291 helix: 0.98 (0.24), residues: 489 sheet: -1.24 (0.43), residues: 151 loop : -1.00 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 23 TYR 0.028 0.002 TYR A 603 PHE 0.012 0.001 PHE A 426 TRP 0.010 0.001 TRP A 614 HIS 0.004 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.19 (10460) covalent geometry : angle 0.71697 / 0.42 (14242) hydrogen bonds : bond 0.10670 / 7.19 ( 432) hydrogen bonds : angle 5.35520 / 3.82 ( 1212) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 100 average time/residue: 0.0908 time to fit residues: 12.9797 Evaluate side-chains 90 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.0370 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN A 157 GLN A 201 HIS A 229 HIS A 476 ASN A 480 GLN ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 139 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.150844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.092273 restraints weight = 16884.635| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.46 r_work: 0.3008 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10461 Z= 0.147 Angle : 0.584 6.163 14242 Z= 0.290 Chirality : 0.040 0.164 1591 Planarity : 0.005 0.046 1867 Dihedral : 4.829 48.367 1411 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.27 % Favored : 94.66 % Rotamer: Outliers : 2.45 % Allowed : 20.89 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.23), residues: 1291 helix: 1.17 (0.24), residues: 489 sheet: -1.21 (0.41), residues: 151 loop : -0.95 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.020 0.002 TYR B 140 PHE 0.012 0.001 PHE A 146 TRP 0.013 0.001 TRP A 677 HIS 0.005 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (10460) covalent geometry : angle 0.58433 / 0.29 (14242) hydrogen bonds : bond 0.03820 / 2.68 ( 432) hydrogen bonds : angle 4.59247 / 3.34 ( 1212) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7711 (t0) cc_final: 0.7449 (t0) REVERT: A 476 ASN cc_start: 0.6182 (OUTLIER) cc_final: 0.5752 (t0) REVERT: A 610 HIS cc_start: 0.7887 (m90) cc_final: 0.7418 (m90) REVERT: B 99 ARG cc_start: 0.8377 (mtp-110) cc_final: 0.8079 (mmm-85) REVERT: B 118 GLN cc_start: 0.7843 (mp10) cc_final: 0.7547 (mp10) outliers start: 27 outliers final: 19 residues processed: 123 average time/residue: 0.1008 time to fit residues: 17.5263 Evaluate side-chains 107 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 95 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 119 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 78 optimal weight: 0.0670 chunk 99 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 107 optimal weight: 0.0040 chunk 120 optimal weight: 2.9990 overall best weight: 0.5732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 HIS A 739 HIS ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.150847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.094903 restraints weight = 16973.188| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.38 r_work: 0.3055 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10461 Z= 0.116 Angle : 0.567 6.260 14242 Z= 0.278 Chirality : 0.039 0.165 1591 Planarity : 0.005 0.047 1867 Dihedral : 4.640 48.509 1409 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.88 % Favored : 95.04 % Rotamer: Outliers : 2.82 % Allowed : 20.71 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.23), residues: 1291 helix: 1.25 (0.24), residues: 496 sheet: -1.05 (0.42), residues: 153 loop : -0.90 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 23 TYR 0.009 0.001 TYR A 683 PHE 0.010 0.001 PHE A 481 TRP 0.011 0.001 TRP A 677 HIS 0.009 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (10460) covalent geometry : angle 0.56667 / 0.28 (14242) hydrogen bonds : bond 0.03488 / 2.44 ( 432) hydrogen bonds : angle 4.42417 / 3.22 ( 1212) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7754 (t0) cc_final: 0.7542 (t0) REVERT: A 610 HIS cc_start: 0.7900 (m90) cc_final: 0.7414 (m90) REVERT: B 99 ARG cc_start: 0.8398 (mtp-110) cc_final: 0.8073 (mmm-85) REVERT: B 118 GLN cc_start: 0.7871 (mp10) cc_final: 0.7579 (mp10) REVERT: C 131 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6738 (mp10) outliers start: 31 outliers final: 14 residues processed: 122 average time/residue: 0.0941 time to fit residues: 16.3480 Evaluate side-chains 104 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 95 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 33 optimal weight: 0.0370 chunk 6 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 106 optimal weight: 0.1980 chunk 115 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 739 HIS C 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.149799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.095578 restraints weight = 17007.290| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.43 r_work: 0.3039 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10461 Z= 0.134 Angle : 0.566 6.224 14242 Z= 0.278 Chirality : 0.039 0.167 1591 Planarity : 0.005 0.043 1867 Dihedral : 4.650 48.375 1409 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 3.09 % Allowed : 20.71 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.23), residues: 1291 helix: 1.35 (0.24), residues: 485 sheet: -0.88 (0.42), residues: 154 loop : -0.86 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 231 TYR 0.010 0.001 TYR A 683 PHE 0.010 0.001 PHE A 146 TRP 0.009 0.001 TRP A 677 HIS 0.008 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (10460) covalent geometry : angle 0.56598 / 0.28 (14242) hydrogen bonds : bond 0.03449 / 2.44 ( 432) hydrogen bonds : angle 4.37762 / 3.18 ( 1212) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7845 (t0) cc_final: 0.7575 (t0) REVERT: A 610 HIS cc_start: 0.7918 (m90) cc_final: 0.7386 (m90) REVERT: B 99 ARG cc_start: 0.8411 (mtp-110) cc_final: 0.7418 (mmm-85) REVERT: B 118 GLN cc_start: 0.7918 (mp10) cc_final: 0.7609 (mp10) REVERT: C 131 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.6769 (mp10) outliers start: 34 outliers final: 19 residues processed: 123 average time/residue: 0.0829 time to fit residues: 14.8370 Evaluate side-chains 112 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 95 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 47 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 739 HIS C 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.149644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.088993 restraints weight = 16842.391| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.65 r_work: 0.3052 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10461 Z= 0.135 Angle : 0.568 7.483 14242 Z= 0.277 Chirality : 0.039 0.175 1591 Planarity : 0.004 0.042 1867 Dihedral : 4.642 48.273 1409 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.88 % Favored : 95.04 % Rotamer: Outliers : 2.54 % Allowed : 21.34 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.07 (0.24), residues: 1291 helix: 1.39 (0.24), residues: 485 sheet: -0.70 (0.42), residues: 154 loop : -0.78 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 231 TYR 0.011 0.001 TYR C 75 PHE 0.009 0.001 PHE A 146 TRP 0.009 0.001 TRP A 614 HIS 0.008 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 (10460) covalent geometry : angle 0.56754 / 0.28 (14242) hydrogen bonds : bond 0.03421 / 2.43 ( 432) hydrogen bonds : angle 4.38479 / 3.18 ( 1212) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7996 (t0) cc_final: 0.7660 (t0) REVERT: A 592 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 610 HIS cc_start: 0.7982 (m90) cc_final: 0.7415 (m90) REVERT: A 628 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7881 (mm-30) REVERT: B 99 ARG cc_start: 0.8504 (mtp-110) cc_final: 0.8088 (mtp-110) REVERT: B 118 GLN cc_start: 0.8102 (mp10) cc_final: 0.7787 (mp10) REVERT: C 75 TYR cc_start: 0.6142 (t80) cc_final: 0.5879 (t80) REVERT: C 80 ASP cc_start: 0.8576 (t70) cc_final: 0.8206 (t0) REVERT: C 131 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6865 (mp10) outliers start: 28 outliers final: 20 residues processed: 117 average time/residue: 0.0960 time to fit residues: 16.0439 Evaluate side-chains 111 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 95 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 631 ASN A 739 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.149910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.089486 restraints weight = 17097.196| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.63 r_work: 0.3053 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10461 Z= 0.131 Angle : 0.568 7.436 14242 Z= 0.275 Chirality : 0.039 0.177 1591 Planarity : 0.004 0.042 1867 Dihedral : 4.610 48.200 1409 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 2.82 % Allowed : 21.34 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.24), residues: 1291 helix: 1.42 (0.24), residues: 485 sheet: -0.61 (0.42), residues: 154 loop : -0.73 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 118 TYR 0.009 0.001 TYR A 683 PHE 0.021 0.001 PHE C 136 TRP 0.010 0.001 TRP A 614 HIS 0.009 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (10460) covalent geometry : angle 0.56766 / 0.28 (14242) hydrogen bonds : bond 0.03346 / 2.38 ( 432) hydrogen bonds : angle 4.35388 / 3.15 ( 1212) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 592 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7434 (mt-10) REVERT: A 610 HIS cc_start: 0.7986 (m90) cc_final: 0.7472 (m90) REVERT: A 628 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7878 (mm-30) REVERT: A 631 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7981 (m110) REVERT: B 99 ARG cc_start: 0.8500 (mtp-110) cc_final: 0.8105 (mtm-85) REVERT: B 118 GLN cc_start: 0.8216 (mp10) cc_final: 0.7895 (mp10) REVERT: B 145 LEU cc_start: 0.8859 (mp) cc_final: 0.8546 (tp) REVERT: C 75 TYR cc_start: 0.6113 (t80) cc_final: 0.5765 (t80) REVERT: C 80 ASP cc_start: 0.8585 (t70) cc_final: 0.8213 (t0) REVERT: C 118 ARG cc_start: 0.8831 (mmp80) cc_final: 0.8584 (mmp80) REVERT: C 131 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6900 (mp10) outliers start: 31 outliers final: 20 residues processed: 112 average time/residue: 0.0824 time to fit residues: 13.1891 Evaluate side-chains 113 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 631 ASN Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 95 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN A 739 HIS C 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.149995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.089468 restraints weight = 16919.190| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.64 r_work: 0.3051 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10461 Z= 0.126 Angle : 0.565 7.689 14242 Z= 0.274 Chirality : 0.039 0.155 1591 Planarity : 0.004 0.042 1867 Dihedral : 4.605 44.912 1409 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.20 % Rotamer: Outliers : 2.72 % Allowed : 21.98 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.19 (0.24), residues: 1291 helix: 1.45 (0.24), residues: 486 sheet: -0.54 (0.42), residues: 154 loop : -0.70 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 114 TYR 0.020 0.001 TYR B 140 PHE 0.011 0.001 PHE C 136 TRP 0.011 0.001 TRP A 614 HIS 0.009 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (10460) covalent geometry : angle 0.56502 / 0.27 (14242) hydrogen bonds : bond 0.03285 / 2.35 ( 432) hydrogen bonds : angle 4.33943 / 3.15 ( 1212) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9135 (mp) REVERT: A 603 TYR cc_start: 0.7947 (p90) cc_final: 0.7666 (p90) REVERT: A 610 HIS cc_start: 0.8014 (m90) cc_final: 0.7524 (m90) REVERT: A 628 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7846 (mm-30) REVERT: B 99 ARG cc_start: 0.8502 (mtp-110) cc_final: 0.8145 (mtm-85) REVERT: B 118 GLN cc_start: 0.8217 (mp10) cc_final: 0.7890 (mp10) REVERT: B 145 LEU cc_start: 0.8858 (mp) cc_final: 0.8548 (tp) REVERT: C 75 TYR cc_start: 0.6243 (t80) cc_final: 0.5715 (t80) REVERT: C 80 ASP cc_start: 0.8607 (t70) cc_final: 0.8210 (t0) REVERT: C 118 ARG cc_start: 0.8829 (mmp80) cc_final: 0.8623 (mmp80) REVERT: C 131 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6938 (mp10) outliers start: 30 outliers final: 22 residues processed: 114 average time/residue: 0.1001 time to fit residues: 16.1267 Evaluate side-chains 113 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 95 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 127 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 88 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 72 optimal weight: 0.0870 chunk 53 optimal weight: 0.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.149087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.088523 restraints weight = 16832.551| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.63 r_work: 0.3056 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 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 : 0.003 0.040 10461 Z= 0.113 Angle : 0.558 7.853 14242 Z= 0.270 Chirality : 0.039 0.173 1591 Planarity : 0.004 0.044 1867 Dihedral : 4.548 44.666 1409 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.12 % Rotamer: Outliers : 2.36 % Allowed : 22.62 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.29 (0.24), residues: 1291 helix: 1.55 (0.24), residues: 480 sheet: -0.47 (0.42), residues: 154 loop : -0.65 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 118 TYR 0.011 0.001 TYR A 735 PHE 0.019 0.001 PHE C 136 TRP 0.013 0.001 TRP A 614 HIS 0.009 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (10460) covalent geometry : angle 0.55840 / 0.27 (14242) hydrogen bonds : bond 0.03162 / 2.25 ( 432) hydrogen bonds : angle 4.25420 / 3.07 ( 1212) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.8019 (t0) cc_final: 0.7695 (t0) REVERT: A 470 ASP cc_start: 0.7871 (m-30) cc_final: 0.7635 (m-30) REVERT: A 603 TYR cc_start: 0.7925 (p90) cc_final: 0.7639 (p90) REVERT: A 610 HIS cc_start: 0.7959 (m90) cc_final: 0.7482 (m90) REVERT: A 628 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7830 (mm-30) REVERT: A 958 TRP cc_start: 0.8768 (OUTLIER) cc_final: 0.8364 (m-10) REVERT: B 99 ARG cc_start: 0.8481 (mtp-110) cc_final: 0.8116 (mtm-85) REVERT: B 118 GLN cc_start: 0.8226 (mp10) cc_final: 0.7904 (mp10) REVERT: B 145 LEU cc_start: 0.8867 (mp) cc_final: 0.8563 (tp) REVERT: C 21 TYR cc_start: 0.7456 (p90) cc_final: 0.7215 (p90) REVERT: C 75 TYR cc_start: 0.6052 (t80) cc_final: 0.5655 (t80) REVERT: C 80 ASP cc_start: 0.8610 (t70) cc_final: 0.8208 (t0) REVERT: C 131 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6921 (mp10) outliers start: 26 outliers final: 19 residues processed: 114 average time/residue: 0.1041 time to fit residues: 16.8697 Evaluate side-chains 116 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 95 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.150619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.097196 restraints weight = 17046.351| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.31 r_work: 0.3067 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10461 Z= 0.138 Angle : 0.579 7.991 14242 Z= 0.280 Chirality : 0.039 0.260 1591 Planarity : 0.004 0.044 1867 Dihedral : 4.580 44.458 1409 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.88 % Favored : 95.04 % Rotamer: Outliers : 2.45 % Allowed : 22.62 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.24), residues: 1291 helix: 1.50 (0.24), residues: 486 sheet: -0.50 (0.42), residues: 154 loop : -0.66 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 118 TYR 0.010 0.001 TYR A 435 PHE 0.023 0.001 PHE D 149 TRP 0.012 0.001 TRP A 614 HIS 0.009 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (10460) covalent geometry : angle 0.57858 / 0.28 (14242) hydrogen bonds : bond 0.03316 / 2.37 ( 432) hydrogen bonds : angle 4.29358 / 3.10 ( 1212) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9119 (mp) REVERT: A 470 ASP cc_start: 0.7942 (m-30) cc_final: 0.7709 (m-30) REVERT: A 610 HIS cc_start: 0.8017 (m90) cc_final: 0.7654 (m-70) REVERT: A 628 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7773 (mm-30) REVERT: A 958 TRP cc_start: 0.8799 (OUTLIER) cc_final: 0.8397 (m-10) REVERT: B 99 ARG cc_start: 0.8502 (mtp-110) cc_final: 0.8139 (mtm-85) REVERT: B 118 GLN cc_start: 0.8282 (mp10) cc_final: 0.7964 (mp10) REVERT: B 145 LEU cc_start: 0.8871 (mp) cc_final: 0.8556 (tp) REVERT: C 75 TYR cc_start: 0.6371 (t80) cc_final: 0.5967 (t80) REVERT: C 80 ASP cc_start: 0.8638 (t70) cc_final: 0.8238 (t0) REVERT: C 131 GLN cc_start: 0.7242 (OUTLIER) cc_final: 0.6972 (mp10) outliers start: 27 outliers final: 21 residues processed: 109 average time/residue: 0.1041 time to fit residues: 15.9346 Evaluate side-chains 111 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 62 optimal weight: 0.0470 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.151376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.095181 restraints weight = 16878.055| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.42 r_work: 0.3048 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10461 Z= 0.115 Angle : 0.573 8.544 14242 Z= 0.277 Chirality : 0.039 0.242 1591 Planarity : 0.004 0.044 1867 Dihedral : 4.563 44.671 1409 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.27 % Rotamer: Outliers : 2.27 % Allowed : 22.43 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.36 (0.24), residues: 1291 helix: 1.61 (0.24), residues: 479 sheet: -0.44 (0.42), residues: 154 loop : -0.60 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 114 TYR 0.012 0.001 TYR A 735 PHE 0.022 0.001 PHE D 149 TRP 0.014 0.001 TRP A 614 HIS 0.011 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (10460) covalent geometry : angle 0.57282 / 0.28 (14242) hydrogen bonds : bond 0.03139 / 2.25 ( 432) hydrogen bonds : angle 4.24376 / 3.07 ( 1212) Misc. bond : bond 0.00001 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9117 (mp) REVERT: A 470 ASP cc_start: 0.7702 (m-30) cc_final: 0.7488 (m-30) REVERT: A 603 TYR cc_start: 0.7917 (p90) cc_final: 0.7664 (p90) REVERT: A 610 HIS cc_start: 0.7964 (m90) cc_final: 0.7616 (m-70) REVERT: A 628 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7702 (mm-30) REVERT: A 958 TRP cc_start: 0.8737 (OUTLIER) cc_final: 0.8322 (m-10) REVERT: B 99 ARG cc_start: 0.8406 (mtp-110) cc_final: 0.8125 (ttm110) REVERT: B 118 GLN cc_start: 0.8234 (mp10) cc_final: 0.7918 (mp10) REVERT: B 145 LEU cc_start: 0.8824 (mp) cc_final: 0.8501 (tp) REVERT: C 21 TYR cc_start: 0.7522 (p90) cc_final: 0.7287 (p90) REVERT: C 75 TYR cc_start: 0.6317 (t80) cc_final: 0.5947 (t80) REVERT: C 80 ASP cc_start: 0.8596 (t70) cc_final: 0.8196 (t0) REVERT: C 131 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6977 (mp10) outliers start: 25 outliers final: 19 residues processed: 105 average time/residue: 0.0985 time to fit residues: 14.3920 Evaluate side-chains 111 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 113 optimal weight: 5.9990 chunk 82 optimal weight: 0.0270 chunk 44 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 94 optimal weight: 0.4980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 HIS ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.154040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.091725 restraints weight = 17472.099| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.74 r_work: 0.3079 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10461 Z= 0.106 Angle : 0.565 8.653 14242 Z= 0.273 Chirality : 0.039 0.235 1591 Planarity : 0.004 0.046 1867 Dihedral : 4.473 44.991 1409 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.12 % Rotamer: Outliers : 2.18 % Allowed : 22.62 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.43 (0.24), residues: 1291 helix: 1.67 (0.24), residues: 480 sheet: -0.38 (0.43), residues: 154 loop : -0.57 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 114 TYR 0.007 0.001 TYR A 247 PHE 0.022 0.001 PHE D 149 TRP 0.013 0.001 TRP A 614 HIS 0.010 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (10460) covalent geometry : angle 0.56529 / 0.27 (14242) hydrogen bonds : bond 0.02983 / 2.12 ( 432) hydrogen bonds : angle 4.15890 / 3.01 ( 1212) Misc. bond : bond 0.00002 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2670.85 seconds wall clock time: 46 minutes 18.34 seconds (2778.34 seconds total)