Starting phenix.real_space_refine on Sun Dec 29 10:28:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sv8_40782/12_2024/8sv8_40782.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sv8_40782/12_2024/8sv8_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_40782/12_2024/8sv8_40782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sv8_40782/12_2024/8sv8_40782.map" model { file = "/net/cci-nas-00/data/ceres_data/8sv8_40782/12_2024/8sv8_40782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sv8_40782/12_2024/8sv8_40782.cif" } resolution = 3.38 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= 0.004 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 7.01, per 1000 atoms: 0.69 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: 2.93 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.55 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: 3.53 Time building geometry restraints manager: 3.35 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: 2.370 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 27.740 Find NCS groups from input model: 0.150 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 10460 Z= 0.244 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 (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: -0.43 (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 TRP 0.010 0.001 TRP A 614 HIS 0.004 0.001 HIS A 817 PHE 0.012 0.001 PHE A 426 TYR 0.028 0.002 TYR A 603 ARG 0.008 0.001 ARG C 23 *********************** 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 : 1.217 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: 0.2442 time to fit residues: 34.8852 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 : 1.246 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 116 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 157 GLN A 201 HIS A 229 HIS ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10460 Z= 0.350 Angle : 0.633 6.213 14242 Z= 0.315 Chirality : 0.042 0.166 1591 Planarity : 0.005 0.050 1867 Dihedral : 5.009 50.269 1411 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.65 % Favored : 94.27 % Rotamer: Outliers : 2.72 % Allowed : 20.53 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.50 (0.23), residues: 1291 helix: 1.03 (0.24), residues: 479 sheet: -1.36 (0.40), residues: 158 loop : -1.08 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 677 HIS 0.005 0.001 HIS A 264 PHE 0.016 0.002 PHE A 881 TYR 0.019 0.002 TYR B 140 ARG 0.007 0.001 ARG B 92 *********************** 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: 30 poor density : 101 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7942 (t0) cc_final: 0.7653 (t0) REVERT: A 468 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7568 (t0) REVERT: A 610 HIS cc_start: 0.8103 (m90) cc_final: 0.7599 (m90) REVERT: B 99 ARG cc_start: 0.8292 (mtp-110) cc_final: 0.7959 (mmm-85) REVERT: B 118 GLN cc_start: 0.8013 (mp10) cc_final: 0.7754 (mp10) REVERT: C 70 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8428 (m-10) outliers start: 30 outliers final: 19 residues processed: 122 average time/residue: 0.2504 time to fit residues: 43.3224 Evaluate side-chains 112 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 256 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 884 SER 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 70 PHE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 99 THR 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 64 optimal weight: 30.0000 chunk 36 optimal weight: 0.0470 chunk 96 optimal weight: 5.9990 chunk 79 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 103 optimal weight: 0.4980 chunk 115 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS A 229 HIS A 476 ASN A 480 GLN A 739 HIS C 139 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10460 Z= 0.158 Angle : 0.555 6.327 14242 Z= 0.273 Chirality : 0.039 0.155 1591 Planarity : 0.005 0.044 1867 Dihedral : 4.705 50.064 1409 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.12 % Rotamer: Outliers : 3.36 % Allowed : 20.44 % 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 (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: -0.16 (0.24), residues: 1291 helix: 1.29 (0.24), residues: 486 sheet: -1.15 (0.42), residues: 153 loop : -0.90 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 677 HIS 0.009 0.001 HIS A 682 PHE 0.009 0.001 PHE A 146 TYR 0.009 0.001 TYR B 140 ARG 0.004 0.000 ARG C 23 *********************** 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 140 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7844 (t0) cc_final: 0.7588 (t0) REVERT: A 610 HIS cc_start: 0.8127 (m90) cc_final: 0.7760 (m-70) REVERT: B 118 GLN cc_start: 0.7993 (mp10) cc_final: 0.7711 (mp10) REVERT: C 70 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8374 (m-10) REVERT: C 128 LEU cc_start: 0.9077 (mm) cc_final: 0.8854 (mm) REVERT: C 131 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6778 (mp10) outliers start: 37 outliers final: 16 residues processed: 129 average time/residue: 0.2762 time to fit residues: 50.2675 Evaluate side-chains 111 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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 160 CYS 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 70 PHE Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 131 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10460 Z= 0.287 Angle : 0.591 6.372 14242 Z= 0.293 Chirality : 0.040 0.166 1591 Planarity : 0.005 0.041 1867 Dihedral : 4.797 50.296 1409 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.34 % Favored : 94.58 % Rotamer: Outliers : 3.09 % Allowed : 21.25 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.17 (0.23), residues: 1291 helix: 1.15 (0.24), residues: 497 sheet: -1.03 (0.41), residues: 153 loop : -0.86 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 677 HIS 0.008 0.001 HIS A 229 PHE 0.014 0.001 PHE C 136 TYR 0.030 0.002 TYR B 140 ARG 0.013 0.000 ARG A 231 *********************** 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 : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7306 (tm-30) REVERT: A 603 TYR cc_start: 0.7848 (p90) cc_final: 0.7542 (p90) REVERT: A 610 HIS cc_start: 0.8129 (m90) cc_final: 0.7567 (m90) REVERT: B 99 ARG cc_start: 0.8273 (mtp-110) cc_final: 0.7910 (mtp-110) REVERT: B 118 GLN cc_start: 0.8046 (mp10) cc_final: 0.7760 (mp10) REVERT: C 70 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8387 (m-80) REVERT: C 128 LEU cc_start: 0.9101 (mm) cc_final: 0.8872 (mm) REVERT: C 131 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6714 (mp10) outliers start: 34 outliers final: 21 residues processed: 123 average time/residue: 0.2415 time to fit residues: 42.0934 Evaluate side-chains 114 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 364 LEU 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 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 70 PHE 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 103 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 105 optimal weight: 0.0980 chunk 85 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS A 476 ASN A 631 ASN A 739 HIS C 84 GLN C 139 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10460 Z= 0.164 Angle : 0.554 7.895 14242 Z= 0.271 Chirality : 0.039 0.157 1591 Planarity : 0.004 0.042 1867 Dihedral : 4.659 49.762 1409 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.20 % Rotamer: Outliers : 2.36 % Allowed : 21.98 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.10 (0.24), residues: 1291 helix: 1.39 (0.24), residues: 485 sheet: -0.74 (0.42), residues: 154 loop : -0.73 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 614 HIS 0.010 0.001 HIS A 229 PHE 0.009 0.001 PHE A 619 TYR 0.010 0.001 TYR B 140 ARG 0.004 0.000 ARG C 118 *********************** 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 129 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7971 (t0) cc_final: 0.7667 (t0) REVERT: A 592 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7888 (mt-10) REVERT: A 603 TYR cc_start: 0.7865 (p90) cc_final: 0.7603 (p90) REVERT: A 610 HIS cc_start: 0.8126 (m90) cc_final: 0.7565 (m90) REVERT: A 628 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7755 (mm-30) REVERT: B 99 ARG cc_start: 0.8218 (mtp-110) cc_final: 0.7876 (mtp-110) REVERT: B 118 GLN cc_start: 0.8156 (mp10) cc_final: 0.7863 (mp10) REVERT: C 70 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8262 (m-80) REVERT: C 80 ASP cc_start: 0.8528 (t70) cc_final: 0.8161 (t0) REVERT: C 118 ARG cc_start: 0.8752 (mmp80) cc_final: 0.8531 (mmp80) REVERT: C 128 LEU cc_start: 0.9086 (mm) cc_final: 0.8813 (mm) REVERT: C 131 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6754 (mp10) outliers start: 26 outliers final: 15 residues processed: 118 average time/residue: 0.2598 time to fit residues: 43.4986 Evaluate side-chains 111 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 254 THR 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 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 70 PHE Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 81 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 30 optimal weight: 0.1980 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10460 Z= 0.288 Angle : 0.590 7.514 14242 Z= 0.290 Chirality : 0.040 0.156 1591 Planarity : 0.005 0.042 1867 Dihedral : 4.781 50.044 1409 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.42 % Favored : 94.50 % Rotamer: Outliers : 3.00 % Allowed : 21.53 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.02 (0.24), residues: 1291 helix: 1.21 (0.24), residues: 492 sheet: -0.81 (0.41), residues: 153 loop : -0.74 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 614 HIS 0.010 0.001 HIS A 229 PHE 0.012 0.001 PHE A 881 TYR 0.012 0.002 TYR A 435 ARG 0.004 0.000 ARG A 231 *********************** 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 127 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9094 (mp) REVERT: A 303 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8906 (mp) REVERT: A 592 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7950 (mt-10) REVERT: A 603 TYR cc_start: 0.7906 (p90) cc_final: 0.7625 (p90) REVERT: A 610 HIS cc_start: 0.8143 (m90) cc_final: 0.7653 (m90) REVERT: A 628 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7777 (mm-30) REVERT: A 958 TRP cc_start: 0.8747 (OUTLIER) cc_final: 0.8414 (m-10) REVERT: B 99 ARG cc_start: 0.8280 (mtp-110) cc_final: 0.7957 (mtm-85) REVERT: B 118 GLN cc_start: 0.8251 (mp10) cc_final: 0.8027 (mp10) REVERT: B 145 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8599 (tp) REVERT: C 70 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: C 80 ASP cc_start: 0.8555 (t70) cc_final: 0.8166 (t0) REVERT: C 118 ARG cc_start: 0.8793 (mmp80) cc_final: 0.8573 (mmp80) REVERT: C 128 LEU cc_start: 0.9113 (mm) cc_final: 0.8848 (mm) REVERT: C 131 GLN cc_start: 0.7043 (OUTLIER) cc_final: 0.6819 (mp10) outliers start: 33 outliers final: 17 residues processed: 116 average time/residue: 0.2580 time to fit residues: 41.9873 Evaluate side-chains 112 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 249 ARG Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 364 LEU 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 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 B residue 145 LEU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 90 optimal weight: 0.0970 chunk 104 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 75 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 739 HIS A 936 GLN C 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10460 Z= 0.172 Angle : 0.558 7.897 14242 Z= 0.272 Chirality : 0.039 0.190 1591 Planarity : 0.004 0.042 1867 Dihedral : 4.659 45.388 1409 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.12 % Rotamer: Outliers : 2.09 % Allowed : 22.52 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.21 (0.24), residues: 1291 helix: 1.44 (0.24), residues: 486 sheet: -0.62 (0.42), residues: 154 loop : -0.64 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 614 HIS 0.010 0.001 HIS A 682 PHE 0.008 0.001 PHE A 146 TYR 0.016 0.001 TYR C 75 ARG 0.003 0.000 ARG C 114 *********************** 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 120 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 TYR cc_start: 0.7847 (p90) cc_final: 0.7563 (p90) REVERT: A 610 HIS cc_start: 0.8140 (m90) cc_final: 0.7639 (m90) REVERT: A 628 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7607 (mm-30) REVERT: A 710 GLN cc_start: 0.2427 (OUTLIER) cc_final: 0.1476 (pp30) REVERT: A 958 TRP cc_start: 0.8694 (OUTLIER) cc_final: 0.8388 (m-10) REVERT: B 99 ARG cc_start: 0.8185 (mtp-110) cc_final: 0.7919 (mtm-85) REVERT: B 118 GLN cc_start: 0.8306 (mp10) cc_final: 0.7981 (mp10) REVERT: C 70 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8290 (m-80) REVERT: C 80 ASP cc_start: 0.8555 (t70) cc_final: 0.8157 (t0) outliers start: 23 outliers final: 15 residues processed: 109 average time/residue: 0.2717 time to fit residues: 41.0908 Evaluate side-chains 108 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 710 GLN 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 70 PHE Chi-restraints excluded: chain C residue 76 HIS 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 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 49 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 739 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10460 Z= 0.198 Angle : 0.579 9.473 14242 Z= 0.281 Chirality : 0.039 0.178 1591 Planarity : 0.004 0.043 1867 Dihedral : 4.637 45.045 1409 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.11 % Favored : 94.81 % 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 (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: 0.26 (0.24), residues: 1291 helix: 1.48 (0.24), residues: 486 sheet: -0.56 (0.42), residues: 154 loop : -0.63 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 614 HIS 0.009 0.001 HIS A 229 PHE 0.016 0.001 PHE C 136 TYR 0.015 0.001 TYR C 75 ARG 0.005 0.000 ARG A 249 *********************** 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 116 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9112 (mp) REVERT: A 603 TYR cc_start: 0.7859 (p90) cc_final: 0.7548 (p90) REVERT: A 610 HIS cc_start: 0.8161 (m90) cc_final: 0.7798 (m-70) REVERT: A 628 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7547 (mm-30) REVERT: A 691 HIS cc_start: 0.6801 (t-90) cc_final: 0.6520 (t-90) REVERT: A 710 GLN cc_start: 0.2427 (OUTLIER) cc_final: 0.1476 (pp30) REVERT: A 927 THR cc_start: 0.7232 (OUTLIER) cc_final: 0.6777 (t) REVERT: A 958 TRP cc_start: 0.8705 (OUTLIER) cc_final: 0.8338 (m-10) REVERT: B 99 ARG cc_start: 0.8166 (mtp-110) cc_final: 0.7881 (mtm-85) REVERT: B 118 GLN cc_start: 0.8316 (mp10) cc_final: 0.7972 (mp10) REVERT: C 70 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8232 (m-80) REVERT: C 80 ASP cc_start: 0.8553 (t70) cc_final: 0.8144 (t0) outliers start: 27 outliers final: 18 residues processed: 106 average time/residue: 0.2706 time to fit residues: 40.2350 Evaluate side-chains 110 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 117 LEU 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 710 GLN Chi-restraints excluded: chain A residue 927 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 70 PHE 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 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 118 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 103 optimal weight: 0.1980 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 739 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10460 Z= 0.174 Angle : 0.566 8.204 14242 Z= 0.275 Chirality : 0.039 0.164 1591 Planarity : 0.004 0.043 1867 Dihedral : 4.562 45.622 1409 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.20 % Rotamer: Outliers : 2.45 % Allowed : 22.52 % 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 (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: 0.35 (0.24), residues: 1291 helix: 1.58 (0.24), residues: 480 sheet: -0.43 (0.43), residues: 154 loop : -0.58 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 614 HIS 0.009 0.001 HIS A 229 PHE 0.015 0.001 PHE C 136 TYR 0.008 0.001 TYR C 75 ARG 0.005 0.000 ARG C 118 *********************** 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 116 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9118 (mp) REVERT: A 603 TYR cc_start: 0.7902 (p90) cc_final: 0.7648 (p90) REVERT: A 610 HIS cc_start: 0.8149 (m90) cc_final: 0.7785 (m-70) REVERT: A 628 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7573 (mm-30) REVERT: A 710 GLN cc_start: 0.2397 (OUTLIER) cc_final: 0.1474 (pp30) REVERT: A 864 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8779 (mt) REVERT: A 927 THR cc_start: 0.7233 (OUTLIER) cc_final: 0.6781 (t) REVERT: A 958 TRP cc_start: 0.8679 (OUTLIER) cc_final: 0.8302 (m-10) REVERT: B 99 ARG cc_start: 0.8166 (mtp-110) cc_final: 0.7958 (ttm110) REVERT: B 118 GLN cc_start: 0.8297 (mp10) cc_final: 0.7926 (mp10) REVERT: C 21 TYR cc_start: 0.7573 (p90) cc_final: 0.7344 (p90) REVERT: C 70 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8231 (m-80) REVERT: C 80 ASP cc_start: 0.8565 (t70) cc_final: 0.8143 (t0) outliers start: 27 outliers final: 18 residues processed: 108 average time/residue: 0.2701 time to fit residues: 40.5703 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 : 1.211 ------------------------------------------------------------------------------- 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 254 THR 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 710 GLN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 927 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 70 PHE 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 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 74 optimal weight: 0.0070 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 78 optimal weight: 0.0270 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10460 Z= 0.149 Angle : 0.562 8.579 14242 Z= 0.272 Chirality : 0.038 0.153 1591 Planarity : 0.004 0.044 1867 Dihedral : 4.448 46.566 1409 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.96 % Favored : 94.97 % Rotamer: Outliers : 2.00 % Allowed : 22.80 % 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 (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: 0.45 (0.24), residues: 1291 helix: 1.65 (0.24), residues: 482 sheet: -0.31 (0.42), residues: 154 loop : -0.55 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 614 HIS 0.009 0.001 HIS A 229 PHE 0.014 0.001 PHE C 136 TYR 0.015 0.001 TYR C 75 ARG 0.005 0.000 ARG C 118 ********************** 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 123 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7946 (t0) cc_final: 0.7668 (t0) REVERT: A 603 TYR cc_start: 0.7778 (p90) cc_final: 0.7480 (p90) REVERT: A 610 HIS cc_start: 0.8176 (m90) cc_final: 0.7824 (m-70) REVERT: A 628 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 710 GLN cc_start: 0.2352 (OUTLIER) cc_final: 0.1404 (pp30) REVERT: A 864 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8770 (mt) REVERT: A 958 TRP cc_start: 0.8658 (OUTLIER) cc_final: 0.8253 (m-10) REVERT: B 118 GLN cc_start: 0.8273 (mp10) cc_final: 0.7894 (mp10) REVERT: C 21 TYR cc_start: 0.7442 (p90) cc_final: 0.7238 (p90) REVERT: C 70 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: C 80 ASP cc_start: 0.8579 (t70) cc_final: 0.8156 (t0) outliers start: 22 outliers final: 17 residues processed: 115 average time/residue: 0.2592 time to fit residues: 42.6701 Evaluate side-chains 112 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU 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 710 GLN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 991 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 70 PHE Chi-restraints excluded: chain C residue 76 HIS 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 149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 chunk 101 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.149147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.088568 restraints weight = 16660.374| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.61 r_work: 0.3072 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10460 Z= 0.200 Angle : 0.577 8.507 14242 Z= 0.279 Chirality : 0.039 0.147 1591 Planarity : 0.004 0.045 1867 Dihedral : 4.481 45.614 1409 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 2.27 % Allowed : 22.89 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.36 (0.24), residues: 1291 helix: 1.55 (0.24), residues: 484 sheet: -0.33 (0.42), residues: 154 loop : -0.60 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 614 HIS 0.010 0.001 HIS A 682 PHE 0.016 0.001 PHE C 136 TYR 0.009 0.001 TYR A 435 ARG 0.006 0.000 ARG C 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2497.35 seconds wall clock time: 46 minutes 22.19 seconds (2782.19 seconds total)