Starting phenix.real_space_refine on Thu May 1 07:02:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sv8_40782/05_2025/8sv8_40782.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sv8_40782/05_2025/8sv8_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_40782/05_2025/8sv8_40782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sv8_40782/05_2025/8sv8_40782.map" model { file = "/net/cci-nas-00/data/ceres_data/8sv8_40782/05_2025/8sv8_40782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sv8_40782/05_2025/8sv8_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-5669/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: 6.81, per 1000 atoms: 0.67 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: 2.55 Conformation dependent library (CDL) restraints added in 1.1 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: 1.41 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: 3.43 Time building geometry restraints manager: 3.04 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: 3.660 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.310 Find NCS groups from input model: 0.130 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.660 ------------------------------------------------------------------------------- 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 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.10670 ( 432) hydrogen bonds : angle 5.35520 ( 1212) covalent geometry : bond 0.00370 (10460) covalent geometry : angle 0.71664 (14242) Misc. bond : bond 0.00010 ( 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 : 1.201 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: 0.2423 time to fit residues: 34.5614 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 : 1.060 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.148529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.094233 restraints weight = 16885.969| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.64 r_work: 0.2993 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 10461 Z= 0.221 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 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 432) hydrogen bonds : angle 4.75397 ( 1212) covalent geometry : bond 0.00539 (10460) covalent geometry : angle 0.63305 (14242) Misc. bond : bond 0.00007 ( 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: 30 poor density : 101 time to evaluate : 1.164 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: 0.7567 (t0) REVERT: A 610 HIS cc_start: 0.7896 (m90) cc_final: 0.7450 (m90) REVERT: B 99 ARG cc_start: 0.8452 (mtp-110) cc_final: 0.8153 (mmm-85) REVERT: B 118 GLN cc_start: 0.7915 (mp10) cc_final: 0.7657 (mp10) REVERT: C 70 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8446 (m-10) outliers start: 30 outliers final: 19 residues processed: 122 average time/residue: 0.2940 time to fit residues: 50.9191 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 : 1.219 ------------------------------------------------------------------------------- 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 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 3 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.0040 chunk 100 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.150374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.090018 restraints weight = 17124.121| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.63 r_work: 0.3071 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1122 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= 0.113 Angle : 0.557 6.309 14242 Z= 0.275 Chirality : 0.039 0.156 1591 Planarity : 0.005 0.044 1867 Dihedral : 4.739 45.163 1409 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.12 % Rotamer: Outliers : 3.36 % Allowed : 20.62 % Favored : 76.02 % 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: -0.16 (0.24), residues: 1291 helix: 1.30 (0.24), residues: 485 sheet: -1.16 (0.42), residues: 153 loop : -0.90 (0.24), residues: 653 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 A 683 ARG 0.004 0.000 ARG C 23 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 432) hydrogen bonds : angle 4.45311 ( 1212) covalent geometry : bond 0.00258 (10460) covalent geometry : angle 0.55747 (14242) Misc. bond : bond 0.00008 ( 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 141 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7890 (t0) cc_final: 0.7611 (t0) REVERT: A 603 TYR cc_start: 0.7818 (p90) cc_final: 0.7462 (p90) REVERT: A 610 HIS cc_start: 0.7987 (m90) cc_final: 0.7631 (m-70) REVERT: B 118 GLN cc_start: 0.7976 (mp10) cc_final: 0.7700 (mp10) REVERT: C 70 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8501 (m-10) REVERT: C 128 LEU cc_start: 0.9089 (mm) cc_final: 0.8885 (mm) REVERT: C 131 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.6792 (mp10) outliers start: 37 outliers final: 17 residues processed: 128 average time/residue: 0.2445 time to fit residues: 45.8054 Evaluate side-chains 113 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 469 MET 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 74 optimal weight: 3.9990 chunk 67 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 87 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 739 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.149401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.093023 restraints weight = 16860.961| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.41 r_work: 0.3019 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10461 Z= 0.139 Angle : 0.568 6.204 14242 Z= 0.280 Chirality : 0.039 0.164 1591 Planarity : 0.005 0.042 1867 Dihedral : 4.737 45.181 1409 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.11 % Favored : 94.81 % Rotamer: Outliers : 3.09 % Allowed : 21.07 % 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 (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: 1.26 (0.24), residues: 492 sheet: -0.98 (0.41), residues: 154 loop : -0.85 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 677 HIS 0.009 0.001 HIS A 229 PHE 0.012 0.001 PHE C 136 TYR 0.029 0.001 TYR B 140 ARG 0.012 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 432) hydrogen bonds : angle 4.42259 ( 1212) covalent geometry : bond 0.00335 (10460) covalent geometry : angle 0.56758 (14242) Misc. bond : bond 0.00019 ( 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 135 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7850 (t0) cc_final: 0.7553 (t0) REVERT: A 603 TYR cc_start: 0.7885 (p90) cc_final: 0.7582 (p90) REVERT: A 610 HIS cc_start: 0.7939 (m90) cc_final: 0.7439 (m90) REVERT: B 99 ARG cc_start: 0.8421 (mtp-110) cc_final: 0.8070 (mtp-110) REVERT: B 118 GLN cc_start: 0.7922 (mp10) cc_final: 0.7635 (mp10) REVERT: C 70 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8310 (m-80) REVERT: C 128 LEU cc_start: 0.9074 (mm) cc_final: 0.8835 (mm) REVERT: C 131 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6803 (mp10) outliers start: 34 outliers final: 20 residues processed: 124 average time/residue: 0.2887 time to fit residues: 51.7357 Evaluate side-chains 117 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 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 62 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 118 optimal weight: 0.4980 chunk 39 optimal weight: 0.0870 chunk 15 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 overall best weight: 1.0562 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.149188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.092942 restraints weight = 17013.194| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.53 r_work: 0.2982 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10461 Z= 0.151 Angle : 0.570 7.415 14242 Z= 0.280 Chirality : 0.039 0.159 1591 Planarity : 0.005 0.044 1867 Dihedral : 4.711 44.969 1409 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.11 % Favored : 94.81 % Rotamer: Outliers : 3.18 % Allowed : 21.44 % 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: -0.02 (0.24), residues: 1291 helix: 1.22 (0.24), residues: 498 sheet: -0.87 (0.41), residues: 154 loop : -0.75 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 614 HIS 0.010 0.001 HIS A 229 PHE 0.009 0.001 PHE A 146 TYR 0.010 0.001 TYR A 435 ARG 0.009 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 432) hydrogen bonds : angle 4.41699 ( 1212) covalent geometry : bond 0.00366 (10460) covalent geometry : angle 0.57001 (14242) Misc. bond : bond 0.00002 ( 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 135 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9111 (mp) REVERT: A 592 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7509 (mt-10) REVERT: A 603 TYR cc_start: 0.8007 (p90) cc_final: 0.7755 (p90) REVERT: A 610 HIS cc_start: 0.7968 (m90) cc_final: 0.7471 (m90) REVERT: A 628 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7887 (mm-30) REVERT: A 631 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7961 (m110) REVERT: A 958 TRP cc_start: 0.8757 (OUTLIER) cc_final: 0.8434 (m-10) REVERT: B 99 ARG cc_start: 0.8453 (mtp-110) cc_final: 0.8078 (mtp-110) REVERT: B 118 GLN cc_start: 0.8130 (mp10) cc_final: 0.7844 (mp10) REVERT: C 70 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8394 (m-80) REVERT: C 80 ASP cc_start: 0.8569 (t70) cc_final: 0.8198 (t0) REVERT: C 118 ARG cc_start: 0.8858 (mmp80) cc_final: 0.8625 (mmp80) REVERT: C 128 LEU cc_start: 0.9122 (mm) cc_final: 0.8874 (mm) REVERT: C 131 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6841 (mp10) outliers start: 35 outliers final: 19 residues processed: 125 average time/residue: 0.2589 time to fit residues: 47.2103 Evaluate side-chains 115 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 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 631 ASN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 110 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 74 optimal weight: 0.0170 chunk 23 optimal weight: 4.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.150481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.090275 restraints weight = 17004.184| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.62 r_work: 0.3067 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1772 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= 0.122 Angle : 0.560 7.582 14242 Z= 0.273 Chirality : 0.039 0.147 1591 Planarity : 0.004 0.043 1867 Dihedral : 4.663 45.025 1409 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.34 % Favored : 94.58 % Rotamer: Outliers : 2.63 % Allowed : 22.25 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.24), residues: 1291 helix: 1.37 (0.24), residues: 486 sheet: -0.72 (0.41), residues: 154 loop : -0.68 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 614 HIS 0.009 0.001 HIS A 229 PHE 0.009 0.001 PHE A 146 TYR 0.010 0.001 TYR A 735 ARG 0.005 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 432) hydrogen bonds : angle 4.35249 ( 1212) covalent geometry : bond 0.00290 (10460) covalent geometry : angle 0.56002 (14242) Misc. bond : bond 0.00008 ( 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 127 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 ASP cc_start: 0.7911 (m-30) cc_final: 0.7661 (m-30) REVERT: A 603 TYR cc_start: 0.7949 (p90) cc_final: 0.7665 (p90) REVERT: A 610 HIS cc_start: 0.7997 (m90) cc_final: 0.7505 (m90) REVERT: A 628 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7929 (mm-30) REVERT: A 631 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8157 (m-40) REVERT: B 99 ARG cc_start: 0.8481 (mtp-110) cc_final: 0.8094 (mtp-110) REVERT: B 118 GLN cc_start: 0.8238 (mp10) cc_final: 0.7945 (mp10) REVERT: B 145 LEU cc_start: 0.8847 (mp) cc_final: 0.8514 (tp) REVERT: C 70 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: C 80 ASP cc_start: 0.8628 (t70) cc_final: 0.8226 (t0) REVERT: C 118 ARG cc_start: 0.8873 (mmp80) cc_final: 0.8671 (mmp80) REVERT: C 128 LEU cc_start: 0.9108 (mm) cc_final: 0.8844 (mm) REVERT: C 131 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6924 (mp10) outliers start: 29 outliers final: 17 residues processed: 116 average time/residue: 0.2539 time to fit residues: 41.6755 Evaluate side-chains 116 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 109 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 631 ASN A 739 HIS C 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.148973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.095126 restraints weight = 17238.414| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.49 r_work: 0.3024 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10461 Z= 0.184 Angle : 0.596 7.849 14242 Z= 0.292 Chirality : 0.040 0.268 1591 Planarity : 0.005 0.045 1867 Dihedral : 4.751 44.664 1409 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.27 % Favored : 94.66 % Rotamer: Outliers : 2.63 % Allowed : 22.34 % 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: -0.03 (0.24), residues: 1291 helix: 1.18 (0.24), residues: 492 sheet: -0.87 (0.41), residues: 154 loop : -0.71 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 614 HIS 0.009 0.001 HIS A 229 PHE 0.016 0.001 PHE C 136 TYR 0.016 0.002 TYR C 75 ARG 0.007 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 432) hydrogen bonds : angle 4.46378 ( 1212) covalent geometry : bond 0.00452 (10460) covalent geometry : angle 0.59607 (14242) Misc. bond : bond 0.00009 ( 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 120 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9105 (mp) REVERT: A 592 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7511 (mt-10) REVERT: A 603 TYR cc_start: 0.7982 (p90) cc_final: 0.7654 (p90) REVERT: A 610 HIS cc_start: 0.7992 (m90) cc_final: 0.7585 (m90) REVERT: A 628 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7786 (mm-30) REVERT: A 710 GLN cc_start: 0.2157 (OUTLIER) cc_final: 0.1347 (pp30) REVERT: B 99 ARG cc_start: 0.8412 (mtp-110) cc_final: 0.8068 (mtm-85) REVERT: B 118 GLN cc_start: 0.8222 (mp10) cc_final: 0.7917 (mp10) REVERT: B 145 LEU cc_start: 0.8841 (mp) cc_final: 0.8526 (tp) REVERT: C 70 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8519 (m-80) REVERT: C 80 ASP cc_start: 0.8596 (t70) cc_final: 0.8218 (t0) REVERT: C 131 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6924 (mp10) outliers start: 29 outliers final: 19 residues processed: 111 average time/residue: 0.3672 time to fit residues: 59.2872 Evaluate side-chains 109 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 92 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 119 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.150235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.094705 restraints weight = 17057.417| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.11 r_work: 0.3052 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2068 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= 0.126 Angle : 0.583 8.562 14242 Z= 0.285 Chirality : 0.039 0.223 1591 Planarity : 0.004 0.044 1867 Dihedral : 4.706 44.896 1409 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.20 % Rotamer: Outliers : 2.45 % Allowed : 22.71 % 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: 0.10 (0.24), residues: 1291 helix: 1.25 (0.24), residues: 498 sheet: -0.71 (0.41), residues: 154 loop : -0.65 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 614 HIS 0.010 0.001 HIS A 682 PHE 0.017 0.001 PHE C 136 TYR 0.014 0.001 TYR C 75 ARG 0.004 0.000 ARG C 114 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 432) hydrogen bonds : angle 4.34562 ( 1212) covalent geometry : bond 0.00300 (10460) covalent geometry : angle 0.58300 (14242) Misc. bond : bond 0.00005 ( 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 118 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 TYR cc_start: 0.7991 (p90) cc_final: 0.7723 (p90) REVERT: A 610 HIS cc_start: 0.8017 (m90) cc_final: 0.7703 (m-70) REVERT: A 628 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7678 (mm-30) REVERT: A 710 GLN cc_start: 0.2137 (OUTLIER) cc_final: 0.1337 (pp30) REVERT: B 99 ARG cc_start: 0.8370 (mtp-110) cc_final: 0.8076 (mtm-85) REVERT: B 118 GLN cc_start: 0.8206 (mp10) cc_final: 0.7902 (mp10) REVERT: B 145 LEU cc_start: 0.8821 (mp) cc_final: 0.8518 (tp) REVERT: C 70 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8451 (m-80) REVERT: C 80 ASP cc_start: 0.8596 (t70) cc_final: 0.8204 (t0) REVERT: C 131 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6971 (mp10) outliers start: 27 outliers final: 22 residues processed: 107 average time/residue: 0.3173 time to fit residues: 49.1056 Evaluate side-chains 113 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 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 943 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain B residue 83 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 57 optimal weight: 0.0010 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.150532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.093842 restraints weight = 17046.028| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.27 r_work: 0.3045 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2165 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= 0.117 Angle : 0.573 8.514 14242 Z= 0.279 Chirality : 0.039 0.221 1591 Planarity : 0.004 0.045 1867 Dihedral : 4.656 45.993 1409 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 2.63 % Allowed : 22.25 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.28 (0.24), residues: 1291 helix: 1.51 (0.24), residues: 480 sheet: -0.56 (0.42), residues: 154 loop : -0.59 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 614 HIS 0.010 0.001 HIS A 682 PHE 0.016 0.001 PHE C 136 TYR 0.008 0.001 TYR A 547 ARG 0.005 0.000 ARG C 118 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 432) hydrogen bonds : angle 4.25390 ( 1212) covalent geometry : bond 0.00278 (10460) covalent geometry : angle 0.57337 (14242) Misc. bond : bond 0.00001 ( 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 120 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9119 (mp) REVERT: A 603 TYR cc_start: 0.7978 (p90) cc_final: 0.7678 (p90) REVERT: A 610 HIS cc_start: 0.7975 (m90) cc_final: 0.7680 (m-70) REVERT: A 628 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7608 (mm-30) REVERT: A 734 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6260 (pp) REVERT: A 864 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8746 (mt) REVERT: A 927 THR cc_start: 0.7211 (OUTLIER) cc_final: 0.6758 (t) REVERT: B 99 ARG cc_start: 0.8390 (mtp-110) cc_final: 0.8078 (mtm-85) REVERT: B 118 GLN cc_start: 0.8210 (mp10) cc_final: 0.7915 (mp10) REVERT: B 145 LEU cc_start: 0.8839 (mp) cc_final: 0.8490 (tp) REVERT: C 70 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8376 (m-80) REVERT: C 80 ASP cc_start: 0.8610 (t70) cc_final: 0.8195 (t0) REVERT: C 131 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6933 (mp10) outliers start: 29 outliers final: 18 residues processed: 110 average time/residue: 0.3292 time to fit residues: 51.7549 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 : 1.155 ------------------------------------------------------------------------------- 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 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 734 LEU 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 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 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 111 optimal weight: 0.2980 chunk 79 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 87 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.150747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.093777 restraints weight = 16883.495| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.33 r_work: 0.3010 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2293 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= 0.127 Angle : 0.578 8.690 14242 Z= 0.281 Chirality : 0.039 0.194 1591 Planarity : 0.004 0.046 1867 Dihedral : 4.653 46.213 1409 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.88 % Favored : 95.04 % Rotamer: Outliers : 2.45 % Allowed : 22.25 % 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 (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: 0.24 (0.24), residues: 1291 helix: 1.39 (0.24), residues: 492 sheet: -0.55 (0.42), residues: 154 loop : -0.58 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 614 HIS 0.010 0.001 HIS A 682 PHE 0.015 0.001 PHE C 136 TYR 0.012 0.001 TYR A 735 ARG 0.004 0.000 ARG C 114 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 432) hydrogen bonds : angle 4.27195 ( 1212) covalent geometry : bond 0.00304 (10460) covalent geometry : angle 0.57844 (14242) Misc. bond : bond 0.00007 ( 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 116 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9119 (mp) REVERT: A 603 TYR cc_start: 0.8035 (p90) cc_final: 0.7772 (p90) REVERT: A 610 HIS cc_start: 0.7941 (m90) cc_final: 0.7670 (m-70) REVERT: A 628 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7535 (mm-30) REVERT: A 710 GLN cc_start: 0.2011 (OUTLIER) cc_final: 0.1239 (pp30) REVERT: A 734 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6209 (pp) REVERT: A 864 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8741 (mt) REVERT: A 927 THR cc_start: 0.7270 (OUTLIER) cc_final: 0.6813 (t) REVERT: B 99 ARG cc_start: 0.8401 (mtp-110) cc_final: 0.8150 (ttm110) REVERT: B 118 GLN cc_start: 0.8247 (mp10) cc_final: 0.7927 (mp10) REVERT: B 145 LEU cc_start: 0.8861 (mp) cc_final: 0.8523 (tp) REVERT: C 70 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8572 (m-80) REVERT: C 80 ASP cc_start: 0.8625 (t70) cc_final: 0.8179 (t0) REVERT: C 131 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.7032 (mp10) outliers start: 27 outliers final: 19 residues processed: 107 average time/residue: 0.2581 time to fit residues: 39.2015 Evaluate side-chains 113 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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 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 734 LEU 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 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 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 6 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 115 optimal weight: 0.0000 chunk 8 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.149275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.091682 restraints weight = 16931.763| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.34 r_work: 0.2980 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10461 Z= 0.185 Angle : 0.616 8.610 14242 Z= 0.302 Chirality : 0.040 0.184 1591 Planarity : 0.005 0.082 1867 Dihedral : 4.785 46.141 1409 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.34 % Favored : 94.58 % Rotamer: Outliers : 2.54 % Allowed : 22.52 % 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: 0.06 (0.24), residues: 1291 helix: 1.26 (0.24), residues: 492 sheet: -0.69 (0.41), residues: 154 loop : -0.69 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 614 HIS 0.010 0.001 HIS A 682 PHE 0.016 0.001 PHE A 619 TYR 0.013 0.002 TYR A 435 ARG 0.009 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 432) hydrogen bonds : angle 4.39491 ( 1212) covalent geometry : bond 0.00453 (10460) covalent geometry : angle 0.61650 (14242) Misc. bond : bond 0.00020 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6093.69 seconds wall clock time: 108 minutes 13.43 seconds (6493.43 seconds total)