Starting phenix.real_space_refine on Mon Jul 28 12:19:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sv8_40782/07_2025/8sv8_40782.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sv8_40782/07_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_40782/07_2025/8sv8_40782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sv8_40782/07_2025/8sv8_40782.map" model { file = "/net/cci-nas-00/data/ceres_data/8sv8_40782/07_2025/8sv8_40782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sv8_40782/07_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 7.57, per 1000 atoms: 0.74 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: 2.84 Conformation dependent library (CDL) restraints added in 1.3 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: 1.70 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: 3.72 Time building geometry restraints manager: 3.26 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 - 1.83: 13759 1.83 - 3.67: 408 3.67 - 5.50: 58 5.50 - 7.34: 16 7.34 - 9.17: 1 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: 639 35.83 - 53.75: 163 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: 1301 0.051 - 0.102: 255 0.102 - 0.152: 26 0.152 - 0.203: 5 0.203 - 0.254: 4 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=" C3' AMP B1101 " pdb=" C2' AMP B1101 " pdb=" C4' AMP B1101 " pdb=" O3' AMP B1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.32e+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: 142.610 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.650 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.100 ------------------------------------------------------------------------------- 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= 0.187 Angle : 0.728 9.175 14242 Z= 0.418 Chirality : 0.042 0.254 1591 Planarity : 0.006 0.066 1867 Dihedral : 16.380 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 0.00373 (10460) covalent geometry : angle 0.72819 (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 : 1.255 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: 0.2659 time to fit residues: 37.8188 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 : 1.101 ------------------------------------------------------------------------------- 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 A 480 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.148724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.095010 restraints weight = 16912.851| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.75 r_work: 0.2997 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10461 Z= 0.226 Angle : 0.639 6.408 14242 Z= 0.317 Chirality : 0.042 0.171 1591 Planarity : 0.005 0.048 1867 Dihedral : 4.699 36.539 1411 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.65 % Favored : 94.27 % Rotamer: Outliers : 2.72 % Allowed : 20.62 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.47 (0.23), residues: 1291 helix: 1.03 (0.24), residues: 483 sheet: -1.34 (0.40), residues: 158 loop : -1.07 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 677 HIS 0.005 0.001 HIS A 817 PHE 0.015 0.002 PHE A 881 TYR 0.023 0.002 TYR B 140 ARG 0.006 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 432) hydrogen bonds : angle 4.72595 ( 1212) covalent geometry : bond 0.00550 (10460) covalent geometry : angle 0.63950 (14242) Misc. bond : bond 0.00005 ( 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 130 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 ASN cc_start: 0.6234 (OUTLIER) cc_final: 0.5784 (t0) REVERT: A 610 HIS cc_start: 0.7962 (m90) cc_final: 0.7497 (m90) REVERT: B 99 ARG cc_start: 0.8454 (mtp-110) cc_final: 0.7836 (mmm-85) REVERT: B 118 GLN cc_start: 0.7923 (mp10) cc_final: 0.7660 (mp10) REVERT: C 70 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8411 (m-10) outliers start: 30 outliers final: 21 residues processed: 121 average time/residue: 0.2431 time to fit residues: 42.0053 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 : 1.209 ------------------------------------------------------------------------------- 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 361 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 724 HIS 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: 0.5980 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 739 HIS C 139 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.149910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.094713 restraints weight = 17094.520| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.69 r_work: 0.3016 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1123 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= 0.132 Angle : 0.576 6.208 14242 Z= 0.282 Chirality : 0.039 0.160 1591 Planarity : 0.005 0.046 1867 Dihedral : 4.484 33.492 1411 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 3.27 % Allowed : 20.44 % 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: -0.30 (0.23), residues: 1291 helix: 1.16 (0.24), residues: 491 sheet: -1.21 (0.40), residues: 163 loop : -0.99 (0.24), residues: 637 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 0.010 0.001 PHE A 481 TYR 0.009 0.001 TYR A 435 ARG 0.004 0.000 ARG C 23 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 432) hydrogen bonds : angle 4.51658 ( 1212) covalent geometry : bond 0.00313 (10460) covalent geometry : angle 0.57641 (14242) Misc. bond : bond 0.00036 ( 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 138 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7780 (t0) cc_final: 0.7485 (t0) REVERT: A 283 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7273 (tm-30) REVERT: A 603 TYR cc_start: 0.7818 (p90) cc_final: 0.7457 (p90) REVERT: A 610 HIS cc_start: 0.7935 (m90) cc_final: 0.7630 (m-70) REVERT: B 118 GLN cc_start: 0.7922 (mp10) cc_final: 0.7644 (mp10) REVERT: C 70 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8459 (m-10) REVERT: C 128 LEU cc_start: 0.9084 (mm) cc_final: 0.8869 (mm) REVERT: C 131 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6791 (mp10) outliers start: 36 outliers final: 19 residues processed: 129 average time/residue: 0.4099 time to fit residues: 75.2920 Evaluate side-chains 115 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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 243 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 401 LEU 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 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 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: 0.8980 chunk 67 optimal weight: 0.0170 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 87 optimal weight: 0.3980 chunk 8 optimal weight: 0.0470 chunk 53 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS A 739 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.150408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.095724 restraints weight = 16831.058| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.57 r_work: 0.3044 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10461 Z= 0.108 Angle : 0.559 6.353 14242 Z= 0.273 Chirality : 0.039 0.167 1591 Planarity : 0.005 0.043 1867 Dihedral : 4.268 32.973 1409 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.11 % Favored : 94.81 % Rotamer: Outliers : 2.91 % Allowed : 21.07 % 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: -0.01 (0.24), residues: 1291 helix: 1.37 (0.24), residues: 486 sheet: -0.90 (0.42), residues: 154 loop : -0.83 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 677 HIS 0.010 0.001 HIS A 229 PHE 0.013 0.001 PHE C 136 TYR 0.026 0.001 TYR B 140 ARG 0.016 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 432) hydrogen bonds : angle 4.37194 ( 1212) covalent geometry : bond 0.00248 (10460) covalent geometry : angle 0.55882 (14242) Misc. bond : bond 0.00043 ( 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: 32 poor density : 103 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7781 (t0) cc_final: 0.7495 (t0) REVERT: A 603 TYR cc_start: 0.7843 (p90) cc_final: 0.7540 (p90) REVERT: A 610 HIS cc_start: 0.7972 (m90) cc_final: 0.7480 (m90) REVERT: B 99 ARG cc_start: 0.8390 (mtp-110) cc_final: 0.7968 (mmm-85) REVERT: B 118 GLN cc_start: 0.7933 (mp10) cc_final: 0.7643 (mp10) REVERT: C 70 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8433 (m-10) REVERT: C 74 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8307 (tt) REVERT: C 128 LEU cc_start: 0.9095 (mm) cc_final: 0.8848 (mm) REVERT: C 131 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6810 (mp10) outliers start: 32 outliers final: 15 residues processed: 124 average time/residue: 0.2374 time to fit residues: 41.9833 Evaluate side-chains 113 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 74 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 62 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.0060 chunk 101 optimal weight: 0.9980 chunk 46 optimal weight: 0.0770 chunk 47 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.4980 overall best weight: 0.4354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS A 739 HIS C 84 GLN C 139 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.150876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.096916 restraints weight = 16972.495| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.44 r_work: 0.3039 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10461 Z= 0.104 Angle : 0.555 7.788 14242 Z= 0.269 Chirality : 0.038 0.160 1591 Planarity : 0.004 0.042 1867 Dihedral : 4.151 32.169 1409 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 2.54 % Allowed : 21.89 % Favored : 75.57 % 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: 0.15 (0.24), residues: 1291 helix: 1.46 (0.24), residues: 486 sheet: -0.65 (0.42), residues: 154 loop : -0.74 (0.24), residues: 651 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 623 TYR 0.013 0.001 TYR B 140 ARG 0.005 0.000 ARG C 118 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 432) hydrogen bonds : angle 4.28592 ( 1212) covalent geometry : bond 0.00241 (10460) covalent geometry : angle 0.55456 (14242) Misc. bond : bond 0.00035 ( 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 129 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7861 (t0) cc_final: 0.7585 (t0) REVERT: A 592 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7422 (mt-10) REVERT: A 603 TYR cc_start: 0.7849 (p90) cc_final: 0.7584 (p90) REVERT: A 610 HIS cc_start: 0.7941 (m90) cc_final: 0.7432 (m90) REVERT: A 628 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7842 (mm-30) REVERT: B 99 ARG cc_start: 0.8409 (mtp-110) cc_final: 0.7972 (mmm-85) REVERT: B 118 GLN cc_start: 0.8054 (mp10) cc_final: 0.7753 (mp10) REVERT: C 70 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8370 (m-10) REVERT: C 80 ASP cc_start: 0.8559 (t70) cc_final: 0.8194 (t0) REVERT: C 118 ARG cc_start: 0.8842 (mmp80) cc_final: 0.8637 (mmp80) outliers start: 28 outliers final: 19 residues processed: 119 average time/residue: 0.2337 time to fit residues: 39.5881 Evaluate side-chains 113 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1012 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 81 GLU Chi-restraints excluded: chain C residue 117 ILE 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: 5.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.148486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.087949 restraints weight = 16997.716| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.61 r_work: 0.3015 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10461 Z= 0.179 Angle : 0.599 7.289 14242 Z= 0.291 Chirality : 0.041 0.183 1591 Planarity : 0.005 0.042 1867 Dihedral : 4.269 30.641 1409 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.11 % Favored : 94.81 % Rotamer: Outliers : 2.82 % Allowed : 21.89 % 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: -0.00 (0.23), residues: 1291 helix: 1.24 (0.24), residues: 491 sheet: -0.73 (0.41), residues: 154 loop : -0.76 (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 481 TYR 0.025 0.002 TYR B 140 ARG 0.004 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.03662 ( 432) hydrogen bonds : angle 4.43698 ( 1212) covalent geometry : bond 0.00439 (10460) covalent geometry : angle 0.59913 (14242) Misc. bond : bond 0.00026 ( 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 129 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9120 (mp) REVERT: A 283 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7560 (tm-30) REVERT: A 592 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7481 (mt-10) REVERT: A 603 TYR cc_start: 0.7982 (p90) cc_final: 0.7716 (p90) REVERT: A 610 HIS cc_start: 0.7997 (m90) cc_final: 0.7520 (m90) REVERT: A 628 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7880 (mm-30) REVERT: A 691 HIS cc_start: 0.6769 (t-90) cc_final: 0.6471 (t-90) REVERT: A 958 TRP cc_start: 0.8801 (OUTLIER) cc_final: 0.8478 (m-10) REVERT: B 99 ARG cc_start: 0.8517 (mtp-110) cc_final: 0.8143 (mtm-85) REVERT: B 118 GLN cc_start: 0.8235 (mp10) cc_final: 0.7936 (mp10) REVERT: C 70 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8535 (m-80) REVERT: C 80 ASP cc_start: 0.8625 (t70) cc_final: 0.8233 (t0) REVERT: C 125 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8983 (mt) outliers start: 31 outliers final: 19 residues processed: 120 average time/residue: 0.2508 time to fit residues: 43.2546 Evaluate side-chains 116 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 256 VAL 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 519 THR Chi-restraints excluded: chain A residue 958 TRP 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 125 LEU 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: 2.9990 chunk 57 optimal weight: 0.0980 chunk 63 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 0.0060 chunk 117 optimal weight: 4.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- 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 C 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.150367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.090687 restraints weight = 17212.066| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.59 r_work: 0.3080 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1900 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= 0.130 Angle : 0.577 7.789 14242 Z= 0.280 Chirality : 0.039 0.161 1591 Planarity : 0.004 0.042 1867 Dihedral : 4.200 28.439 1409 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.12 % 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: 0.16 (0.24), residues: 1291 helix: 1.32 (0.24), residues: 492 sheet: -0.61 (0.42), residues: 154 loop : -0.64 (0.24), residues: 645 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 0.008 0.001 TYR A 683 ARG 0.004 0.000 ARG C 118 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 432) hydrogen bonds : angle 4.32925 ( 1212) covalent geometry : bond 0.00312 (10460) covalent geometry : angle 0.57744 (14242) Misc. bond : bond 0.00014 ( 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 122 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 TYR cc_start: 0.8016 (p90) cc_final: 0.7750 (p90) REVERT: A 610 HIS cc_start: 0.7990 (m90) cc_final: 0.7532 (m90) REVERT: A 628 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7828 (mm-30) REVERT: A 691 HIS cc_start: 0.6775 (t-90) cc_final: 0.6475 (t-90) REVERT: B 99 ARG cc_start: 0.8440 (mtp-110) cc_final: 0.8122 (mtm-85) REVERT: B 118 GLN cc_start: 0.8243 (mp10) cc_final: 0.7936 (mp10) REVERT: B 145 LEU cc_start: 0.8817 (mp) cc_final: 0.8490 (tp) REVERT: C 70 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8398 (m-80) REVERT: C 80 ASP cc_start: 0.8651 (t70) cc_final: 0.8237 (t0) outliers start: 27 outliers final: 19 residues processed: 113 average time/residue: 0.3413 time to fit residues: 55.8317 Evaluate side-chains 114 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 249 ARG Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 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 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: 0.9980 chunk 95 optimal weight: 0.0770 chunk 89 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.150849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097546 restraints weight = 16996.955| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.21 r_work: 0.3071 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10461 Z= 0.117 Angle : 0.572 7.850 14242 Z= 0.276 Chirality : 0.039 0.193 1591 Planarity : 0.004 0.042 1867 Dihedral : 4.122 27.329 1409 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.11 % Favored : 94.81 % 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: 0.28 (0.24), residues: 1291 helix: 1.51 (0.24), residues: 480 sheet: -0.55 (0.42), residues: 154 loop : -0.60 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 614 HIS 0.009 0.001 HIS A 229 PHE 0.016 0.001 PHE C 136 TYR 0.014 0.001 TYR C 75 ARG 0.005 0.000 ARG C 118 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 432) hydrogen bonds : angle 4.26084 ( 1212) covalent geometry : bond 0.00276 (10460) covalent geometry : angle 0.57245 (14242) Misc. bond : bond 0.00013 ( 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 121 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9116 (mp) REVERT: A 603 TYR cc_start: 0.8002 (p90) cc_final: 0.7740 (p90) REVERT: A 610 HIS cc_start: 0.7991 (m90) cc_final: 0.7663 (m-70) REVERT: A 628 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7668 (mm-30) REVERT: A 691 HIS cc_start: 0.6730 (t-90) cc_final: 0.6409 (t-90) REVERT: A 710 GLN cc_start: 0.2112 (OUTLIER) cc_final: 0.1303 (pp30) REVERT: B 99 ARG cc_start: 0.8326 (mtp-110) cc_final: 0.8022 (mtm-85) REVERT: B 118 GLN cc_start: 0.8199 (mp10) cc_final: 0.7888 (mp10) REVERT: B 145 LEU cc_start: 0.8757 (mp) cc_final: 0.8454 (tp) REVERT: C 70 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8312 (m-80) REVERT: C 80 ASP cc_start: 0.8589 (t70) cc_final: 0.8204 (t0) outliers start: 27 outliers final: 19 residues processed: 112 average time/residue: 0.2539 time to fit residues: 39.8112 Evaluate side-chains 112 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 710 GLN 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 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: 1.9990 chunk 26 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.150953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.091725 restraints weight = 17056.879| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.58 r_work: 0.3084 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2124 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= 0.124 Angle : 0.580 8.017 14242 Z= 0.279 Chirality : 0.039 0.167 1591 Planarity : 0.004 0.044 1867 Dihedral : 4.120 26.496 1409 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.20 % Rotamer: Outliers : 2.27 % Allowed : 22.80 % 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: 0.30 (0.24), residues: 1291 helix: 1.53 (0.24), residues: 480 sheet: -0.53 (0.42), residues: 154 loop : -0.59 (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 0.017 0.001 PHE C 136 TYR 0.014 0.001 TYR B 140 ARG 0.004 0.000 ARG C 114 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 432) hydrogen bonds : angle 4.25676 ( 1212) covalent geometry : bond 0.00298 (10460) covalent geometry : angle 0.57956 (14242) Misc. bond : bond 0.00008 ( 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 119 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9124 (mp) REVERT: A 603 TYR cc_start: 0.7976 (p90) cc_final: 0.7693 (p90) REVERT: A 610 HIS cc_start: 0.8039 (m90) cc_final: 0.7691 (m-70) REVERT: A 628 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7636 (mm-30) REVERT: A 691 HIS cc_start: 0.6761 (t-90) cc_final: 0.6437 (t-90) REVERT: A 710 GLN cc_start: 0.2216 (OUTLIER) cc_final: 0.1359 (pp30) REVERT: B 99 ARG cc_start: 0.8438 (mtp-110) cc_final: 0.8164 (ttm110) REVERT: B 118 GLN cc_start: 0.8255 (mp10) cc_final: 0.7948 (mp10) REVERT: B 145 LEU cc_start: 0.8838 (mp) cc_final: 0.8508 (tp) REVERT: C 70 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: C 80 ASP cc_start: 0.8654 (t70) cc_final: 0.8244 (t0) outliers start: 25 outliers final: 21 residues processed: 110 average time/residue: 0.3269 time to fit residues: 50.7965 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 : 1.180 ------------------------------------------------------------------------------- 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 83 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 710 GLN 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 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: 0.4980 chunk 79 optimal weight: 6.9990 chunk 95 optimal weight: 0.1980 chunk 119 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 9.9990 chunk 87 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 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 476 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.151216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.095846 restraints weight = 16852.817| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.29 r_work: 0.3053 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10461 Z= 0.110 Angle : 0.575 8.484 14242 Z= 0.276 Chirality : 0.039 0.160 1591 Planarity : 0.004 0.046 1867 Dihedral : 4.047 25.965 1409 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.96 % Favored : 94.97 % Rotamer: Outliers : 2.09 % Allowed : 22.98 % 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: 0.39 (0.24), residues: 1291 helix: 1.61 (0.24), residues: 479 sheet: -0.44 (0.42), residues: 154 loop : -0.56 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 614 HIS 0.011 0.001 HIS A 682 PHE 0.022 0.001 PHE D 149 TYR 0.012 0.001 TYR A 735 ARG 0.005 0.000 ARG C 118 Details of bonding type rmsd hydrogen bonds : bond 0.03078 ( 432) hydrogen bonds : angle 4.19375 ( 1212) covalent geometry : bond 0.00261 (10460) covalent geometry : angle 0.57456 (14242) Misc. bond : bond 0.00008 ( 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 118 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9117 (mp) REVERT: A 603 TYR cc_start: 0.7998 (p90) cc_final: 0.7737 (p90) REVERT: A 610 HIS cc_start: 0.7977 (m90) cc_final: 0.7679 (m-70) REVERT: A 628 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7573 (mm-30) REVERT: A 710 GLN cc_start: 0.2136 (OUTLIER) cc_final: 0.1324 (pp30) REVERT: A 864 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8744 (mt) REVERT: B 99 ARG cc_start: 0.8360 (mtp-110) cc_final: 0.8128 (ttm110) REVERT: B 118 GLN cc_start: 0.8229 (mp10) cc_final: 0.7919 (mp10) REVERT: B 145 LEU cc_start: 0.8784 (mp) cc_final: 0.8473 (tp) REVERT: C 21 TYR cc_start: 0.7626 (p90) cc_final: 0.7336 (p90) REVERT: C 70 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8295 (m-80) REVERT: C 80 ASP cc_start: 0.8605 (t70) cc_final: 0.8210 (t0) outliers start: 23 outliers final: 16 residues processed: 108 average time/residue: 0.3135 time to fit residues: 47.1819 Evaluate side-chains 111 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain A residue 864 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 117 ILE 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: 0.1980 chunk 59 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 124 optimal weight: 20.0000 chunk 119 optimal weight: 0.9990 chunk 115 optimal weight: 0.1980 chunk 8 optimal weight: 0.7980 chunk 80 optimal weight: 0.4980 chunk 57 optimal weight: 0.0970 chunk 113 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.150408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.091240 restraints weight = 16743.467| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.28 r_work: 0.3072 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10461 Z= 0.102 Angle : 0.572 8.666 14242 Z= 0.275 Chirality : 0.038 0.145 1591 Planarity : 0.004 0.047 1867 Dihedral : 3.985 25.540 1409 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 2.00 % Allowed : 23.25 % Favored : 74.75 % 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: 0.45 (0.24), residues: 1291 helix: 1.67 (0.24), residues: 480 sheet: -0.37 (0.42), residues: 154 loop : -0.55 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 614 HIS 0.011 0.001 HIS A 682 PHE 0.021 0.001 PHE D 149 TYR 0.010 0.001 TYR B 140 ARG 0.006 0.000 ARG C 114 Details of bonding type rmsd hydrogen bonds : bond 0.02945 ( 432) hydrogen bonds : angle 4.12664 ( 1212) covalent geometry : bond 0.00237 (10460) covalent geometry : angle 0.57174 (14242) Misc. bond : bond 0.00010 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6963.91 seconds wall clock time: 128 minutes 47.84 seconds (7727.84 seconds total)