Starting phenix.real_space_refine on Wed Feb 4 02:24:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vdl_64987/02_2026/9vdl_64987.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vdl_64987/02_2026/9vdl_64987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vdl_64987/02_2026/9vdl_64987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vdl_64987/02_2026/9vdl_64987.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vdl_64987/02_2026/9vdl_64987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vdl_64987/02_2026/9vdl_64987.map" } resolution = 2.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.072 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 47 5.16 5 Be 1 3.05 5 C 5116 2.51 5 N 1341 2.21 5 O 1732 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8241 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7970 Classifications: {'peptide': 1000} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 969} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "A" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 271 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 270} Link IDs: {None: 270} Time building chain proxies: 1.62, per 1000 atoms: 0.20 Number of scatterers: 8241 At special positions: 0 Unit cell: (84.976, 80.464, 138.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 47 16.00 Mg 1 11.99 F 3 9.00 O 1732 8.00 N 1341 7.00 C 5116 6.00 Be 1 4.00 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=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 214.9 milliseconds 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 6 sheets defined 56.6% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 67 through 78 Processing helix chain 'A' and resid 79 through 91 removed outlier: 4.433A pdb=" N PHE A 85 " --> pdb=" O PHE A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 102 through 136 removed outlier: 3.633A pdb=" N TRP A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Proline residue: A 108 - end of helix removed outlier: 3.646A pdb=" N GLU A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.531A pdb=" N ARG A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 219 removed outlier: 3.834A pdb=" N GLN A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 276 through 279 Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 294 through 321 Processing helix chain 'A' and resid 327 through 341 removed outlier: 3.545A pdb=" N ASN A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 365 removed outlier: 3.621A pdb=" N LEU A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 414 through 416 No H-bonds generated for 'chain 'A' and resid 414 through 416' Processing helix chain 'A' and resid 417 through 432 removed outlier: 3.850A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 466 Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 499 through 513 Processing helix chain 'A' and resid 570 through 575 Processing helix chain 'A' and resid 583 through 594 removed outlier: 3.549A pdb=" N GLU A 594 " --> pdb=" O ASN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 624 removed outlier: 3.518A pdb=" N ARG A 617 " --> pdb=" O ASP A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 658 through 669 Processing helix chain 'A' and resid 680 through 691 Processing helix chain 'A' and resid 708 through 721 Processing helix chain 'A' and resid 731 through 741 removed outlier: 3.583A pdb=" N VAL A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 761 through 777 Processing helix chain 'A' and resid 786 through 788 No H-bonds generated for 'chain 'A' and resid 786 through 788' Processing helix chain 'A' and resid 789 through 796 Processing helix chain 'A' and resid 808 through 814 Processing helix chain 'A' and resid 822 through 830 removed outlier: 4.289A pdb=" N ARG A 826 " --> pdb=" O LYS A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 864 Processing helix chain 'A' and resid 874 through 882 removed outlier: 3.508A pdb=" N ILE A 878 " --> pdb=" O GLY A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 894 removed outlier: 3.925A pdb=" N PHE A 887 " --> pdb=" O ILE A 883 " (cutoff:3.500A) Proline residue: A 888 - end of helix Processing helix chain 'A' and resid 899 through 906 Processing helix chain 'A' and resid 907 through 915 removed outlier: 3.931A pdb=" N LYS A 911 " --> pdb=" O PRO A 907 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP A 912 " --> pdb=" O GLU A 908 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 913 " --> pdb=" O LEU A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 946 Processing helix chain 'A' and resid 952 through 973 Processing helix chain 'A' and resid 977 through 998 removed outlier: 3.521A pdb=" N THR A 981 " --> pdb=" O HIS A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1008 Processing helix chain 'A' and resid 1009 through 1024 Processing helix chain 'A' and resid 1024 through 1036 Processing helix chain 'A' and resid 1040 through 1045 removed outlier: 4.070A pdb=" N LYS A1044 " --> pdb=" O PRO A1040 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1040 through 1045' Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42 Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 151 removed outlier: 3.810A pdb=" N SER A 140 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 270 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP A 172 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 201 Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 373 removed outlier: 6.703A pdb=" N THR A 780 " --> pdb=" O CYS A 798 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL A 800 " --> pdb=" O THR A 780 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ALA A 782 " --> pdb=" O VAL A 800 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL A 802 " --> pdb=" O ALA A 782 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY A 784 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU A 779 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL A 673 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N CYS A 757 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N MET A 675 " --> pdb=" O CYS A 757 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N VAL A 756 " --> pdb=" O CYS A 725 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 727 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N CYS A 758 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A 729 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP A 699 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL A 728 " --> pdb=" O ASP A 699 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS A 701 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N SER A 730 " --> pdb=" O HIS A 701 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 412 through 413 removed outlier: 5.121A pdb=" N GLU A 400 " --> pdb=" O GLN A 654 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY A 650 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU A 406 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU A 648 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU A 645 " --> pdb=" O LYS A 603 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS A 603 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS A 647 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 563 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG A 550 " --> pdb=" O PHE A 544 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 544 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ARG A 556 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE A 538 " --> pdb=" O ARG A 556 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER A 523 " --> pdb=" O ARG A 519 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG A 519 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN A 525 " --> pdb=" O VAL A 517 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 470 through 473 451 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 0.56 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: 2129 1.33 - 1.45: 1393 1.45 - 1.57: 4533 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8131 Sorted by residual: bond pdb=" F3 BFD A 391 " pdb="BE BFD A 391 " ideal model delta sigma weight residual 1.529 1.762 -0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" F2 BFD A 391 " pdb="BE BFD A 391 " ideal model delta sigma weight residual 1.535 1.750 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" F1 BFD A 391 " pdb="BE BFD A 391 " ideal model delta sigma weight residual 1.542 1.750 -0.208 2.00e-02 2.50e+03 1.09e+02 bond pdb=" CG BFD A 391 " pdb=" OD1 BFD A 391 " ideal model delta sigma weight residual 1.269 1.446 -0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" CB BFD A 391 " pdb=" CG BFD A 391 " ideal model delta sigma weight residual 1.529 1.497 0.032 2.00e-02 2.50e+03 2.48e+00 ... (remaining 8126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 11001 3.83 - 7.66: 19 7.66 - 11.49: 5 11.49 - 15.32: 1 15.32 - 19.15: 4 Bond angle restraints: 11030 Sorted by residual: angle pdb=" CA BFD A 391 " pdb=" C BFD A 391 " pdb=" O BFD A 391 " ideal model delta sigma weight residual 120.80 139.95 -19.15 1.70e+00 3.46e-01 1.27e+02 angle pdb=" O BFD A 391 " pdb=" C BFD A 391 " pdb=" N LYS A 392 " ideal model delta sigma weight residual 123.00 113.37 9.63 1.60e+00 3.91e-01 3.62e+01 angle pdb=" F2 BFD A 391 " pdb="BE BFD A 391 " pdb=" F3 BFD A 391 " ideal model delta sigma weight residual 112.60 96.26 16.34 3.00e+00 1.11e-01 2.97e+01 angle pdb=" F1 BFD A 391 " pdb="BE BFD A 391 " pdb=" F3 BFD A 391 " ideal model delta sigma weight residual 111.29 95.45 15.84 3.00e+00 1.11e-01 2.79e+01 angle pdb=" OD1 BFD A 391 " pdb="BE BFD A 391 " pdb=" F1 BFD A 391 " ideal model delta sigma weight residual 102.38 117.82 -15.44 3.00e+00 1.11e-01 2.65e+01 ... (remaining 11025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4222 17.76 - 35.52: 445 35.52 - 53.29: 148 53.29 - 71.05: 33 71.05 - 88.81: 19 Dihedral angle restraints: 4867 sinusoidal: 1935 harmonic: 2932 Sorted by residual: dihedral pdb=" CA THR A 882 " pdb=" C THR A 882 " pdb=" N ILE A 883 " pdb=" CA ILE A 883 " ideal model delta harmonic sigma weight residual -180.00 -156.57 -23.43 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ASP A 245 " pdb=" C ASP A 245 " pdb=" N PRO A 246 " pdb=" CA PRO A 246 " ideal model delta harmonic sigma weight residual 180.00 160.44 19.56 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA VAL A 889 " pdb=" C VAL A 889 " pdb=" N PHE A 890 " pdb=" CA PHE A 890 " ideal model delta harmonic sigma weight residual 180.00 162.56 17.44 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 4864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 687 0.028 - 0.056: 363 0.056 - 0.084: 141 0.084 - 0.112: 80 0.112 - 0.140: 11 Chirality restraints: 1282 Sorted by residual: chirality pdb=" CA PRO A 888 " pdb=" N PRO A 888 " pdb=" C PRO A 888 " pdb=" CB PRO A 888 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA ILE A 563 " pdb=" N ILE A 563 " pdb=" C ILE A 563 " pdb=" CB ILE A 563 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE A 174 " pdb=" N ILE A 174 " pdb=" C ILE A 174 " pdb=" CB ILE A 174 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 1279 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 887 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A 888 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 888 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 888 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 245 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO A 246 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 246 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 246 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 81 " 0.011 2.00e-02 2.50e+03 1.02e-02 1.83e+00 pdb=" CG PHE A 81 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 81 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 81 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 81 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 81 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 81 " 0.002 2.00e-02 2.50e+03 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 141 2.62 - 3.19: 7166 3.19 - 3.76: 13743 3.76 - 4.33: 20257 4.33 - 4.90: 31779 Nonbonded interactions: 73086 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O HOH A1247 " model vdw 2.045 2.170 nonbonded pdb=" F3 BFD A 391 " pdb="MG MG A1101 " model vdw 2.045 2.120 nonbonded pdb=" OD2 BFD A 391 " pdb="MG MG A1101 " model vdw 2.057 2.170 nonbonded pdb=" OG1 THR A 537 " pdb=" OE2 GLU A 558 " model vdw 2.148 3.040 nonbonded pdb=" OG1 THR A 143 " pdb=" O GLY A 146 " model vdw 2.157 3.040 ... (remaining 73081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.870 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.006 0.233 8131 Z= 0.287 Angle : 0.683 19.152 11030 Z= 0.340 Chirality : 0.043 0.140 1282 Planarity : 0.004 0.053 1384 Dihedral : 17.667 88.811 2975 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.84 % Allowed : 20.00 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.27), residues: 993 helix: 1.37 (0.24), residues: 504 sheet: 0.39 (0.38), residues: 171 loop : 0.48 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 597 TYR 0.015 0.002 TYR A 611 PHE 0.023 0.002 PHE A 81 TRP 0.011 0.002 TRP A 976 HIS 0.005 0.001 HIS A 848 Details of bonding type rmsd covalent geometry : bond 0.00605 ( 8131) covalent geometry : angle 0.68350 (11030) hydrogen bonds : bond 0.13936 ( 451) hydrogen bonds : angle 5.75798 ( 1299) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.298 Fit side-chains REVERT: A 52 ARG cc_start: 0.7186 (ttp80) cc_final: 0.6361 (tmt170) outliers start: 34 outliers final: 32 residues processed: 150 average time/residue: 0.4387 time to fit residues: 70.3405 Evaluate side-chains 146 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 911 LYS Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 965 GLU Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1046 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 398 GLN A 844 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.138984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.106345 restraints weight = 8846.765| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.68 r_work: 0.3125 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8131 Z= 0.167 Angle : 0.551 9.907 11030 Z= 0.294 Chirality : 0.043 0.154 1282 Planarity : 0.004 0.041 1384 Dihedral : 8.871 68.570 1151 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.52 % Allowed : 18.87 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.27), residues: 993 helix: 1.46 (0.23), residues: 508 sheet: 0.69 (0.40), residues: 150 loop : 0.43 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 597 TYR 0.015 0.002 TYR A 611 PHE 0.021 0.002 PHE A 85 TRP 0.011 0.002 TRP A 976 HIS 0.004 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8131) covalent geometry : angle 0.55126 (11030) hydrogen bonds : bond 0.04784 ( 451) hydrogen bonds : angle 4.75957 ( 1299) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.345 Fit side-chains REVERT: A 52 ARG cc_start: 0.7416 (ttp80) cc_final: 0.6725 (tmt170) REVERT: A 535 ASN cc_start: 0.8352 (t0) cc_final: 0.8141 (t0) REVERT: A 562 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7971 (mm-30) REVERT: A 959 THR cc_start: 0.8647 (m) cc_final: 0.8436 (m) REVERT: A 1045 LEU cc_start: 0.4476 (OUTLIER) cc_final: 0.3844 (pp) outliers start: 40 outliers final: 24 residues processed: 150 average time/residue: 0.5039 time to fit residues: 80.9454 Evaluate side-chains 141 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 965 GLU Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1046 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 86 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.105901 restraints weight = 8839.918| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.69 r_work: 0.3119 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8131 Z= 0.171 Angle : 0.548 9.291 11030 Z= 0.291 Chirality : 0.043 0.134 1282 Planarity : 0.004 0.033 1384 Dihedral : 8.207 68.697 1134 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.41 % Allowed : 18.31 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.26), residues: 993 helix: 1.45 (0.23), residues: 509 sheet: 0.69 (0.40), residues: 150 loop : 0.36 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 597 TYR 0.014 0.002 TYR A 611 PHE 0.021 0.002 PHE A 85 TRP 0.012 0.002 TRP A1014 HIS 0.004 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8131) covalent geometry : angle 0.54832 (11030) hydrogen bonds : bond 0.04654 ( 451) hydrogen bonds : angle 4.64728 ( 1299) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.317 Fit side-chains REVERT: A 52 ARG cc_start: 0.7450 (ttp80) cc_final: 0.6692 (tmt170) REVERT: A 519 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8850 (ttt90) REVERT: A 521 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7719 (mp10) REVERT: A 562 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7954 (mm-30) REVERT: A 626 HIS cc_start: 0.5311 (OUTLIER) cc_final: 0.4112 (m-70) REVERT: A 664 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: A 1045 LEU cc_start: 0.4478 (OUTLIER) cc_final: 0.3788 (pp) outliers start: 39 outliers final: 22 residues processed: 146 average time/residue: 0.5203 time to fit residues: 80.7025 Evaluate side-chains 145 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 519 ARG Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 965 GLU Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1045 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.106422 restraints weight = 9009.969| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.71 r_work: 0.3126 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8131 Z= 0.150 Angle : 0.526 8.337 11030 Z= 0.280 Chirality : 0.042 0.133 1282 Planarity : 0.004 0.032 1384 Dihedral : 7.468 67.720 1128 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.86 % Allowed : 18.64 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.26), residues: 993 helix: 1.51 (0.23), residues: 511 sheet: 0.48 (0.40), residues: 156 loop : 0.34 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 597 TYR 0.013 0.002 TYR A 611 PHE 0.020 0.002 PHE A 85 TRP 0.012 0.001 TRP A1014 HIS 0.004 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8131) covalent geometry : angle 0.52552 (11030) hydrogen bonds : bond 0.04380 ( 451) hydrogen bonds : angle 4.54083 ( 1299) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 0.321 Fit side-chains REVERT: A 37 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7017 (mtm-85) REVERT: A 52 ARG cc_start: 0.7418 (ttp80) cc_final: 0.6687 (tmt170) REVERT: A 97 MET cc_start: 0.7181 (mpp) cc_final: 0.6949 (mpp) REVERT: A 519 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8783 (ttt90) REVERT: A 521 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7729 (mp10) REVERT: A 626 HIS cc_start: 0.5339 (OUTLIER) cc_final: 0.4116 (m-70) REVERT: A 664 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: A 959 THR cc_start: 0.8635 (m) cc_final: 0.8375 (m) REVERT: A 1045 LEU cc_start: 0.4482 (OUTLIER) cc_final: 0.3800 (pp) outliers start: 43 outliers final: 28 residues processed: 156 average time/residue: 0.4905 time to fit residues: 81.3690 Evaluate side-chains 151 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 519 ARG Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 844 GLN Chi-restraints excluded: chain A residue 965 GLU Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1001 PHE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1045 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 93 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.138316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.105432 restraints weight = 8903.059| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.69 r_work: 0.3113 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8131 Z= 0.186 Angle : 0.562 10.592 11030 Z= 0.297 Chirality : 0.044 0.137 1282 Planarity : 0.004 0.033 1384 Dihedral : 7.465 68.787 1125 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 5.42 % Allowed : 18.76 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.26), residues: 993 helix: 1.43 (0.23), residues: 512 sheet: 0.67 (0.40), residues: 150 loop : 0.33 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 597 TYR 0.015 0.002 TYR A 611 PHE 0.022 0.002 PHE A 85 TRP 0.012 0.002 TRP A1014 HIS 0.004 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 8131) covalent geometry : angle 0.56194 (11030) hydrogen bonds : bond 0.04678 ( 451) hydrogen bonds : angle 4.58486 ( 1299) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 117 time to evaluate : 0.329 Fit side-chains REVERT: A 52 ARG cc_start: 0.7483 (ttp80) cc_final: 0.6699 (tmt170) REVERT: A 96 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.6010 (mp0) REVERT: A 97 MET cc_start: 0.7182 (mpp) cc_final: 0.6920 (mpp) REVERT: A 519 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8854 (ttt90) REVERT: A 521 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7756 (mp10) REVERT: A 626 HIS cc_start: 0.5338 (OUTLIER) cc_final: 0.4105 (m-70) REVERT: A 664 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: A 959 THR cc_start: 0.8664 (m) cc_final: 0.8439 (m) REVERT: A 1045 LEU cc_start: 0.4513 (OUTLIER) cc_final: 0.3877 (pp) outliers start: 48 outliers final: 28 residues processed: 152 average time/residue: 0.5394 time to fit residues: 87.2883 Evaluate side-chains 149 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 519 ARG Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 965 GLU Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1001 PHE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1045 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.106614 restraints weight = 8857.860| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.69 r_work: 0.3128 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8131 Z= 0.144 Angle : 0.524 10.041 11030 Z= 0.277 Chirality : 0.042 0.132 1282 Planarity : 0.003 0.034 1384 Dihedral : 7.224 67.493 1125 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.63 % Allowed : 19.44 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.26), residues: 993 helix: 1.56 (0.23), residues: 509 sheet: 0.63 (0.40), residues: 151 loop : 0.40 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 597 TYR 0.013 0.001 TYR A 611 PHE 0.020 0.001 PHE A 85 TRP 0.013 0.001 TRP A1014 HIS 0.004 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8131) covalent geometry : angle 0.52388 (11030) hydrogen bonds : bond 0.04273 ( 451) hydrogen bonds : angle 4.49980 ( 1299) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.259 Fit side-chains REVERT: A 37 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7009 (mtm-85) REVERT: A 52 ARG cc_start: 0.7444 (ttp80) cc_final: 0.6707 (tmt170) REVERT: A 96 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.6010 (mp0) REVERT: A 97 MET cc_start: 0.7160 (mpp) cc_final: 0.6732 (mpp) REVERT: A 519 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8784 (ttt90) REVERT: A 521 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7737 (mp10) REVERT: A 626 HIS cc_start: 0.5365 (OUTLIER) cc_final: 0.4148 (m-70) REVERT: A 637 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7444 (tt0) REVERT: A 664 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: A 926 ILE cc_start: 0.8703 (mt) cc_final: 0.8416 (mp) REVERT: A 1045 LEU cc_start: 0.4479 (OUTLIER) cc_final: 0.3791 (pp) outliers start: 41 outliers final: 22 residues processed: 148 average time/residue: 0.5842 time to fit residues: 91.8889 Evaluate side-chains 149 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 519 ARG Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 965 GLU Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1001 PHE Chi-restraints excluded: chain A residue 1045 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.103609 restraints weight = 8974.927| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.70 r_work: 0.3088 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 8131 Z= 0.280 Angle : 0.652 12.168 11030 Z= 0.342 Chirality : 0.048 0.151 1282 Planarity : 0.004 0.038 1384 Dihedral : 7.107 68.804 1118 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.86 % Allowed : 19.66 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 993 helix: 1.24 (0.23), residues: 511 sheet: 0.52 (0.39), residues: 151 loop : 0.28 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 597 TYR 0.018 0.002 TYR A 611 PHE 0.026 0.002 PHE A 85 TRP 0.013 0.002 TRP A 976 HIS 0.005 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00661 ( 8131) covalent geometry : angle 0.65232 (11030) hydrogen bonds : bond 0.05333 ( 451) hydrogen bonds : angle 4.70284 ( 1299) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 0.345 Fit side-chains REVERT: A 52 ARG cc_start: 0.7487 (ttp80) cc_final: 0.6676 (tmt170) REVERT: A 96 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.6017 (mp0) REVERT: A 97 MET cc_start: 0.7184 (mpp) cc_final: 0.6856 (mpp) REVERT: A 519 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8835 (ttt90) REVERT: A 521 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7769 (mp10) REVERT: A 626 HIS cc_start: 0.5488 (OUTLIER) cc_final: 0.4291 (m-70) REVERT: A 637 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7467 (tt0) REVERT: A 664 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: A 1045 LEU cc_start: 0.4590 (OUTLIER) cc_final: 0.3996 (pp) outliers start: 43 outliers final: 28 residues processed: 148 average time/residue: 0.5427 time to fit residues: 85.4550 Evaluate side-chains 145 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 519 ARG Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 965 GLU Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1001 PHE Chi-restraints excluded: chain A residue 1045 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.140256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.107996 restraints weight = 9004.361| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.69 r_work: 0.3146 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8131 Z= 0.122 Angle : 0.512 10.036 11030 Z= 0.270 Chirality : 0.041 0.133 1282 Planarity : 0.003 0.037 1384 Dihedral : 6.482 59.954 1118 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.50 % Allowed : 21.13 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.27), residues: 993 helix: 1.51 (0.23), residues: 509 sheet: 0.63 (0.41), residues: 151 loop : 0.42 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 597 TYR 0.012 0.001 TYR A 611 PHE 0.020 0.001 PHE A 85 TRP 0.014 0.001 TRP A1014 HIS 0.002 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8131) covalent geometry : angle 0.51178 (11030) hydrogen bonds : bond 0.04016 ( 451) hydrogen bonds : angle 4.49220 ( 1299) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.334 Fit side-chains REVERT: A 37 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7003 (mtm-85) REVERT: A 52 ARG cc_start: 0.7426 (ttp80) cc_final: 0.6727 (tmt170) REVERT: A 96 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.5966 (mp0) REVERT: A 97 MET cc_start: 0.7178 (mpp) cc_final: 0.6734 (mpp) REVERT: A 521 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7769 (mp10) REVERT: A 626 HIS cc_start: 0.5512 (OUTLIER) cc_final: 0.4344 (m-70) REVERT: A 637 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7475 (tt0) REVERT: A 1045 LEU cc_start: 0.4523 (OUTLIER) cc_final: 0.3877 (pp) outliers start: 31 outliers final: 19 residues processed: 149 average time/residue: 0.4947 time to fit residues: 78.6839 Evaluate side-chains 145 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 965 GLU Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1001 PHE Chi-restraints excluded: chain A residue 1045 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.139637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.107320 restraints weight = 8943.161| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.68 r_work: 0.3138 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8131 Z= 0.134 Angle : 0.524 10.452 11030 Z= 0.276 Chirality : 0.042 0.134 1282 Planarity : 0.003 0.035 1384 Dihedral : 6.405 57.615 1118 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.28 % Allowed : 21.24 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.27), residues: 993 helix: 1.50 (0.23), residues: 511 sheet: 0.73 (0.41), residues: 150 loop : 0.37 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 597 TYR 0.013 0.001 TYR A 611 PHE 0.020 0.001 PHE A 85 TRP 0.013 0.001 TRP A1014 HIS 0.004 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8131) covalent geometry : angle 0.52436 (11030) hydrogen bonds : bond 0.04142 ( 451) hydrogen bonds : angle 4.46586 ( 1299) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.354 Fit side-chains REVERT: A 37 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7011 (mtm-85) REVERT: A 52 ARG cc_start: 0.7460 (ttp80) cc_final: 0.6749 (tmt170) REVERT: A 96 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.5992 (mp0) REVERT: A 521 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7727 (mp10) REVERT: A 626 HIS cc_start: 0.5510 (OUTLIER) cc_final: 0.4361 (m-70) REVERT: A 637 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7473 (tt0) REVERT: A 1045 LEU cc_start: 0.4503 (OUTLIER) cc_final: 0.3849 (pp) outliers start: 29 outliers final: 22 residues processed: 147 average time/residue: 0.5523 time to fit residues: 86.4902 Evaluate side-chains 147 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 965 GLU Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1001 PHE Chi-restraints excluded: chain A residue 1045 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 0.0170 chunk 8 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.107093 restraints weight = 8855.002| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.67 r_work: 0.3136 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8131 Z= 0.143 Angle : 0.535 10.423 11030 Z= 0.281 Chirality : 0.042 0.134 1282 Planarity : 0.004 0.039 1384 Dihedral : 6.387 57.266 1118 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.39 % Allowed : 21.24 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.26), residues: 993 helix: 1.49 (0.23), residues: 511 sheet: 0.77 (0.41), residues: 150 loop : 0.36 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 597 TYR 0.013 0.001 TYR A1028 PHE 0.020 0.001 PHE A 85 TRP 0.013 0.001 TRP A1014 HIS 0.004 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8131) covalent geometry : angle 0.53510 (11030) hydrogen bonds : bond 0.04213 ( 451) hydrogen bonds : angle 4.48234 ( 1299) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.272 Fit side-chains REVERT: A 37 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7008 (mtm-85) REVERT: A 52 ARG cc_start: 0.7449 (ttp80) cc_final: 0.6745 (tmt170) REVERT: A 96 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.5994 (mp0) REVERT: A 521 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7748 (mp10) REVERT: A 626 HIS cc_start: 0.5497 (OUTLIER) cc_final: 0.4320 (m-70) REVERT: A 637 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7472 (tt0) REVERT: A 844 GLN cc_start: 0.8657 (mt0) cc_final: 0.8398 (mt0) REVERT: A 959 THR cc_start: 0.8559 (m) cc_final: 0.8307 (m) REVERT: A 1045 LEU cc_start: 0.4511 (OUTLIER) cc_final: 0.3857 (pp) outliers start: 30 outliers final: 23 residues processed: 145 average time/residue: 0.4915 time to fit residues: 76.1914 Evaluate side-chains 150 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 965 GLU Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1001 PHE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1046 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.137977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.105550 restraints weight = 8963.293| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.68 r_work: 0.3114 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8131 Z= 0.189 Angle : 0.580 10.884 11030 Z= 0.304 Chirality : 0.044 0.135 1282 Planarity : 0.004 0.035 1384 Dihedral : 6.432 61.820 1115 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.39 % Allowed : 21.36 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.26), residues: 993 helix: 1.39 (0.23), residues: 511 sheet: 0.71 (0.40), residues: 150 loop : 0.33 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 597 TYR 0.016 0.002 TYR A 611 PHE 0.023 0.002 PHE A 85 TRP 0.012 0.002 TRP A1014 HIS 0.005 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 8131) covalent geometry : angle 0.58050 (11030) hydrogen bonds : bond 0.04648 ( 451) hydrogen bonds : angle 4.56574 ( 1299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3621.52 seconds wall clock time: 62 minutes 13.16 seconds (3733.16 seconds total)