Starting phenix.real_space_refine on Thu Jul 2 15:45:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rpi_24615/07_2026/7rpi_24615.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rpi_24615/07_2026/7rpi_24615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7rpi_24615/07_2026/7rpi_24615.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rpi_24615/07_2026/7rpi_24615.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rpi_24615/07_2026/7rpi_24615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rpi_24615/07_2026/7rpi_24615.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rpi_24615/07_2026/7rpi_24615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rpi_24615/07_2026/7rpi_24615.map" } resolution = 2.5 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= 0.005 sd= 0.579 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 S 65 5.16 5 Na 2 4.78 5 C 5741 2.51 5 N 1184 2.21 5 O 1534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8526 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 926, 7358 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 926, 7358 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885} Chain breaks: 3 bond proxies already assigned to first conformer: 7550 Chain: "A" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1163 Unusual residues: {' NA': 2, 'AV0': 2, 'NAG': 5, 'Y01': 26} Classifications: {'undetermined': 35, 'water': 43} Link IDs: {None: 77} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.67, per 1000 atoms: 0.31 Number of scatterers: 8526 At special positions: 0 Unit cell: (86.005, 87.675, 127.755, 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 65 16.00 Na 2 11.00 O 1534 8.00 N 1184 7.00 C 5741 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 366 " distance=2.05 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 829 " - pdb=" SG CYS A 849 " distance=2.05 Simple disulfide: pdb=" SG CYS A 863 " - pdb=" SG CYS A 872 " distance=2.04 Simple disulfide: pdb=" SG CYS A 871 " - pdb=" SG CYS A 887 " distance=2.04 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 Links applied NAG-ASN " NAG A2129 " - " ASN A 915 " " NAG A2130 " - " ASN A 834 " " NAG A2131 " - " ASN A 475 " " NAG A2132 " - " ASN A 390 " " NAG A2133 " - " ASN A 362 " Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 500.4 milliseconds 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1766 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 2 sheets defined 66.1% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 187 through 209 removed outlier: 3.552A pdb=" N VAL A 191 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 242 Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.827A pdb=" N GLU A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 removed outlier: 3.564A pdb=" N CYS A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.630A pdb=" N LEU A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 361 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 370 through 390 removed outlier: 5.239A pdb=" N LYS A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N HIS A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 490 through 502 removed outlier: 3.827A pdb=" N GLN A 496 " --> pdb=" O HIS A 492 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 522 Processing helix chain 'A' and resid 523 through 548 removed outlier: 3.653A pdb=" N THR A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 560 through 569 Processing helix chain 'A' and resid 570 through 587 removed outlier: 3.642A pdb=" N VAL A 575 " --> pdb=" O ASP A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 620 removed outlier: 5.557A pdb=" N LEU A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N SER A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 624 Processing helix chain 'A' and resid 626 through 648 Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 661 through 666 Processing helix chain 'A' and resid 682 through 706 removed outlier: 4.586A pdb=" N GLN A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 removed outlier: 3.720A pdb=" N CYS A 710 " --> pdb=" O LYS A 706 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 736 Processing helix chain 'A' and resid 746 through 750 Processing helix chain 'A' and resid 757 through 765 removed outlier: 3.689A pdb=" N ASP A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 769 Processing helix chain 'A' and resid 770 through 775 Processing helix chain 'A' and resid 818 through 833 Processing helix chain 'A' and resid 849 through 859 removed outlier: 3.608A pdb=" N THR A 853 " --> pdb=" O CYS A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 869 Processing helix chain 'A' and resid 880 through 899 removed outlier: 3.978A pdb=" N LYS A 889 " --> pdb=" O GLU A 885 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP A 896 " --> pdb=" O ILE A 892 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG A 897 " --> pdb=" O MET A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 954 Processing helix chain 'A' and resid 969 through 1002 Processing helix chain 'A' and resid 1003 through 1028 Processing helix chain 'A' and resid 1035 through 1061 removed outlier: 3.590A pdb=" N ILE A1040 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A1044 " --> pdb=" O ILE A1040 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASP A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1094 removed outlier: 5.434A pdb=" N SER A1079 " --> pdb=" O SER A1075 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ALA A1080 " --> pdb=" O ARG A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1123 Processing helix chain 'A' and resid 1123 through 1133 Processing sheet with id=AA1, first strand: chain 'A' and resid 450 through 458 removed outlier: 4.013A pdb=" N SER A 300 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA A 305 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL A 483 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 909 through 912 removed outlier: 3.577A pdb=" N ALA A 920 " --> pdb=" O ARG A 911 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU A 923 " --> pdb=" O TRP A 789 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N TRP A 789 " --> pdb=" O LEU A 923 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE A 925 " --> pdb=" O VAL A 787 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL A 787 " --> pdb=" O PHE A 925 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N SER A 927 " --> pdb=" O ILE A 785 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE A 785 " --> pdb=" O SER A 927 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE A 929 " --> pdb=" O MET A 783 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1287 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: 1.07 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1340 1.32 - 1.45: 2192 1.45 - 1.58: 5065 1.58 - 1.70: 69 1.70 - 1.83: 98 Bond restraints: 8764 Sorted by residual: bond pdb=" N MET A 557 " pdb=" CA BMET A 557 " ideal model delta sigma weight residual 1.458 1.357 0.102 1.27e-02 6.20e+03 6.43e+01 bond pdb=" N GLU A1031 " pdb=" CA GLU A1031 " ideal model delta sigma weight residual 1.454 1.400 0.053 1.23e-02 6.61e+03 1.86e+01 bond pdb=" C ASP A 578 " pdb=" O ASP A 578 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.15e-02 7.56e+03 1.66e+01 bond pdb=" CA GLU A1031 " pdb=" CB GLU A1031 " ideal model delta sigma weight residual 1.535 1.462 0.073 1.93e-02 2.68e+03 1.42e+01 bond pdb=" CB THR A1122 " pdb=" OG1 THR A1122 " ideal model delta sigma weight residual 1.433 1.373 0.060 1.60e-02 3.91e+03 1.42e+01 ... (remaining 8759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 10331 2.65 - 5.31: 1646 5.31 - 7.96: 76 7.96 - 10.61: 8 10.61 - 13.26: 1 Bond angle restraints: 12062 Sorted by residual: angle pdb=" N ARG A 341 " pdb=" CA ARG A 341 " pdb=" C ARG A 341 " ideal model delta sigma weight residual 108.76 122.02 -13.26 1.69e+00 3.50e-01 6.16e+01 angle pdb=" N MET A 557 " pdb=" CA BMET A 557 " pdb=" C MET A 557 " ideal model delta sigma weight residual 111.75 120.36 -8.61 1.28e+00 6.10e-01 4.52e+01 angle pdb=" CA PHE A 759 " pdb=" CB PHE A 759 " pdb=" CG PHE A 759 " ideal model delta sigma weight residual 113.80 120.40 -6.60 1.00e+00 1.00e+00 4.36e+01 angle pdb=" CA PHE A 549 " pdb=" CB PHE A 549 " pdb=" CG PHE A 549 " ideal model delta sigma weight residual 113.80 120.17 -6.37 1.00e+00 1.00e+00 4.06e+01 angle pdb=" CA ASP A 293 " pdb=" CB ASP A 293 " pdb=" CG ASP A 293 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.00e+00 1.00e+00 3.87e+01 ... (remaining 12057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.89: 4654 26.89 - 53.79: 156 53.79 - 80.68: 16 80.68 - 107.57: 6 107.57 - 134.47: 2 Dihedral angle restraints: 4834 sinusoidal: 2106 harmonic: 2728 Sorted by residual: dihedral pdb=" CA VAL A1048 " pdb=" C VAL A1048 " pdb=" N ASP A1049 " pdb=" CA ASP A1049 " ideal model delta harmonic sigma weight residual 180.00 -150.68 -29.32 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA TYR A 420 " pdb=" C TYR A 420 " pdb=" N ASN A 421 " pdb=" CA ASN A 421 " ideal model delta harmonic sigma weight residual -180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA TYR A 443 " pdb=" C TYR A 443 " pdb=" N ALA A 444 " pdb=" CA ALA A 444 " ideal model delta harmonic sigma weight residual -180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 4831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 922 0.095 - 0.191: 432 0.191 - 0.286: 69 0.286 - 0.381: 15 0.381 - 0.477: 3 Chirality restraints: 1441 Sorted by residual: chirality pdb=" CA GLU A1031 " pdb=" N GLU A1031 " pdb=" C GLU A1031 " pdb=" CB GLU A1031 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA BMET A 557 " pdb=" N MET A 557 " pdb=" C MET A 557 " pdb=" CB BMET A 557 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA ASP A 916 " pdb=" N ASP A 916 " pdb=" C ASP A 916 " pdb=" CB ASP A 916 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 1438 not shown) Planarity restraints: 1344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 834 " -0.102 2.00e-02 2.50e+03 1.05e-01 1.37e+02 pdb=" CG ASN A 834 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN A 834 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 834 " 0.157 2.00e-02 2.50e+03 pdb=" C1 NAG A2130 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 313 " 0.145 2.00e-02 2.50e+03 7.20e-02 1.30e+02 pdb=" CG TRP A 313 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 313 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP A 313 " -0.051 2.00e-02 2.50e+03 pdb=" NE1 TRP A 313 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP A 313 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 313 " -0.090 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 313 " 0.084 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 313 " -0.043 2.00e-02 2.50e+03 pdb=" CH2 TRP A 313 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 915 " -0.091 2.00e-02 2.50e+03 1.01e-01 1.28e+02 pdb=" CG ASN A 915 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 915 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 915 " 0.164 2.00e-02 2.50e+03 pdb=" C1 NAG A2129 " -0.119 2.00e-02 2.50e+03 ... (remaining 1341 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 140 2.72 - 3.26: 8270 3.26 - 3.81: 12726 3.81 - 4.35: 18480 4.35 - 4.90: 29510 Nonbonded interactions: 69126 Sorted by model distance: nonbonded pdb=" OD1 ASP A1049 " pdb="NA NA A2134 " model vdw 2.170 2.470 nonbonded pdb=" O GLY A1045 " pdb="NA NA A2134 " model vdw 2.205 2.470 nonbonded pdb=" OD1 ASP A 572 " pdb="NA NA A2135 " model vdw 2.213 2.470 nonbonded pdb=" OD2 ASP A 572 " pdb="NA NA A2135 " model vdw 2.245 2.470 nonbonded pdb="NA NA A2135 " pdb=" O HOH A2231 " model vdw 2.261 2.470 ... (remaining 69121 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 8.970 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:5.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 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 : 0.016 0.102 8777 Z= 0.895 Angle : 1.828 13.262 12093 Z= 1.186 Chirality : 0.106 0.477 1441 Planarity : 0.014 0.100 1339 Dihedral : 13.821 134.467 3044 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.12 % Allowed : 1.72 % Favored : 98.16 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.25), residues: 919 helix: -0.43 (0.19), residues: 558 sheet: 0.48 (0.94), residues: 29 loop : -0.29 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 301 TYR 0.114 0.021 TYR A 635 PHE 0.063 0.014 PHE A1109 TRP 0.145 0.028 TRP A 313 HIS 0.008 0.003 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.01586 / 0.89 ( 8764) covalent geometry : angle 1.81803 / 1.18 (12062) SS BOND : bond 0.01033 / 0.49 ( 8) SS BOND : angle 1.43047 / 0.82 ( 16) hydrogen bonds : bond 0.19508 / 12.89 ( 441) hydrogen bonds : angle 7.16071 / 5.09 ( 1287) link_NAG-ASN : bond 0.01743 / 0.98 ( 5) link_NAG-ASN : angle 5.71678 / 3.37 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 TRP cc_start: 0.7100 (m-10) cc_final: 0.6769 (m-10) REVERT: A 194 MET cc_start: 0.5966 (mtp) cc_final: 0.5583 (mmp) REVERT: A 647 MET cc_start: 0.7973 (mmp) cc_final: 0.7606 (mmt) REVERT: A 698 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6555 (mm-30) REVERT: A 700 SER cc_start: 0.7653 (t) cc_final: 0.7056 (m) REVERT: A 701 ARG cc_start: 0.7019 (mmt90) cc_final: 0.6546 (tpm170) REVERT: A 702 ILE cc_start: 0.6853 (mm) cc_final: 0.6584 (mm) REVERT: A 860 ASN cc_start: 0.7009 (m-40) cc_final: 0.6679 (t0) REVERT: A 937 LYS cc_start: 0.7678 (mtmt) cc_final: 0.7445 (mtmm) REVERT: A 943 LYS cc_start: 0.7334 (mtpp) cc_final: 0.6813 (mmmt) REVERT: A 997 MET cc_start: 0.7552 (mtm) cc_final: 0.7263 (mtp) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.5248 time to fit residues: 72.0525 Evaluate side-chains 87 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.0870 chunk 74 optimal weight: 0.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 ASN A 340 GLN A 421 ASN A 465 ASN A 470 ASN A 856 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.187936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.133849 restraints weight = 8669.575| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.05 r_work: 0.3379 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8777 Z= 0.141 Angle : 0.709 9.959 12093 Z= 0.340 Chirality : 0.042 0.225 1441 Planarity : 0.004 0.035 1339 Dihedral : 11.280 143.835 1373 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.35 % Allowed : 6.39 % Favored : 92.26 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.50 % 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: 1.57 (0.28), residues: 919 helix: 1.54 (0.21), residues: 568 sheet: 0.73 (0.91), residues: 29 loop : 0.31 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 363 TYR 0.015 0.002 TYR A 619 PHE 0.017 0.002 PHE A 608 TRP 0.018 0.002 TRP A 474 HIS 0.007 0.001 HIS A 827 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 8764) covalent geometry : angle 0.69052 / 0.34 (12062) SS BOND : bond 0.00433 / 0.20 ( 8) SS BOND : angle 1.18043 / 0.74 ( 16) hydrogen bonds : bond 0.05547 / 3.62 ( 441) hydrogen bonds : angle 4.68743 / 3.33 ( 1287) link_NAG-ASN : bond 0.00429 / 0.29 ( 5) link_NAG-ASN : angle 4.56457 / 2.65 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.7234 (mtp) cc_final: 0.6554 (mmp) REVERT: A 223 GLU cc_start: 0.8109 (tt0) cc_final: 0.7471 (pm20) REVERT: A 340 GLN cc_start: 0.7236 (tt0) cc_final: 0.6975 (mt0) REVERT: A 515 LEU cc_start: 0.7955 (mt) cc_final: 0.7662 (tp) REVERT: A 698 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6592 (mm-30) REVERT: A 700 SER cc_start: 0.8019 (t) cc_final: 0.7525 (m) REVERT: A 701 ARG cc_start: 0.7416 (mmt90) cc_final: 0.6948 (tpm170) REVERT: A 771 MET cc_start: 0.7762 (mpp) cc_final: 0.7526 (mmp) REVERT: A 887 CYS cc_start: 0.7497 (m) cc_final: 0.7048 (m) REVERT: A 962 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6936 (mtm110) outliers start: 11 outliers final: 5 residues processed: 107 average time/residue: 0.5157 time to fit residues: 58.9498 Evaluate side-chains 90 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 962 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 75 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.187060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.133333 restraints weight = 10595.096| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.05 r_work: 0.3384 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8777 Z= 0.127 Angle : 0.651 9.176 12093 Z= 0.301 Chirality : 0.042 0.363 1441 Planarity : 0.004 0.043 1339 Dihedral : 10.795 141.329 1373 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.35 % Allowed : 9.21 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.95 (0.28), residues: 919 helix: 1.94 (0.22), residues: 573 sheet: 0.88 (0.94), residues: 29 loop : 0.24 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 341 TYR 0.014 0.002 TYR A 619 PHE 0.018 0.001 PHE A 608 TRP 0.014 0.001 TRP A 650 HIS 0.004 0.001 HIS A 827 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 8764) covalent geometry : angle 0.63797 / 0.30 (12062) SS BOND : bond 0.00369 / 0.18 ( 8) SS BOND : angle 0.89327 / 0.54 ( 16) hydrogen bonds : bond 0.05101 / 3.32 ( 441) hydrogen bonds : angle 4.41457 / 3.13 ( 1287) link_NAG-ASN : bond 0.00914 / 0.52 ( 5) link_NAG-ASN : angle 3.69116 / 2.07 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.7327 (mtp) cc_final: 0.6561 (mmp) REVERT: A 223 GLU cc_start: 0.8230 (tt0) cc_final: 0.7393 (pm20) REVERT: A 256 TYR cc_start: 0.5425 (t80) cc_final: 0.5219 (t80) REVERT: A 339 CYS cc_start: 0.7219 (p) cc_final: 0.6701 (p) REVERT: A 515 LEU cc_start: 0.7814 (mt) cc_final: 0.7543 (tt) REVERT: A 700 SER cc_start: 0.7919 (t) cc_final: 0.7384 (m) REVERT: A 701 ARG cc_start: 0.7404 (mmt90) cc_final: 0.6765 (tpm170) REVERT: A 771 MET cc_start: 0.7641 (mpp) cc_final: 0.7384 (mmp) REVERT: A 887 CYS cc_start: 0.7590 (m) cc_final: 0.7169 (m) outliers start: 11 outliers final: 6 residues processed: 103 average time/residue: 0.5132 time to fit residues: 56.6452 Evaluate side-chains 92 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 997 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.190369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.139038 restraints weight = 12567.105| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.98 r_work: 0.3513 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8777 Z= 0.130 Angle : 0.638 7.599 12093 Z= 0.297 Chirality : 0.042 0.384 1441 Planarity : 0.004 0.044 1339 Dihedral : 10.652 138.915 1373 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.84 % Allowed : 9.83 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.01 (0.28), residues: 919 helix: 2.06 (0.22), residues: 573 sheet: 0.92 (0.91), residues: 29 loop : 0.10 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 774 TYR 0.013 0.002 TYR A 644 PHE 0.018 0.001 PHE A 608 TRP 0.014 0.001 TRP A 650 HIS 0.002 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 8764) covalent geometry : angle 0.62996 / 0.29 (12062) SS BOND : bond 0.00366 / 0.18 ( 8) SS BOND : angle 1.08551 / 0.65 ( 16) hydrogen bonds : bond 0.05127 / 3.32 ( 441) hydrogen bonds : angle 4.39646 / 3.11 ( 1287) link_NAG-ASN : bond 0.01142 / 0.62 ( 5) link_NAG-ASN : angle 2.81405 / 1.66 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.7441 (mtp) cc_final: 0.6700 (mmp) REVERT: A 223 GLU cc_start: 0.8294 (tt0) cc_final: 0.7497 (pm20) REVERT: A 363 ARG cc_start: 0.7422 (mpt90) cc_final: 0.7130 (mtt-85) REVERT: A 515 LEU cc_start: 0.7902 (mt) cc_final: 0.7644 (tt) REVERT: A 700 SER cc_start: 0.8032 (t) cc_final: 0.7519 (m) REVERT: A 701 ARG cc_start: 0.7422 (mmt90) cc_final: 0.6873 (tpm170) REVERT: A 771 MET cc_start: 0.7714 (mpp) cc_final: 0.7366 (mmp) REVERT: A 887 CYS cc_start: 0.7563 (m) cc_final: 0.7141 (m) REVERT: A 943 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7579 (tptt) outliers start: 15 outliers final: 7 residues processed: 104 average time/residue: 0.5114 time to fit residues: 57.0548 Evaluate side-chains 97 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 943 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.189410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.138046 restraints weight = 10765.371| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.99 r_work: 0.3509 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8777 Z= 0.137 Angle : 0.650 8.442 12093 Z= 0.301 Chirality : 0.042 0.357 1441 Planarity : 0.004 0.041 1339 Dihedral : 10.655 136.823 1373 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.47 % Allowed : 11.18 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.02 (0.28), residues: 919 helix: 2.13 (0.22), residues: 568 sheet: 0.88 (0.91), residues: 29 loop : -0.01 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 754 TYR 0.013 0.002 TYR A 644 PHE 0.018 0.002 PHE A 608 TRP 0.013 0.001 TRP A 650 HIS 0.002 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 8764) covalent geometry : angle 0.64306 / 0.30 (12062) SS BOND : bond 0.00364 / 0.17 ( 8) SS BOND : angle 0.87655 / 0.53 ( 16) hydrogen bonds : bond 0.05343 / 3.46 ( 441) hydrogen bonds : angle 4.41969 / 3.13 ( 1287) link_NAG-ASN : bond 0.01014 / 0.54 ( 5) link_NAG-ASN : angle 2.60576 / 1.52 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.287 Fit side-chains REVERT: A 194 MET cc_start: 0.7325 (mtp) cc_final: 0.6578 (mmp) REVERT: A 223 GLU cc_start: 0.8325 (tt0) cc_final: 0.7616 (pm20) REVERT: A 363 ARG cc_start: 0.7418 (mpt90) cc_final: 0.7103 (mtt-85) REVERT: A 515 LEU cc_start: 0.7896 (mt) cc_final: 0.7608 (tt) REVERT: A 700 SER cc_start: 0.8005 (t) cc_final: 0.7480 (m) REVERT: A 701 ARG cc_start: 0.7311 (mmt90) cc_final: 0.6757 (tpm170) REVERT: A 771 MET cc_start: 0.7678 (mpp) cc_final: 0.7308 (mmp) REVERT: A 887 CYS cc_start: 0.7529 (m) cc_final: 0.7119 (m) REVERT: A 937 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7320 (mmpt) REVERT: A 943 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7560 (tptt) outliers start: 12 outliers final: 6 residues processed: 99 average time/residue: 0.4983 time to fit residues: 52.9752 Evaluate side-chains 95 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 997 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 3 optimal weight: 0.0870 chunk 65 optimal weight: 7.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.191076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.141681 restraints weight = 9194.897| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.85 r_work: 0.3553 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8777 Z= 0.118 Angle : 0.612 8.417 12093 Z= 0.283 Chirality : 0.041 0.346 1441 Planarity : 0.004 0.042 1339 Dihedral : 10.464 137.154 1373 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.84 % Allowed : 11.55 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.11 (0.29), residues: 919 helix: 2.25 (0.22), residues: 566 sheet: 0.97 (0.92), residues: 29 loop : -0.05 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 962 TYR 0.011 0.001 TYR A 545 PHE 0.014 0.001 PHE A 608 TRP 0.012 0.001 TRP A 650 HIS 0.002 0.000 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 8764) covalent geometry : angle 0.60540 / 0.28 (12062) SS BOND : bond 0.00379 / 0.18 ( 8) SS BOND : angle 1.21022 / 0.73 ( 16) hydrogen bonds : bond 0.04629 / 3.00 ( 441) hydrogen bonds : angle 4.32384 / 3.07 ( 1287) link_NAG-ASN : bond 0.00894 / 0.49 ( 5) link_NAG-ASN : angle 2.42687 / 1.46 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.214 Fit side-chains REVERT: A 194 MET cc_start: 0.7299 (mtp) cc_final: 0.6592 (mmp) REVERT: A 223 GLU cc_start: 0.8206 (tt0) cc_final: 0.7542 (pm20) REVERT: A 363 ARG cc_start: 0.7389 (mpt90) cc_final: 0.7086 (mtt-85) REVERT: A 515 LEU cc_start: 0.7845 (mt) cc_final: 0.7598 (tt) REVERT: A 700 SER cc_start: 0.8003 (t) cc_final: 0.7490 (m) REVERT: A 701 ARG cc_start: 0.7312 (mmt90) cc_final: 0.6774 (tpm170) REVERT: A 771 MET cc_start: 0.7677 (mpp) cc_final: 0.7310 (mmp) REVERT: A 887 CYS cc_start: 0.7457 (m) cc_final: 0.7049 (m) REVERT: A 937 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7288 (mmpt) REVERT: A 943 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7609 (tptt) outliers start: 15 outliers final: 4 residues processed: 97 average time/residue: 0.4787 time to fit residues: 49.8368 Evaluate side-chains 93 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 943 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.189299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.138253 restraints weight = 10910.908| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.98 r_work: 0.3509 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8777 Z= 0.139 Angle : 0.646 8.622 12093 Z= 0.299 Chirality : 0.042 0.341 1441 Planarity : 0.004 0.043 1339 Dihedral : 10.671 137.548 1373 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.72 % Allowed : 11.67 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.96 (0.28), residues: 919 helix: 2.14 (0.22), residues: 568 sheet: 0.89 (0.89), residues: 29 loop : -0.17 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 754 TYR 0.013 0.002 TYR A 644 PHE 0.021 0.002 PHE A 585 TRP 0.013 0.001 TRP A 650 HIS 0.002 0.000 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 8764) covalent geometry : angle 0.63964 / 0.30 (12062) SS BOND : bond 0.00414 / 0.20 ( 8) SS BOND : angle 0.99949 / 0.61 ( 16) hydrogen bonds : bond 0.05337 / 3.46 ( 441) hydrogen bonds : angle 4.41074 / 3.13 ( 1287) link_NAG-ASN : bond 0.00874 / 0.47 ( 5) link_NAG-ASN : angle 2.45209 / 1.46 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.7381 (mtp) cc_final: 0.6648 (mmp) REVERT: A 223 GLU cc_start: 0.8256 (tt0) cc_final: 0.7592 (pm20) REVERT: A 363 ARG cc_start: 0.7424 (mpt90) cc_final: 0.7133 (mtt-85) REVERT: A 515 LEU cc_start: 0.7952 (mt) cc_final: 0.7668 (tt) REVERT: A 700 SER cc_start: 0.8022 (t) cc_final: 0.7505 (m) REVERT: A 701 ARG cc_start: 0.7341 (mmt90) cc_final: 0.6756 (tpm170) REVERT: A 887 CYS cc_start: 0.7467 (m) cc_final: 0.7100 (m) REVERT: A 937 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7350 (mmpt) REVERT: A 943 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7608 (tptt) outliers start: 14 outliers final: 6 residues processed: 96 average time/residue: 0.4460 time to fit residues: 46.2713 Evaluate side-chains 94 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 943 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 55 optimal weight: 0.8980 chunk 38 optimal weight: 0.0060 chunk 17 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 0.0870 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.193223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.143534 restraints weight = 11320.444| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.88 r_work: 0.3546 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8777 Z= 0.107 Angle : 0.589 9.151 12093 Z= 0.272 Chirality : 0.040 0.337 1441 Planarity : 0.004 0.044 1339 Dihedral : 10.275 137.811 1373 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.49 % Allowed : 13.02 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.15 (0.29), residues: 919 helix: 2.33 (0.22), residues: 566 sheet: 0.93 (0.93), residues: 29 loop : -0.13 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 754 TYR 0.011 0.001 TYR A 545 PHE 0.011 0.001 PHE A 608 TRP 0.012 0.001 TRP A 650 HIS 0.001 0.000 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 ( 8764) covalent geometry : angle 0.58407 / 0.27 (12062) SS BOND : bond 0.00343 / 0.17 ( 8) SS BOND : angle 0.72647 / 0.45 ( 16) hydrogen bonds : bond 0.04129 / 2.68 ( 441) hydrogen bonds : angle 4.23213 / 3.01 ( 1287) link_NAG-ASN : bond 0.00821 / 0.47 ( 5) link_NAG-ASN : angle 2.28651 / 1.39 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.301 Fit side-chains REVERT: A 194 MET cc_start: 0.7516 (mtp) cc_final: 0.6835 (mmp) REVERT: A 223 GLU cc_start: 0.8226 (tt0) cc_final: 0.7651 (pm20) REVERT: A 363 ARG cc_start: 0.7415 (mpt90) cc_final: 0.7116 (mtt-85) REVERT: A 436 MET cc_start: 0.4339 (OUTLIER) cc_final: 0.4135 (mpt) REVERT: A 700 SER cc_start: 0.8095 (t) cc_final: 0.7607 (m) REVERT: A 701 ARG cc_start: 0.7424 (mmt90) cc_final: 0.6886 (tpm170) REVERT: A 746 GLU cc_start: 0.7676 (pt0) cc_final: 0.7320 (mm-30) REVERT: A 887 CYS cc_start: 0.7563 (m) cc_final: 0.7176 (m) REVERT: A 937 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7414 (mmpt) REVERT: A 943 LYS cc_start: 0.8257 (mtpp) cc_final: 0.7756 (tptt) outliers start: 4 outliers final: 2 residues processed: 90 average time/residue: 0.5038 time to fit residues: 48.8509 Evaluate side-chains 90 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 937 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 66 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 81 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.191848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141334 restraints weight = 11294.001| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.05 r_work: 0.3534 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8777 Z= 0.114 Angle : 0.600 9.220 12093 Z= 0.277 Chirality : 0.040 0.324 1441 Planarity : 0.004 0.044 1339 Dihedral : 10.250 138.254 1373 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.49 % Allowed : 13.02 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.15 (0.29), residues: 919 helix: 2.34 (0.22), residues: 566 sheet: 0.95 (0.92), residues: 29 loop : -0.16 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 962 TYR 0.011 0.001 TYR A 545 PHE 0.013 0.001 PHE A 608 TRP 0.014 0.001 TRP A 650 HIS 0.001 0.000 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 8764) covalent geometry : angle 0.59488 / 0.28 (12062) SS BOND : bond 0.00355 / 0.17 ( 8) SS BOND : angle 0.73668 / 0.46 ( 16) hydrogen bonds : bond 0.04511 / 2.92 ( 441) hydrogen bonds : angle 4.26000 / 3.03 ( 1287) link_NAG-ASN : bond 0.00784 / 0.44 ( 5) link_NAG-ASN : angle 2.25559 / 1.36 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.278 Fit side-chains REVERT: A 194 MET cc_start: 0.7383 (mtp) cc_final: 0.6674 (mmp) REVERT: A 223 GLU cc_start: 0.8241 (tt0) cc_final: 0.7566 (pm20) REVERT: A 363 ARG cc_start: 0.7340 (mpt90) cc_final: 0.7067 (mtt-85) REVERT: A 700 SER cc_start: 0.7961 (t) cc_final: 0.7439 (m) REVERT: A 701 ARG cc_start: 0.7312 (mmt90) cc_final: 0.6747 (tpm170) REVERT: A 746 GLU cc_start: 0.7516 (pt0) cc_final: 0.7203 (mm-30) REVERT: A 887 CYS cc_start: 0.7521 (m) cc_final: 0.7106 (m) REVERT: A 937 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7343 (mmpt) REVERT: A 943 LYS cc_start: 0.8198 (mtpp) cc_final: 0.7653 (tptt) outliers start: 4 outliers final: 2 residues processed: 96 average time/residue: 0.4554 time to fit residues: 47.1778 Evaluate side-chains 93 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 937 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 78 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 0.0270 chunk 91 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.190963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.140568 restraints weight = 12672.307| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.03 r_work: 0.3502 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8777 Z= 0.123 Angle : 0.619 9.297 12093 Z= 0.286 Chirality : 0.041 0.324 1441 Planarity : 0.004 0.044 1339 Dihedral : 10.322 138.494 1373 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.61 % Allowed : 13.27 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.11 (0.29), residues: 919 helix: 2.30 (0.22), residues: 566 sheet: 1.05 (0.92), residues: 29 loop : -0.16 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 962 TYR 0.011 0.001 TYR A 644 PHE 0.016 0.001 PHE A 608 TRP 0.013 0.001 TRP A 650 HIS 0.001 0.000 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 8764) covalent geometry : angle 0.61339 / 0.28 (12062) SS BOND : bond 0.00375 / 0.18 ( 8) SS BOND : angle 0.97370 / 0.59 ( 16) hydrogen bonds : bond 0.04787 / 3.10 ( 441) hydrogen bonds : angle 4.30883 / 3.06 ( 1287) link_NAG-ASN : bond 0.00793 / 0.44 ( 5) link_NAG-ASN : angle 2.26903 / 1.36 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.243 Fit side-chains REVERT: A 194 MET cc_start: 0.7168 (mtp) cc_final: 0.6500 (mmp) REVERT: A 223 GLU cc_start: 0.8105 (tt0) cc_final: 0.7586 (pm20) REVERT: A 363 ARG cc_start: 0.7345 (mpt90) cc_final: 0.7079 (mtt-85) REVERT: A 700 SER cc_start: 0.7973 (t) cc_final: 0.7470 (m) REVERT: A 701 ARG cc_start: 0.7215 (mmt90) cc_final: 0.6731 (tpm170) REVERT: A 887 CYS cc_start: 0.7347 (m) cc_final: 0.6955 (m) REVERT: A 937 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7320 (mmpt) REVERT: A 943 LYS cc_start: 0.8088 (mtpp) cc_final: 0.7569 (tptt) outliers start: 5 outliers final: 2 residues processed: 95 average time/residue: 0.4752 time to fit residues: 48.6332 Evaluate side-chains 91 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 937 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 860 ASN A 968 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.189820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.135952 restraints weight = 16640.844| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.43 r_work: 0.3466 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8777 Z= 0.132 Angle : 0.638 10.349 12093 Z= 0.295 Chirality : 0.041 0.323 1441 Planarity : 0.004 0.044 1339 Dihedral : 10.456 138.536 1373 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.49 % Allowed : 13.27 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.04 (0.29), residues: 919 helix: 2.25 (0.22), residues: 568 sheet: 1.05 (0.90), residues: 29 loop : -0.22 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 962 TYR 0.012 0.001 TYR A 644 PHE 0.017 0.001 PHE A 608 TRP 0.013 0.001 TRP A 650 HIS 0.002 0.000 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 8764) covalent geometry : angle 0.63276 / 0.29 (12062) SS BOND : bond 0.00375 / 0.18 ( 8) SS BOND : angle 0.88874 / 0.54 ( 16) hydrogen bonds : bond 0.05083 / 3.30 ( 441) hydrogen bonds : angle 4.37033 / 3.10 ( 1287) link_NAG-ASN : bond 0.00796 / 0.44 ( 5) link_NAG-ASN : angle 2.29635 / 1.38 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3646.49 seconds wall clock time: 62 minutes 37.78 seconds (3757.78 seconds total)