Starting phenix.real_space_refine on Fri Feb 14 04:34:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q61_13849/02_2025/7q61_13849.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q61_13849/02_2025/7q61_13849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q61_13849/02_2025/7q61_13849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q61_13849/02_2025/7q61_13849.map" model { file = "/net/cci-nas-00/data/ceres_data/7q61_13849/02_2025/7q61_13849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q61_13849/02_2025/7q61_13849.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 6095 2.51 5 N 1559 2.21 5 O 1835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9535 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1210, 9437 Classifications: {'peptide': 1210} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1147} Chain breaks: 4 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.97, per 1000 atoms: 0.73 Number of scatterers: 9535 At special positions: 0 Unit cell: (89.286, 124.224, 124.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1835 8.00 N 1559 7.00 C 6095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 40 " - pdb=" SG CYS A 78 " distance=2.07 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 557 " distance=2.03 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS A 769 " distance=2.02 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 694 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 847 " distance=2.04 Simple disulfide: pdb=" SG CYS A 845 " - pdb=" SG CYS A 881 " distance=2.03 Simple disulfide: pdb=" SG CYS A 919 " - pdb=" SG CYS A1307 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1123 " distance=2.03 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1501 " - " ASN A 328 " " NAG A1502 " - " ASN A 609 " " NAG A1503 " - " ASN A 857 " " NAG B 1 " - " ASN A 867 " " NAG X 1 " - " ASN A 120 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2252 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 19 sheets defined 15.9% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 508 through 512 removed outlier: 4.001A pdb=" N LYS A 511 " --> pdb=" O ASN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 602 removed outlier: 3.752A pdb=" N LEU A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 670 through 677 Processing helix chain 'A' and resid 837 through 839 No H-bonds generated for 'chain 'A' and resid 837 through 839' Processing helix chain 'A' and resid 970 through 973 Processing helix chain 'A' and resid 974 through 990 removed outlier: 4.031A pdb=" N ALA A 979 " --> pdb=" O MET A 975 " (cutoff:3.500A) Proline residue: A 980 - end of helix removed outlier: 4.145A pdb=" N TYR A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1011 Processing helix chain 'A' and resid 1034 through 1046 Processing helix chain 'A' and resid 1047 through 1051 removed outlier: 4.044A pdb=" N LYS A1050 " --> pdb=" O GLN A1047 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A1051 " --> pdb=" O ALA A1048 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1047 through 1051' Processing helix chain 'A' and resid 1056 through 1070 removed outlier: 3.756A pdb=" N GLN A1060 " --> pdb=" O PRO A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1106 removed outlier: 3.930A pdb=" N LEU A1106 " --> pdb=" O THR A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1125 removed outlier: 4.078A pdb=" N GLN A1119 " --> pdb=" O PRO A1115 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY A1120 " --> pdb=" O MET A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1131 removed outlier: 3.849A pdb=" N THR A1131 " --> pdb=" O SER A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1144 Processing helix chain 'A' and resid 1192 through 1205 Processing helix chain 'A' and resid 1211 through 1226 removed outlier: 3.645A pdb=" N TRP A1224 " --> pdb=" O SER A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1255 removed outlier: 3.640A pdb=" N VAL A1243 " --> pdb=" O GLN A1239 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 82 removed outlier: 8.357A pdb=" N LYS A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.822A pdb=" N PHE A 52 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU A 67 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 54 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 126 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 131 removed outlier: 4.672A pdb=" N THR A 205 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N SER A 156 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 223 Processing sheet with id=AA6, first strand: chain 'A' and resid 229 through 230 removed outlier: 6.624A pdb=" N LEU A 229 " --> pdb=" O SER A 336 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N HIS A 310 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLN A 311 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS A 261 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 278 " --> pdb=" O GLN A 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 398 through 403 removed outlier: 8.903A pdb=" N SER A 358 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N THR A 347 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS A 360 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLN A 436 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER A 341 " --> pdb=" O GLN A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 455 Processing sheet with id=AB1, first strand: chain 'A' and resid 498 through 507 removed outlier: 5.220A pdb=" N LEU A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY A 495 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N SER A 488 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE A 539 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 563 through 567 Processing sheet with id=AB3, first strand: chain 'A' and resid 570 through 571 removed outlier: 3.507A pdb=" N GLN A 571 " --> pdb=" O THR A 785 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP A 595 " --> pdb=" O THR A 736 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR A 736 " --> pdb=" O ASP A 595 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 570 through 571 removed outlier: 3.507A pdb=" N GLN A 571 " --> pdb=" O THR A 785 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 729 through 730 removed outlier: 3.505A pdb=" N ILE A 898 " --> pdb=" O ARG A 730 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 729 through 730 removed outlier: 3.505A pdb=" N ILE A 898 " --> pdb=" O ARG A 730 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 790 through 795 Processing sheet with id=AB8, first strand: chain 'A' and resid 908 through 918 Processing sheet with id=AB9, first strand: chain 'A' and resid 921 through 930 removed outlier: 5.040A pdb=" N LYS A 923 " --> pdb=" O GLY A1304 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A1304 " --> pdb=" O LYS A 923 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1165 through 1166 401 hydrogen bonds defined for protein. 1110 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.71 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 3076 1.36 - 1.50: 2688 1.50 - 1.64: 3914 1.64 - 1.78: 3 1.78 - 1.91: 66 Bond restraints: 9747 Sorted by residual: bond pdb=" CD GLU A 596 " pdb=" OE2 GLU A 596 " ideal model delta sigma weight residual 1.249 1.327 -0.078 1.90e-02 2.77e+03 1.69e+01 bond pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " ideal model delta sigma weight residual 1.808 1.697 0.111 3.30e-02 9.18e+02 1.13e+01 bond pdb=" CB CYS A 40 " pdb=" SG CYS A 40 " ideal model delta sigma weight residual 1.808 1.915 -0.107 3.30e-02 9.18e+02 1.05e+01 bond pdb=" N SER A1024 " pdb=" CA SER A1024 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.37e+00 bond pdb=" N ARG A1029 " pdb=" CA ARG A1029 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 7.03e+00 ... (remaining 9742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.58: 13173 5.58 - 11.15: 65 11.15 - 16.73: 4 16.73 - 22.30: 0 22.30 - 27.88: 1 Bond angle restraints: 13243 Sorted by residual: angle pdb=" CA CYS A 78 " pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " ideal model delta sigma weight residual 114.40 142.28 -27.88 2.30e+00 1.89e-01 1.47e+02 angle pdb=" C ILE A 952 " pdb=" N MET A 953 " pdb=" CA MET A 953 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" CA TYR A1076 " pdb=" CB TYR A1076 " pdb=" CG TYR A1076 " ideal model delta sigma weight residual 113.90 123.65 -9.75 1.80e+00 3.09e-01 2.93e+01 angle pdb=" CA MET A 953 " pdb=" CB MET A 953 " pdb=" CG MET A 953 " ideal model delta sigma weight residual 114.10 124.83 -10.73 2.00e+00 2.50e-01 2.88e+01 angle pdb=" C ASN A 459 " pdb=" CA ASN A 459 " pdb=" CB ASN A 459 " ideal model delta sigma weight residual 117.23 110.43 6.80 1.36e+00 5.41e-01 2.50e+01 ... (remaining 13238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.49: 5567 20.49 - 40.97: 288 40.97 - 61.46: 48 61.46 - 81.95: 20 81.95 - 102.43: 18 Dihedral angle restraints: 5941 sinusoidal: 2432 harmonic: 3509 Sorted by residual: dihedral pdb=" CA PHE A 616 " pdb=" C PHE A 616 " pdb=" N PRO A 617 " pdb=" CA PRO A 617 " ideal model delta harmonic sigma weight residual -180.00 -138.24 -41.76 0 5.00e+00 4.00e-02 6.98e+01 dihedral pdb=" CA PRO A1056 " pdb=" C PRO A1056 " pdb=" N LYS A1057 " pdb=" CA LYS A1057 " ideal model delta harmonic sigma weight residual -180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA TYR A1256 " pdb=" C TYR A1256 " pdb=" N MET A1257 " pdb=" CA MET A1257 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 5938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1181 0.066 - 0.131: 265 0.131 - 0.197: 54 0.197 - 0.263: 16 0.263 - 0.328: 5 Chirality restraints: 1521 Sorted by residual: chirality pdb=" CA CYS A 78 " pdb=" N CYS A 78 " pdb=" C CYS A 78 " pdb=" CB CYS A 78 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" C1 NAG A1502 " pdb=" ND2 ASN A 609 " pdb=" C2 NAG A1502 " pdb=" O5 NAG A1502 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB ILE A 952 " pdb=" CA ILE A 952 " pdb=" CG1 ILE A 952 " pdb=" CG2 ILE A 952 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 1518 not shown) Planarity restraints: 1699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 399 " 0.066 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO A 400 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 400 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 400 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 733 " 0.016 2.00e-02 2.50e+03 2.20e-02 8.43e+00 pdb=" CG PHE A 733 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 733 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 733 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE A 733 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 733 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 733 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A1055 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO A1056 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A1056 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1056 " 0.038 5.00e-02 4.00e+02 ... (remaining 1696 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2327 2.80 - 3.33: 7797 3.33 - 3.85: 15779 3.85 - 4.38: 17633 4.38 - 4.90: 31021 Nonbonded interactions: 74557 Sorted by model distance: nonbonded pdb=" OE2 GLU A 320 " pdb=" OG1 THR A 323 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASP A 127 " pdb=" OH TYR A 131 " model vdw 2.319 3.040 nonbonded pdb=" O CYS A 557 " pdb=" OH TYR A 613 " model vdw 2.329 3.040 nonbonded pdb=" O ALA A 827 " pdb=" OH TYR A 832 " model vdw 2.333 3.040 nonbonded pdb=" OE1 GLN A 161 " pdb=" OG1 THR A 955 " model vdw 2.339 3.040 ... (remaining 74552 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'X' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.570 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.790 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 0.111 9747 Z= 0.391 Angle : 1.092 27.881 13243 Z= 0.550 Chirality : 0.063 0.328 1521 Planarity : 0.009 0.100 1694 Dihedral : 14.479 102.431 3659 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.50 % Favored : 95.25 % Rotamer: Outliers : 0.10 % Allowed : 0.19 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.22), residues: 1200 helix: -3.00 (0.24), residues: 169 sheet: -0.23 (0.23), residues: 486 loop : -1.47 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1065 HIS 0.007 0.001 HIS A 75 PHE 0.050 0.004 PHE A 733 TYR 0.040 0.003 TYR A1076 ARG 0.006 0.001 ARG A 730 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7284 (m90) cc_final: 0.6932 (m90) REVERT: A 395 ASN cc_start: 0.9107 (p0) cc_final: 0.8902 (p0) REVERT: A 548 ASP cc_start: 0.7744 (t70) cc_final: 0.7307 (t70) REVERT: A 1015 MET cc_start: 0.7641 (pmm) cc_final: 0.7375 (pmm) REVERT: A 1045 PHE cc_start: 0.9227 (m-80) cc_final: 0.8761 (m-80) REVERT: A 1311 GLN cc_start: 0.7773 (tt0) cc_final: 0.7512 (tt0) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.9690 time to fit residues: 119.9731 Evaluate side-chains 74 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 0.0470 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 311 GLN A 313 ASN A 332 ASN A 384 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.117675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.081837 restraints weight = 21999.760| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.78 r_work: 0.3331 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9747 Z= 0.276 Angle : 0.707 12.687 13243 Z= 0.351 Chirality : 0.047 0.297 1521 Planarity : 0.006 0.063 1694 Dihedral : 7.991 74.124 1438 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.08 % Favored : 95.75 % Rotamer: Outliers : 1.53 % Allowed : 10.10 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.23), residues: 1200 helix: -1.23 (0.33), residues: 182 sheet: -0.21 (0.23), residues: 494 loop : -1.08 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1065 HIS 0.003 0.001 HIS A1018 PHE 0.018 0.002 PHE A 107 TYR 0.021 0.002 TYR A1076 ARG 0.004 0.000 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8992 (p0) cc_final: 0.8687 (p0) REVERT: A 310 HIS cc_start: 0.7865 (m90) cc_final: 0.7326 (m90) REVERT: A 381 TYR cc_start: 0.8159 (m-10) cc_final: 0.7944 (m-10) REVERT: A 395 ASN cc_start: 0.9461 (p0) cc_final: 0.9198 (p0) REVERT: A 548 ASP cc_start: 0.8383 (t70) cc_final: 0.7988 (t70) REVERT: A 945 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7094 (p90) REVERT: A 953 MET cc_start: 0.5566 (OUTLIER) cc_final: 0.5212 (ppp) REVERT: A 1005 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7170 (m-80) REVERT: A 1015 MET cc_start: 0.7922 (pmm) cc_final: 0.7640 (pmm) REVERT: A 1045 PHE cc_start: 0.9440 (m-80) cc_final: 0.8903 (m-80) REVERT: A 1213 LYS cc_start: 0.8865 (mmpt) cc_final: 0.8511 (mmmt) REVERT: A 1311 GLN cc_start: 0.8430 (tt0) cc_final: 0.8078 (tt0) outliers start: 16 outliers final: 7 residues processed: 89 average time/residue: 0.9340 time to fit residues: 92.1921 Evaluate side-chains 80 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain A residue 1171 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 86 optimal weight: 0.0040 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 4 optimal weight: 0.0570 chunk 74 optimal weight: 0.2980 overall best weight: 0.8714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS ** A 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 HIS A 958 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.116673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.081024 restraints weight = 21984.522| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 4.02 r_work: 0.3252 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9747 Z= 0.233 Angle : 0.676 11.564 13243 Z= 0.329 Chirality : 0.045 0.276 1521 Planarity : 0.005 0.054 1694 Dihedral : 6.663 56.966 1438 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.67 % Rotamer: Outliers : 2.29 % Allowed : 11.92 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.24), residues: 1200 helix: -0.36 (0.37), residues: 181 sheet: -0.13 (0.23), residues: 515 loop : -0.71 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1036 HIS 0.003 0.001 HIS A 75 PHE 0.015 0.002 PHE A 107 TYR 0.023 0.001 TYR A1076 ARG 0.009 0.001 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 302 ASP cc_start: 0.8810 (t0) cc_final: 0.8515 (p0) REVERT: A 310 HIS cc_start: 0.7920 (m90) cc_final: 0.7335 (m90) REVERT: A 381 TYR cc_start: 0.8149 (m-10) cc_final: 0.7891 (m-10) REVERT: A 395 ASN cc_start: 0.9541 (p0) cc_final: 0.9265 (p0) REVERT: A 548 ASP cc_start: 0.8433 (t70) cc_final: 0.8192 (t70) REVERT: A 945 TYR cc_start: 0.8210 (OUTLIER) cc_final: 0.6971 (p90) REVERT: A 966 MET cc_start: -0.3026 (ttt) cc_final: -0.3421 (ttm) REVERT: A 1015 MET cc_start: 0.7987 (pmm) cc_final: 0.7669 (pmm) REVERT: A 1045 PHE cc_start: 0.9510 (m-80) cc_final: 0.8967 (m-80) REVERT: A 1213 LYS cc_start: 0.8883 (mmpt) cc_final: 0.8631 (mmpt) REVERT: A 1311 GLN cc_start: 0.8234 (tt0) cc_final: 0.7830 (tt0) outliers start: 24 outliers final: 13 residues processed: 85 average time/residue: 0.8157 time to fit residues: 77.7059 Evaluate side-chains 82 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1171 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 12 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 0.0030 chunk 60 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 115 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 55 optimal weight: 0.0370 chunk 11 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 overall best weight: 0.2666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.118579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.082468 restraints weight = 21752.404| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.89 r_work: 0.3303 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9747 Z= 0.156 Angle : 0.623 12.378 13243 Z= 0.305 Chirality : 0.044 0.254 1521 Planarity : 0.004 0.056 1694 Dihedral : 5.384 41.380 1438 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.83 % Favored : 96.00 % Rotamer: Outliers : 1.91 % Allowed : 13.92 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.24), residues: 1200 helix: 0.04 (0.38), residues: 182 sheet: 0.07 (0.23), residues: 508 loop : -0.64 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1036 HIS 0.002 0.000 HIS A 75 PHE 0.019 0.001 PHE A 107 TYR 0.017 0.001 TYR A1076 ARG 0.006 0.000 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.9168 (p0) cc_final: 0.8833 (p0) REVERT: A 310 HIS cc_start: 0.7784 (m90) cc_final: 0.7323 (m90) REVERT: A 381 TYR cc_start: 0.8188 (m-10) cc_final: 0.7909 (m-10) REVERT: A 395 ASN cc_start: 0.9543 (p0) cc_final: 0.9264 (p0) REVERT: A 548 ASP cc_start: 0.8339 (t70) cc_final: 0.8117 (t70) REVERT: A 766 MET cc_start: 0.8626 (tmm) cc_final: 0.8399 (ppp) REVERT: A 945 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.6904 (p90) REVERT: A 966 MET cc_start: -0.3081 (ttt) cc_final: -0.3488 (ttm) REVERT: A 1015 MET cc_start: 0.7940 (pmm) cc_final: 0.7600 (pmm) REVERT: A 1045 PHE cc_start: 0.9474 (m-80) cc_final: 0.8934 (m-80) REVERT: A 1213 LYS cc_start: 0.8886 (mmpt) cc_final: 0.8630 (mmpt) REVERT: A 1301 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8464 (pt0) REVERT: A 1311 GLN cc_start: 0.8198 (tt0) cc_final: 0.7794 (tt0) outliers start: 20 outliers final: 9 residues processed: 91 average time/residue: 0.8865 time to fit residues: 90.0254 Evaluate side-chains 81 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1307 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 112 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 chunk 97 optimal weight: 0.0770 chunk 82 optimal weight: 1.9990 overall best weight: 1.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.114671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.080030 restraints weight = 21855.897| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.96 r_work: 0.3209 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9747 Z= 0.352 Angle : 0.692 12.130 13243 Z= 0.342 Chirality : 0.046 0.271 1521 Planarity : 0.004 0.053 1694 Dihedral : 5.361 36.229 1438 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.42 % Favored : 95.33 % Rotamer: Outliers : 3.15 % Allowed : 14.49 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.24), residues: 1200 helix: 0.34 (0.39), residues: 182 sheet: -0.02 (0.23), residues: 515 loop : -0.58 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 856 HIS 0.003 0.001 HIS A 855 PHE 0.017 0.002 PHE A1286 TYR 0.018 0.002 TYR A1076 ARG 0.006 0.001 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7939 (m90) cc_final: 0.7360 (m90) REVERT: A 381 TYR cc_start: 0.8166 (m-10) cc_final: 0.7860 (m-10) REVERT: A 395 ASN cc_start: 0.9548 (p0) cc_final: 0.9283 (p0) REVERT: A 548 ASP cc_start: 0.8523 (t70) cc_final: 0.8206 (t0) REVERT: A 872 THR cc_start: 0.8244 (p) cc_final: 0.7808 (p) REVERT: A 945 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7064 (p90) REVERT: A 966 MET cc_start: -0.3074 (ttt) cc_final: -0.3430 (ttm) REVERT: A 1015 MET cc_start: 0.8010 (pmm) cc_final: 0.7659 (pmm) REVERT: A 1045 PHE cc_start: 0.9484 (m-80) cc_final: 0.8971 (m-80) REVERT: A 1213 LYS cc_start: 0.8920 (mmpt) cc_final: 0.8654 (mmpt) REVERT: A 1301 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8542 (pt0) outliers start: 33 outliers final: 17 residues processed: 93 average time/residue: 0.7392 time to fit residues: 78.0782 Evaluate side-chains 84 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1307 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 855 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.114710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.079907 restraints weight = 21972.246| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 4.04 r_work: 0.3217 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9747 Z= 0.299 Angle : 0.676 13.085 13243 Z= 0.333 Chirality : 0.046 0.264 1521 Planarity : 0.004 0.053 1694 Dihedral : 5.256 35.194 1438 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.33 % Favored : 95.42 % Rotamer: Outliers : 2.67 % Allowed : 15.82 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1200 helix: 0.42 (0.39), residues: 187 sheet: -0.03 (0.23), residues: 515 loop : -0.58 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 619 HIS 0.004 0.001 HIS A 75 PHE 0.017 0.002 PHE A 107 TYR 0.015 0.002 TYR A 620 ARG 0.004 0.000 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.9309 (p0) cc_final: 0.8993 (p0) REVERT: A 381 TYR cc_start: 0.8144 (m-10) cc_final: 0.7910 (m-10) REVERT: A 395 ASN cc_start: 0.9557 (p0) cc_final: 0.9296 (p0) REVERT: A 548 ASP cc_start: 0.8485 (t70) cc_final: 0.8228 (t70) REVERT: A 872 THR cc_start: 0.8325 (p) cc_final: 0.7897 (p) REVERT: A 945 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7025 (p90) REVERT: A 966 MET cc_start: -0.2942 (ttt) cc_final: -0.3338 (ttm) REVERT: A 1015 MET cc_start: 0.8020 (pmm) cc_final: 0.7669 (pmm) REVERT: A 1045 PHE cc_start: 0.9456 (m-80) cc_final: 0.8958 (m-80) REVERT: A 1213 LYS cc_start: 0.8916 (mmpt) cc_final: 0.8645 (mmpt) REVERT: A 1301 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8535 (pt0) outliers start: 28 outliers final: 18 residues processed: 96 average time/residue: 0.8048 time to fit residues: 87.9020 Evaluate side-chains 87 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1307 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 73 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.115131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.080256 restraints weight = 21973.948| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 4.16 r_work: 0.3220 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9747 Z= 0.247 Angle : 0.669 12.930 13243 Z= 0.325 Chirality : 0.045 0.255 1521 Planarity : 0.004 0.053 1694 Dihedral : 5.064 34.227 1438 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.33 % Favored : 95.42 % Rotamer: Outliers : 3.34 % Allowed : 16.49 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1200 helix: 0.47 (0.39), residues: 188 sheet: -0.02 (0.23), residues: 516 loop : -0.48 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 619 HIS 0.003 0.001 HIS A 855 PHE 0.016 0.001 PHE A 518 TYR 0.013 0.001 TYR A1076 ARG 0.004 0.000 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 1.385 Fit side-chains revert: symmetry clash REVERT: A 190 GLU cc_start: 0.8816 (mp0) cc_final: 0.8613 (mp0) REVERT: A 381 TYR cc_start: 0.8100 (m-10) cc_final: 0.7829 (m-10) REVERT: A 395 ASN cc_start: 0.9563 (p0) cc_final: 0.9303 (p0) REVERT: A 462 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8435 (mm) REVERT: A 471 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8616 (tm) REVERT: A 548 ASP cc_start: 0.8469 (t70) cc_final: 0.8229 (t70) REVERT: A 872 THR cc_start: 0.8369 (p) cc_final: 0.7987 (p) REVERT: A 945 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.7040 (p90) REVERT: A 966 MET cc_start: -0.2944 (ttt) cc_final: -0.3325 (ttm) REVERT: A 978 PHE cc_start: 0.9040 (t80) cc_final: 0.8696 (t80) REVERT: A 1015 MET cc_start: 0.8019 (pmm) cc_final: 0.7661 (pmm) REVERT: A 1045 PHE cc_start: 0.9441 (m-80) cc_final: 0.8895 (m-80) REVERT: A 1213 LYS cc_start: 0.8934 (mmpt) cc_final: 0.8653 (mmpt) REVERT: A 1260 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7296 (mm-30) outliers start: 35 outliers final: 20 residues processed: 103 average time/residue: 0.8507 time to fit residues: 98.8302 Evaluate side-chains 96 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1307 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 728 GLN A1047 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.112257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.075204 restraints weight = 22293.981| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.83 r_work: 0.3160 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 9747 Z= 0.451 Angle : 0.780 12.899 13243 Z= 0.381 Chirality : 0.049 0.294 1521 Planarity : 0.005 0.053 1694 Dihedral : 5.468 35.452 1438 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.92 % Favored : 94.83 % Rotamer: Outliers : 3.15 % Allowed : 17.35 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.24), residues: 1200 helix: 0.65 (0.40), residues: 182 sheet: -0.18 (0.22), residues: 511 loop : -0.57 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 763 HIS 0.005 0.001 HIS A 855 PHE 0.018 0.002 PHE A1286 TYR 0.017 0.002 TYR A 620 ARG 0.004 0.001 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.9349 (p0) cc_final: 0.9007 (p0) REVERT: A 381 TYR cc_start: 0.8114 (m-10) cc_final: 0.7864 (m-10) REVERT: A 395 ASN cc_start: 0.9566 (p0) cc_final: 0.9315 (p0) REVERT: A 462 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8510 (mm) REVERT: A 471 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8439 (tm) REVERT: A 548 ASP cc_start: 0.8510 (t70) cc_final: 0.8193 (t0) REVERT: A 872 THR cc_start: 0.8521 (p) cc_final: 0.8179 (p) REVERT: A 945 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7202 (p90) REVERT: A 953 MET cc_start: 0.6201 (ptm) cc_final: 0.5514 (ptp) REVERT: A 1005 PHE cc_start: 0.8570 (m-80) cc_final: 0.8266 (m-80) REVERT: A 1015 MET cc_start: 0.8076 (pmm) cc_final: 0.7730 (pmm) REVERT: A 1045 PHE cc_start: 0.9434 (m-80) cc_final: 0.8916 (m-80) REVERT: A 1213 LYS cc_start: 0.8950 (mmpt) cc_final: 0.8672 (mmpt) REVERT: A 1260 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7234 (mm-30) REVERT: A 1301 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8561 (pt0) outliers start: 33 outliers final: 22 residues processed: 101 average time/residue: 0.9961 time to fit residues: 111.9043 Evaluate side-chains 97 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1307 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.114498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.079918 restraints weight = 21920.161| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 4.22 r_work: 0.3205 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9747 Z= 0.235 Angle : 0.705 12.784 13243 Z= 0.340 Chirality : 0.046 0.268 1521 Planarity : 0.004 0.054 1694 Dihedral : 5.169 34.184 1438 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.08 % Favored : 95.67 % Rotamer: Outliers : 2.67 % Allowed : 18.30 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1200 helix: 0.60 (0.40), residues: 184 sheet: -0.11 (0.23), residues: 513 loop : -0.49 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1065 HIS 0.003 0.000 HIS A 855 PHE 0.016 0.002 PHE A 518 TYR 0.013 0.001 TYR A1232 ARG 0.003 0.000 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 TYR cc_start: 0.8098 (m-10) cc_final: 0.7856 (m-10) REVERT: A 395 ASN cc_start: 0.9564 (p0) cc_final: 0.9310 (p0) REVERT: A 471 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8614 (tm) REVERT: A 548 ASP cc_start: 0.8440 (t70) cc_final: 0.8205 (t70) REVERT: A 872 THR cc_start: 0.8393 (p) cc_final: 0.8023 (p) REVERT: A 945 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7085 (p90) REVERT: A 953 MET cc_start: 0.6110 (ptm) cc_final: 0.5457 (ptp) REVERT: A 1005 PHE cc_start: 0.8402 (m-80) cc_final: 0.8052 (m-80) REVERT: A 1015 MET cc_start: 0.8085 (pmm) cc_final: 0.7739 (pmm) REVERT: A 1045 PHE cc_start: 0.9408 (m-80) cc_final: 0.8872 (m-80) REVERT: A 1213 LYS cc_start: 0.8934 (mmpt) cc_final: 0.8668 (mmpt) REVERT: A 1301 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8545 (pt0) outliers start: 28 outliers final: 19 residues processed: 96 average time/residue: 0.8636 time to fit residues: 92.4218 Evaluate side-chains 93 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1307 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 9 optimal weight: 0.7980 chunk 79 optimal weight: 0.0060 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.115068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.078700 restraints weight = 22108.274| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.84 r_work: 0.3235 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9747 Z= 0.220 Angle : 0.708 12.462 13243 Z= 0.340 Chirality : 0.045 0.262 1521 Planarity : 0.004 0.052 1694 Dihedral : 4.982 33.362 1438 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.25 % Favored : 95.58 % Rotamer: Outliers : 2.57 % Allowed : 18.78 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1200 helix: 0.57 (0.40), residues: 185 sheet: -0.00 (0.23), residues: 504 loop : -0.44 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1065 HIS 0.002 0.000 HIS A 855 PHE 0.017 0.002 PHE A 107 TYR 0.012 0.001 TYR A 625 ARG 0.003 0.000 ARG A 610 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.9303 (p0) cc_final: 0.8900 (p0) REVERT: A 250 MET cc_start: 0.7168 (pmm) cc_final: 0.6410 (pmt) REVERT: A 339 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8329 (tmm) REVERT: A 381 TYR cc_start: 0.8091 (m-10) cc_final: 0.7822 (m-10) REVERT: A 395 ASN cc_start: 0.9557 (p0) cc_final: 0.9295 (p0) REVERT: A 462 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8469 (mm) REVERT: A 471 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8600 (tm) REVERT: A 548 ASP cc_start: 0.8359 (t70) cc_final: 0.8152 (t70) REVERT: A 872 THR cc_start: 0.8386 (p) cc_final: 0.7999 (p) REVERT: A 945 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7102 (p90) REVERT: A 953 MET cc_start: 0.6203 (ptm) cc_final: 0.5672 (ptp) REVERT: A 1015 MET cc_start: 0.8068 (pmm) cc_final: 0.7712 (pmm) REVERT: A 1045 PHE cc_start: 0.9368 (m-80) cc_final: 0.8823 (m-80) REVERT: A 1213 LYS cc_start: 0.8943 (mmpt) cc_final: 0.8666 (mmpt) REVERT: A 1301 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8520 (pt0) outliers start: 27 outliers final: 19 residues processed: 97 average time/residue: 0.8289 time to fit residues: 89.8538 Evaluate side-chains 98 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 945 TYR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1307 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 104 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.112192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.075687 restraints weight = 22338.049| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.72 r_work: 0.3193 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 9747 Z= 0.374 Angle : 0.760 12.817 13243 Z= 0.369 Chirality : 0.048 0.296 1521 Planarity : 0.005 0.054 1694 Dihedral : 5.241 34.579 1438 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.67 % Favored : 95.08 % Rotamer: Outliers : 2.96 % Allowed : 18.59 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.25), residues: 1200 helix: 0.41 (0.39), residues: 193 sheet: -0.13 (0.23), residues: 511 loop : -0.55 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1065 HIS 0.004 0.001 HIS A 855 PHE 0.016 0.002 PHE A 518 TYR 0.012 0.002 TYR A1076 ARG 0.003 0.000 ARG A 610 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6497.37 seconds wall clock time: 116 minutes 17.91 seconds (6977.91 seconds total)