Starting phenix.real_space_refine on Thu Jul 2 06:39:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v6z_31754/07_2026/7v6z_31754.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v6z_31754/07_2026/7v6z_31754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7v6z_31754/07_2026/7v6z_31754.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v6z_31754/07_2026/7v6z_31754.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v6z_31754/07_2026/7v6z_31754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v6z_31754/07_2026/7v6z_31754.map" model { file = "/net/cci-nas-00/data/ceres_data/7v6z_31754/07_2026/7v6z_31754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v6z_31754/07_2026/7v6z_31754.cif" } resolution = 3.64 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= 0.002 sd= 0.048 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 32 5.16 5 C 4626 2.51 5 N 1195 2.21 5 O 1229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s 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: 7082 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 6984 Classifications: {'peptide': 1008} Incomplete info: {'truncation_to_alanine': 260} Link IDs: {'PTRANS': 45, 'TRANS': 962} Chain breaks: 3 Unresolved non-hydrogen bonds: 1021 Unresolved non-hydrogen angles: 1278 Unresolved non-hydrogen dihedrals: 859 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'HIS:plan': 3, 'ARG:plan': 18, 'TYR:plan': 12, 'ASP:plan': 36, 'GLU:plan': 42, 'GLN:plan1': 15, 'PHE:plan': 9, 'ASN:plan1': 12, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 660 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 chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'CLR': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.24, per 1000 atoms: 0.18 Number of scatterers: 7082 At special positions: 0 Unit cell: (88.56, 88.56, 132.84, 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 32 16.00 O 1229 8.00 N 1195 7.00 C 4626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 212 " distance=2.05 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 290 " distance=2.02 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-ASN " NAG A1201 " - " ASN A 127 " " NAG A1202 " - " ASN A 335 " " NAG A1203 " - " ASN A 400 " " NAG B 1 " - " ASN A 986 " Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 327.0 milliseconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 4 sheets defined 66.4% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 60 through 83 Processing helix chain 'A' and resid 83 through 99 removed outlier: 3.831A pdb=" N LEU A 88 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 120 through 133 Processing helix chain 'A' and resid 157 through 173 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 222 through 228 removed outlier: 4.124A pdb=" N LYS A 226 " --> pdb=" O TRP A 222 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 222 through 228' Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.561A pdb=" N ARG A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 354 through 363 removed outlier: 3.838A pdb=" N ARG A 363 " --> pdb=" O TYR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 397 removed outlier: 3.586A pdb=" N ALA A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 removed outlier: 3.649A pdb=" N LEU A 413 " --> pdb=" O THR A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 444 Processing helix chain 'A' and resid 452 through 478 Processing helix chain 'A' and resid 482 through 514 removed outlier: 3.865A pdb=" N LEU A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 3.683A pdb=" N LEU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 549 removed outlier: 4.354A pdb=" N ALA A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 591 removed outlier: 3.891A pdb=" N PHE A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 717 through 732 Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 732 through 756 removed outlier: 3.753A pdb=" N ILE A 740 " --> pdb=" O LYS A 736 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG A 756 " --> pdb=" O TYR A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 767 removed outlier: 4.142A pdb=" N ILE A 766 " --> pdb=" O ASP A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 784 Processing helix chain 'A' and resid 802 through 815 removed outlier: 3.963A pdb=" N TYR A 806 " --> pdb=" O GLN A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 852 Processing helix chain 'A' and resid 863 through 874 Processing helix chain 'A' and resid 874 through 880 Processing helix chain 'A' and resid 904 through 915 Processing helix chain 'A' and resid 916 through 924 removed outlier: 4.257A pdb=" N TYR A 920 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 924 " --> pdb=" O TYR A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 990 Processing helix chain 'A' and resid 999 through 1034 removed outlier: 3.571A pdb=" N PHE A1003 " --> pdb=" O TYR A 999 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A1005 " --> pdb=" O PHE A1001 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLN A1006 " --> pdb=" O LEU A1002 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N TYR A1007 " --> pdb=" O PHE A1003 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A1008 " --> pdb=" O TRP A1004 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A1009 " --> pdb=" O GLU A1005 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG A1011 " --> pdb=" O TYR A1007 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N HIS A1012 " --> pdb=" O ILE A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1061 Processing helix chain 'A' and resid 1065 through 1092 removed outlier: 3.608A pdb=" N PHE A1082 " --> pdb=" O ILE A1078 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE A1090 " --> pdb=" O VAL A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1127 removed outlier: 3.520A pdb=" N MET A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ALA A1110 " --> pdb=" O GLU A1106 " (cutoff:3.500A) Proline residue: A1111 - end of helix removed outlier: 3.555A pdb=" N GLY A1122 " --> pdb=" O SER A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1152 removed outlier: 3.742A pdb=" N VAL A1141 " --> pdb=" O TYR A1137 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A1142 " --> pdb=" O PHE A1138 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A1144 " --> pdb=" O ALA A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1164 Proline residue: A1158 - end of helix removed outlier: 3.543A pdb=" N PHE A1163 " --> pdb=" O VAL A1159 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 215 Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 215 Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA4, first strand: chain 'A' and resid 957 through 965 485 hydrogen bonds defined for protein. 1410 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: 1.13 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1118 1.31 - 1.44: 2015 1.44 - 1.57: 4064 1.57 - 1.70: 1 1.70 - 1.83: 50 Bond restraints: 7248 Sorted by residual: bond pdb=" CA ALA A 171 " pdb=" C ALA A 171 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.26e-02 6.30e+03 4.50e+01 bond pdb=" C VAL A 393 " pdb=" O VAL A 393 " ideal model delta sigma weight residual 1.237 1.313 -0.076 1.17e-02 7.31e+03 4.24e+01 bond pdb=" CA TYR A 774 " pdb=" C TYR A 774 " ideal model delta sigma weight residual 1.524 1.442 0.082 1.29e-02 6.01e+03 4.01e+01 bond pdb=" N SER A 172 " pdb=" CA SER A 172 " ideal model delta sigma weight residual 1.459 1.386 0.073 1.21e-02 6.83e+03 3.64e+01 bond pdb=" CA ALA A 921 " pdb=" C ALA A 921 " ideal model delta sigma weight residual 1.523 1.449 0.074 1.30e-02 5.92e+03 3.27e+01 ... (remaining 7243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 8964 2.46 - 4.92: 773 4.92 - 7.38: 173 7.38 - 9.84: 50 9.84 - 12.30: 12 Bond angle restraints: 9972 Sorted by residual: angle pdb=" N LYS A 297 " pdb=" CA LYS A 297 " pdb=" C LYS A 297 " ideal model delta sigma weight residual 111.28 99.40 11.88 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N LEU A 594 " pdb=" CA LEU A 594 " pdb=" C LEU A 594 " ideal model delta sigma weight residual 111.28 122.43 -11.15 1.09e+00 8.42e-01 1.05e+02 angle pdb=" N TYR A 210 " pdb=" CA TYR A 210 " pdb=" C TYR A 210 " ideal model delta sigma weight residual 109.72 98.10 11.62 1.25e+00 6.40e-01 8.65e+01 angle pdb=" N SER A 40 " pdb=" CA SER A 40 " pdb=" C SER A 40 " ideal model delta sigma weight residual 111.74 99.44 12.30 1.35e+00 5.49e-01 8.30e+01 angle pdb=" N PHE A 729 " pdb=" CA PHE A 729 " pdb=" C PHE A 729 " ideal model delta sigma weight residual 111.07 102.04 9.03 1.07e+00 8.73e-01 7.12e+01 ... (remaining 9967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3797 17.94 - 35.89: 255 35.89 - 53.83: 80 53.83 - 71.77: 17 71.77 - 89.71: 3 Dihedral angle restraints: 4152 sinusoidal: 1225 harmonic: 2927 Sorted by residual: dihedral pdb=" CB CYS A 282 " pdb=" SG CYS A 282 " pdb=" SG CYS A 290 " pdb=" CB CYS A 290 " ideal model delta sinusoidal sigma weight residual 93.00 -177.29 -89.71 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS A 189 " pdb=" SG CYS A 189 " pdb=" SG CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sinusoidal sigma weight residual -86.00 -36.82 -49.18 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" C ILE A 777 " pdb=" N ILE A 777 " pdb=" CA ILE A 777 " pdb=" CB ILE A 777 " ideal model delta harmonic sigma weight residual -122.00 -136.26 14.26 0 2.50e+00 1.60e-01 3.25e+01 ... (remaining 4149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 975 0.120 - 0.239: 206 0.239 - 0.359: 49 0.359 - 0.479: 13 0.479 - 0.598: 4 Chirality restraints: 1247 Sorted by residual: chirality pdb=" CA TRP A1004 " pdb=" N TRP A1004 " pdb=" C TRP A1004 " pdb=" CB TRP A1004 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.94e+00 chirality pdb=" CA ILE A 777 " pdb=" N ILE A 777 " pdb=" C ILE A 777 " pdb=" CB ILE A 777 " both_signs ideal model delta sigma weight residual False 2.43 1.90 0.53 2.00e-01 2.50e+01 7.08e+00 chirality pdb=" CA LEU A 594 " pdb=" N LEU A 594 " pdb=" C LEU A 594 " pdb=" CB LEU A 594 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.84e+00 ... (remaining 1244 not shown) Planarity restraints: 1255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1157 " -0.098 5.00e-02 4.00e+02 1.47e-01 3.47e+01 pdb=" N PRO A1158 " 0.255 5.00e-02 4.00e+02 pdb=" CA PRO A1158 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO A1158 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1153 " 0.023 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C GLY A1153 " -0.079 2.00e-02 2.50e+03 pdb=" O GLY A1153 " 0.029 2.00e-02 2.50e+03 pdb=" N LEU A1154 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 294 " 0.069 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO A 295 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.060 5.00e-02 4.00e+02 ... (remaining 1252 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2308 2.81 - 3.33: 7578 3.33 - 3.85: 11798 3.85 - 4.38: 13600 4.38 - 4.90: 21272 Nonbonded interactions: 56556 Sorted by model distance: nonbonded pdb=" O GLY A1115 " pdb=" OG SER A1118 " model vdw 2.282 3.040 nonbonded pdb=" CG2 ILE A1071 " pdb=" CD1 ILE A1071 " model vdw 2.314 3.104 nonbonded pdb=" N SER A1065 " pdb=" O SER A1065 " model vdw 2.354 2.496 nonbonded pdb=" N ASP A 591 " pdb=" O ASP A 591 " model vdw 2.410 2.496 nonbonded pdb=" N ARG A 772 " pdb=" N GLU A 773 " model vdw 2.436 2.560 ... (remaining 56551 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.170 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.560 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 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 : 0.012 0.085 7256 Z= 0.880 Angle : 1.670 12.301 9993 Z= 1.164 Chirality : 0.114 0.598 1247 Planarity : 0.010 0.147 1251 Dihedral : 14.439 88.724 2251 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.20 % Favored : 96.50 % Rotamer: Outliers : 10.76 % Allowed : 8.91 % Favored : 80.34 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.27), residues: 1000 helix: 2.51 (0.22), residues: 581 sheet: 0.56 (0.75), residues: 47 loop : -1.15 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 280 TYR 0.035 0.003 TYR A 774 PHE 0.023 0.002 PHE A1131 TRP 0.019 0.002 TRP A 837 HIS 0.007 0.002 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.01177 / 0.88 ( 7248) covalent geometry : angle 1.66642 / 1.16 ( 9972) SS BOND : bond 0.01264 / 0.65 ( 3) SS BOND : angle 1.93037 / 1.05 ( 6) hydrogen bonds : bond 0.17478 / 12.13 ( 483) hydrogen bonds : angle 6.92692 / 5.12 ( 1410) link_BETA1-4 : bond 0.00463 / 0.24 ( 1) link_BETA1-4 : angle 1.29096 / 0.66 ( 3) link_NAG-ASN : bond 0.01855 / 0.97 ( 4) link_NAG-ASN : angle 3.63763 / 1.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 204 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 PHE cc_start: 0.7940 (t80) cc_final: 0.7585 (t80) REVERT: A 771 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7236 (m) REVERT: A 829 MET cc_start: 0.7569 (ptp) cc_final: 0.7362 (ptp) REVERT: A 984 CYS cc_start: 0.7857 (m) cc_final: 0.7548 (t) REVERT: A 1099 HIS cc_start: 0.6329 (OUTLIER) cc_final: 0.5892 (t70) outliers start: 64 outliers final: 22 residues processed: 243 average time/residue: 0.0532 time to fit residues: 18.4067 Evaluate side-chains 162 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1150 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 GLN A 154 ASN A 175 HIS ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 296 ASN A 386 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN A1006 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.162085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.126850 restraints weight = 11853.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.131356 restraints weight = 5886.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.134406 restraints weight = 3826.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.135896 restraints weight = 2946.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.137398 restraints weight = 2553.382| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7256 Z= 0.188 Angle : 0.732 7.422 9993 Z= 0.385 Chirality : 0.046 0.244 1247 Planarity : 0.006 0.062 1251 Dihedral : 7.728 56.126 1105 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.80 % Favored : 97.10 % Rotamer: Outliers : 8.57 % Allowed : 16.13 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.26), residues: 1000 helix: 1.72 (0.21), residues: 591 sheet: -0.29 (0.70), residues: 49 loop : -1.15 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 124 TYR 0.025 0.002 TYR A 179 PHE 0.019 0.002 PHE A 786 TRP 0.019 0.002 TRP A 837 HIS 0.007 0.001 HIS A 809 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 ( 7248) covalent geometry : angle 0.72718 / 0.38 ( 9972) SS BOND : bond 0.00136 / 0.07 ( 3) SS BOND : angle 0.21713 / 0.12 ( 6) hydrogen bonds : bond 0.06114 / 4.32 ( 483) hydrogen bonds : angle 5.09001 / 3.79 ( 1410) link_BETA1-4 : bond 0.00198 / 0.10 ( 1) link_BETA1-4 : angle 1.05438 / 0.45 ( 3) link_NAG-ASN : bond 0.00453 / 0.24 ( 4) link_NAG-ASN : angle 2.48334 / 1.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7062 (pt0) REVERT: A 316 LEU cc_start: 0.7680 (mt) cc_final: 0.7457 (mp) REVERT: A 403 GLN cc_start: 0.6520 (mp10) cc_final: 0.6127 (tm-30) REVERT: A 526 CYS cc_start: 0.6502 (OUTLIER) cc_final: 0.6038 (t) REVERT: A 573 MET cc_start: 0.8204 (tmm) cc_final: 0.7869 (tmm) REVERT: A 832 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7494 (m170) REVERT: A 972 ASP cc_start: 0.8132 (m-30) cc_final: 0.7737 (t0) REVERT: A 984 CYS cc_start: 0.7805 (m) cc_final: 0.7259 (t) REVERT: A 1099 HIS cc_start: 0.5963 (OUTLIER) cc_final: 0.5417 (t70) outliers start: 51 outliers final: 32 residues processed: 187 average time/residue: 0.0437 time to fit residues: 12.5490 Evaluate side-chains 168 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.157623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.121913 restraints weight = 12106.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.126125 restraints weight = 6141.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.128908 restraints weight = 4062.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.130703 restraints weight = 3170.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.131441 restraints weight = 2723.347| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7256 Z= 0.207 Angle : 0.726 9.721 9993 Z= 0.377 Chirality : 0.045 0.193 1247 Planarity : 0.006 0.054 1251 Dihedral : 6.759 53.380 1089 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.50 % Favored : 96.40 % Rotamer: Outliers : 11.09 % Allowed : 17.31 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.26), residues: 1000 helix: 1.46 (0.21), residues: 594 sheet: -0.77 (0.69), residues: 49 loop : -1.13 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 756 TYR 0.026 0.002 TYR A 179 PHE 0.018 0.002 PHE A 408 TRP 0.017 0.002 TRP A 837 HIS 0.009 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 ( 7248) covalent geometry : angle 0.72147 / 0.38 ( 9972) SS BOND : bond 0.00337 / 0.16 ( 3) SS BOND : angle 0.90957 / 0.42 ( 6) hydrogen bonds : bond 0.05475 / 3.86 ( 483) hydrogen bonds : angle 4.95131 / 3.71 ( 1410) link_BETA1-4 : bond 0.00494 / 0.26 ( 1) link_BETA1-4 : angle 0.98802 / 0.49 ( 3) link_NAG-ASN : bond 0.00147 / 0.08 ( 4) link_NAG-ASN : angle 2.39997 / 1.30 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 143 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7235 (pt0) REVERT: A 408 PHE cc_start: 0.7766 (t80) cc_final: 0.7462 (t80) REVERT: A 473 LEU cc_start: 0.8566 (tp) cc_final: 0.8239 (tt) REVERT: A 504 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8615 (tt) REVERT: A 526 CYS cc_start: 0.6587 (OUTLIER) cc_final: 0.6142 (t) REVERT: A 573 MET cc_start: 0.8274 (tmm) cc_final: 0.7989 (tmm) REVERT: A 984 CYS cc_start: 0.7913 (m) cc_final: 0.7213 (t) REVERT: A 1072 LEU cc_start: 0.5969 (OUTLIER) cc_final: 0.5564 (mp) REVERT: A 1099 HIS cc_start: 0.5985 (OUTLIER) cc_final: 0.5463 (t70) outliers start: 66 outliers final: 41 residues processed: 186 average time/residue: 0.0422 time to fit residues: 12.1140 Evaluate side-chains 176 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 130 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1013 TRP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1147 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 66 optimal weight: 0.0170 chunk 2 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.161204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.126213 restraints weight = 12040.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.130740 restraints weight = 5878.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.133753 restraints weight = 3795.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.135130 restraints weight = 2897.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.135149 restraints weight = 2521.116| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7256 Z= 0.142 Angle : 0.672 11.946 9993 Z= 0.336 Chirality : 0.043 0.206 1247 Planarity : 0.005 0.049 1251 Dihedral : 6.345 52.852 1087 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.90 % Favored : 97.00 % Rotamer: Outliers : 6.72 % Allowed : 23.03 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.27), residues: 1000 helix: 1.67 (0.21), residues: 595 sheet: -0.52 (0.77), residues: 44 loop : -1.10 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 756 TYR 0.019 0.002 TYR A 920 PHE 0.014 0.001 PHE A1133 TRP 0.017 0.001 TRP A 837 HIS 0.007 0.001 HIS A 809 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 7248) covalent geometry : angle 0.66795 / 0.33 ( 9972) SS BOND : bond 0.00476 / 0.23 ( 3) SS BOND : angle 0.80011 / 0.35 ( 6) hydrogen bonds : bond 0.04664 / 3.28 ( 483) hydrogen bonds : angle 4.71396 / 3.52 ( 1410) link_BETA1-4 : bond 0.00343 / 0.18 ( 1) link_BETA1-4 : angle 0.99652 / 0.46 ( 3) link_NAG-ASN : bond 0.00228 / 0.11 ( 4) link_NAG-ASN : angle 2.21368 / 1.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 403 GLN cc_start: 0.6721 (tm-30) cc_final: 0.6211 (mp10) REVERT: A 408 PHE cc_start: 0.7672 (t80) cc_final: 0.7415 (t80) REVERT: A 422 ASP cc_start: 0.7799 (m-30) cc_final: 0.7440 (m-30) REVERT: A 526 CYS cc_start: 0.6528 (OUTLIER) cc_final: 0.6105 (t) REVERT: A 573 MET cc_start: 0.8259 (tmm) cc_final: 0.8018 (tmm) REVERT: A 774 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.6779 (t80) REVERT: A 972 ASP cc_start: 0.8137 (m-30) cc_final: 0.7822 (t0) REVERT: A 984 CYS cc_start: 0.7920 (m) cc_final: 0.7246 (t) REVERT: A 1099 HIS cc_start: 0.5943 (OUTLIER) cc_final: 0.5417 (t70) outliers start: 40 outliers final: 30 residues processed: 168 average time/residue: 0.0467 time to fit residues: 12.0023 Evaluate side-chains 167 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 788 ASN Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1032 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 0.0000 chunk 56 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.161047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.125693 restraints weight = 12053.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.130045 restraints weight = 5958.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.132937 restraints weight = 3879.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.134250 restraints weight = 2999.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.135172 restraints weight = 2621.874| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7256 Z= 0.143 Angle : 0.668 10.392 9993 Z= 0.331 Chirality : 0.043 0.244 1247 Planarity : 0.005 0.048 1251 Dihedral : 6.025 52.295 1084 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.50 % Favored : 96.40 % Rotamer: Outliers : 7.06 % Allowed : 24.03 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.27), residues: 1000 helix: 1.69 (0.21), residues: 594 sheet: -0.70 (0.76), residues: 44 loop : -1.11 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 756 TYR 0.018 0.002 TYR A 190 PHE 0.017 0.001 PHE A 786 TRP 0.025 0.002 TRP A1037 HIS 0.015 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 7248) covalent geometry : angle 0.66372 / 0.33 ( 9972) SS BOND : bond 0.00049 / 0.03 ( 3) SS BOND : angle 1.55945 / 0.79 ( 6) hydrogen bonds : bond 0.04494 / 3.14 ( 483) hydrogen bonds : angle 4.67182 / 3.49 ( 1410) link_BETA1-4 : bond 0.00476 / 0.25 ( 1) link_BETA1-4 : angle 0.99494 / 0.46 ( 3) link_NAG-ASN : bond 0.00228 / 0.11 ( 4) link_NAG-ASN : angle 2.11100 / 1.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 403 GLN cc_start: 0.6695 (tm-30) cc_final: 0.6110 (mp-120) REVERT: A 408 PHE cc_start: 0.7672 (t80) cc_final: 0.7432 (t80) REVERT: A 475 SER cc_start: 0.8235 (m) cc_final: 0.7990 (p) REVERT: A 526 CYS cc_start: 0.6394 (OUTLIER) cc_final: 0.5895 (t) REVERT: A 774 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.6783 (t80) REVERT: A 783 TYR cc_start: 0.7839 (m-80) cc_final: 0.7559 (m-10) REVERT: A 972 ASP cc_start: 0.8139 (m-30) cc_final: 0.7854 (t0) REVERT: A 984 CYS cc_start: 0.7875 (m) cc_final: 0.7312 (t) REVERT: A 1099 HIS cc_start: 0.5977 (OUTLIER) cc_final: 0.5496 (t70) REVERT: A 1144 ILE cc_start: 0.8279 (tt) cc_final: 0.7912 (pt) outliers start: 42 outliers final: 35 residues processed: 164 average time/residue: 0.0443 time to fit residues: 11.1612 Evaluate side-chains 172 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1032 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 0.0470 chunk 49 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** 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 = 0.4248 r_free = 0.4248 target = 0.160613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.125290 restraints weight = 12144.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.129576 restraints weight = 6023.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.132478 restraints weight = 3949.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.133808 restraints weight = 3054.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.135192 restraints weight = 2667.365| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7256 Z= 0.138 Angle : 0.652 10.488 9993 Z= 0.323 Chirality : 0.042 0.244 1247 Planarity : 0.005 0.047 1251 Dihedral : 5.870 51.654 1083 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.60 % Favored : 96.30 % Rotamer: Outliers : 9.08 % Allowed : 22.52 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.27), residues: 1000 helix: 1.69 (0.21), residues: 594 sheet: -0.72 (0.76), residues: 44 loop : -1.10 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 756 TYR 0.017 0.001 TYR A 190 PHE 0.013 0.001 PHE A 408 TRP 0.020 0.001 TRP A1037 HIS 0.014 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 7248) covalent geometry : angle 0.64739 / 0.32 ( 9972) SS BOND : bond 0.00172 / 0.08 ( 3) SS BOND : angle 1.47185 / 0.81 ( 6) hydrogen bonds : bond 0.04264 / 2.98 ( 483) hydrogen bonds : angle 4.63262 / 3.45 ( 1410) link_BETA1-4 : bond 0.00393 / 0.21 ( 1) link_BETA1-4 : angle 0.99262 / 0.47 ( 3) link_NAG-ASN : bond 0.00220 / 0.11 ( 4) link_NAG-ASN : angle 2.00318 / 1.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 140 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ILE cc_start: 0.8832 (mt) cc_final: 0.8627 (mp) REVERT: A 321 MET cc_start: 0.8330 (ptp) cc_final: 0.8129 (ptp) REVERT: A 403 GLN cc_start: 0.6614 (tm-30) cc_final: 0.6131 (mp10) REVERT: A 408 PHE cc_start: 0.7618 (t80) cc_final: 0.7410 (t80) REVERT: A 473 LEU cc_start: 0.8554 (tp) cc_final: 0.8283 (tp) REVERT: A 475 SER cc_start: 0.8234 (m) cc_final: 0.7901 (p) REVERT: A 569 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7538 (m-10) REVERT: A 774 TYR cc_start: 0.7646 (OUTLIER) cc_final: 0.6731 (t80) REVERT: A 972 ASP cc_start: 0.8115 (m-30) cc_final: 0.7849 (t0) REVERT: A 984 CYS cc_start: 0.7957 (m) cc_final: 0.7592 (t) REVERT: A 1009 SER cc_start: 0.8001 (OUTLIER) cc_final: 0.7790 (p) REVERT: A 1099 HIS cc_start: 0.5866 (OUTLIER) cc_final: 0.5418 (t70) REVERT: A 1144 ILE cc_start: 0.8242 (tt) cc_final: 0.7944 (pt) outliers start: 54 outliers final: 35 residues processed: 174 average time/residue: 0.0429 time to fit residues: 11.5834 Evaluate side-chains 170 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1032 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 30.0000 chunk 12 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.157663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.122460 restraints weight = 12163.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.126650 restraints weight = 6157.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.129477 restraints weight = 4039.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.130837 restraints weight = 3117.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.132259 restraints weight = 2714.219| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7256 Z= 0.168 Angle : 0.678 8.877 9993 Z= 0.338 Chirality : 0.043 0.238 1247 Planarity : 0.005 0.046 1251 Dihedral : 5.817 51.379 1082 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.30 % Favored : 96.60 % Rotamer: Outliers : 7.73 % Allowed : 24.37 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.27), residues: 1000 helix: 1.56 (0.21), residues: 595 sheet: -0.65 (0.78), residues: 44 loop : -1.18 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 756 TYR 0.020 0.002 TYR A 920 PHE 0.018 0.002 PHE A 408 TRP 0.016 0.001 TRP A1037 HIS 0.006 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 7248) covalent geometry : angle 0.67384 / 0.34 ( 9972) SS BOND : bond 0.00131 / 0.07 ( 3) SS BOND : angle 1.31116 / 0.72 ( 6) hydrogen bonds : bond 0.04509 / 3.13 ( 483) hydrogen bonds : angle 4.65689 / 3.46 ( 1410) link_BETA1-4 : bond 0.00440 / 0.23 ( 1) link_BETA1-4 : angle 0.96992 / 0.47 ( 3) link_NAG-ASN : bond 0.00172 / 0.09 ( 4) link_NAG-ASN : angle 2.00449 / 1.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 403 GLN cc_start: 0.6643 (tm-30) cc_final: 0.6258 (mp-120) REVERT: A 475 SER cc_start: 0.8273 (m) cc_final: 0.7922 (p) REVERT: A 569 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7652 (m-10) REVERT: A 774 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.6684 (t80) REVERT: A 984 CYS cc_start: 0.8055 (m) cc_final: 0.7587 (t) REVERT: A 1099 HIS cc_start: 0.5934 (OUTLIER) cc_final: 0.5485 (t70) outliers start: 46 outliers final: 36 residues processed: 166 average time/residue: 0.0425 time to fit residues: 10.7632 Evaluate side-chains 168 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1032 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 30.0000 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 9 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** 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 = 0.4241 r_free = 0.4241 target = 0.159646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.124896 restraints weight = 12199.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.129180 restraints weight = 6074.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.132051 restraints weight = 3958.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.133953 restraints weight = 3041.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.134487 restraints weight = 2585.811| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7256 Z= 0.138 Angle : 0.665 10.456 9993 Z= 0.329 Chirality : 0.042 0.277 1247 Planarity : 0.005 0.045 1251 Dihedral : 5.557 50.963 1080 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.50 % Rotamer: Outliers : 7.06 % Allowed : 26.05 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.27), residues: 1000 helix: 1.69 (0.21), residues: 595 sheet: -0.54 (0.78), residues: 44 loop : -1.14 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 588 TYR 0.024 0.001 TYR A 920 PHE 0.022 0.002 PHE A1133 TRP 0.016 0.001 TRP A1037 HIS 0.006 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 7248) covalent geometry : angle 0.66153 / 0.33 ( 9972) SS BOND : bond 0.00474 / 0.23 ( 3) SS BOND : angle 1.31275 / 0.73 ( 6) hydrogen bonds : bond 0.04155 / 2.91 ( 483) hydrogen bonds : angle 4.58334 / 3.40 ( 1410) link_BETA1-4 : bond 0.00434 / 0.23 ( 1) link_BETA1-4 : angle 0.96569 / 0.45 ( 3) link_NAG-ASN : bond 0.00206 / 0.10 ( 4) link_NAG-ASN : angle 1.90264 / 1.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 403 GLN cc_start: 0.6565 (tm-30) cc_final: 0.6255 (mp10) REVERT: A 475 SER cc_start: 0.8179 (m) cc_final: 0.7881 (p) REVERT: A 569 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7656 (m-10) REVERT: A 573 MET cc_start: 0.8257 (tmm) cc_final: 0.7935 (tmm) REVERT: A 774 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6555 (t80) REVERT: A 972 ASP cc_start: 0.8108 (m-30) cc_final: 0.7889 (t0) REVERT: A 984 CYS cc_start: 0.8079 (m) cc_final: 0.7667 (t) REVERT: A 1144 ILE cc_start: 0.8244 (tt) cc_final: 0.8008 (pt) outliers start: 42 outliers final: 37 residues processed: 163 average time/residue: 0.0370 time to fit residues: 9.2730 Evaluate side-chains 170 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1032 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 54 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 0.0470 chunk 73 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** 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 = 0.4254 r_free = 0.4254 target = 0.160737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.125929 restraints weight = 12027.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.130088 restraints weight = 6030.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.132986 restraints weight = 3992.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.134561 restraints weight = 3084.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.135933 restraints weight = 2660.521| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7256 Z= 0.131 Angle : 0.661 9.981 9993 Z= 0.325 Chirality : 0.041 0.271 1247 Planarity : 0.005 0.045 1251 Dihedral : 5.297 49.875 1078 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.50 % Favored : 96.40 % Rotamer: Outliers : 7.06 % Allowed : 27.39 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.27), residues: 1000 helix: 1.70 (0.21), residues: 602 sheet: -0.34 (0.79), residues: 44 loop : -1.17 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 756 TYR 0.023 0.001 TYR A 920 PHE 0.023 0.001 PHE A 502 TRP 0.016 0.001 TRP A1037 HIS 0.005 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 7248) covalent geometry : angle 0.65819 / 0.32 ( 9972) SS BOND : bond 0.00135 / 0.07 ( 3) SS BOND : angle 1.10561 / 0.61 ( 6) hydrogen bonds : bond 0.03990 / 2.79 ( 483) hydrogen bonds : angle 4.53265 / 3.35 ( 1410) link_BETA1-4 : bond 0.00612 / 0.32 ( 1) link_BETA1-4 : angle 1.00302 / 0.46 ( 3) link_NAG-ASN : bond 0.00249 / 0.12 ( 4) link_NAG-ASN : angle 1.81782 / 1.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6159 (t80) REVERT: A 403 GLN cc_start: 0.6512 (tm-30) cc_final: 0.6251 (mp10) REVERT: A 475 SER cc_start: 0.8168 (m) cc_final: 0.7878 (p) REVERT: A 573 MET cc_start: 0.8200 (tmm) cc_final: 0.7898 (tmm) REVERT: A 774 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6514 (t80) REVERT: A 984 CYS cc_start: 0.8006 (m) cc_final: 0.7577 (t) REVERT: A 1144 ILE cc_start: 0.8172 (tt) cc_final: 0.7967 (pt) outliers start: 42 outliers final: 34 residues processed: 170 average time/residue: 0.0434 time to fit residues: 11.3572 Evaluate side-chains 170 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1032 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 HIS ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.160561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.125691 restraints weight = 12212.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.129903 restraints weight = 6158.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.132791 restraints weight = 4030.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.134322 restraints weight = 3120.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.135645 restraints weight = 2700.953| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7256 Z= 0.139 Angle : 0.685 10.237 9993 Z= 0.335 Chirality : 0.043 0.296 1247 Planarity : 0.005 0.045 1251 Dihedral : 5.295 49.549 1078 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.50 % Rotamer: Outliers : 6.39 % Allowed : 28.24 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.27), residues: 1000 helix: 1.65 (0.21), residues: 601 sheet: -0.31 (0.79), residues: 44 loop : -1.21 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 427 TYR 0.023 0.002 TYR A 920 PHE 0.028 0.002 PHE A 502 TRP 0.015 0.001 TRP A1037 HIS 0.005 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 7248) covalent geometry : angle 0.68295 / 0.34 ( 9972) SS BOND : bond 0.00079 / 0.04 ( 3) SS BOND : angle 0.91341 / 0.50 ( 6) hydrogen bonds : bond 0.04084 / 2.87 ( 483) hydrogen bonds : angle 4.54237 / 3.38 ( 1410) link_BETA1-4 : bond 0.00485 / 0.26 ( 1) link_BETA1-4 : angle 1.06197 / 0.51 ( 3) link_NAG-ASN : bond 0.00311 / 0.16 ( 4) link_NAG-ASN : angle 1.71555 / 0.97 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 362 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.6142 (t80) REVERT: A 403 GLN cc_start: 0.6507 (tm-30) cc_final: 0.6263 (mp10) REVERT: A 475 SER cc_start: 0.8149 (m) cc_final: 0.7875 (p) REVERT: A 561 LEU cc_start: 0.8761 (mt) cc_final: 0.8543 (mt) REVERT: A 573 MET cc_start: 0.8185 (tmm) cc_final: 0.7876 (tmm) REVERT: A 774 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.6560 (t80) REVERT: A 984 CYS cc_start: 0.8150 (m) cc_final: 0.7800 (t) outliers start: 38 outliers final: 33 residues processed: 163 average time/residue: 0.0395 time to fit residues: 10.0050 Evaluate side-chains 172 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1032 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 6 optimal weight: 0.0270 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** 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 = 0.4255 r_free = 0.4255 target = 0.161144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.126683 restraints weight = 12175.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.131031 restraints weight = 6072.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.133993 restraints weight = 3945.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.135564 restraints weight = 3010.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.136963 restraints weight = 2590.516| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7256 Z= 0.133 Angle : 0.692 10.287 9993 Z= 0.338 Chirality : 0.043 0.287 1247 Planarity : 0.005 0.045 1251 Dihedral : 5.265 49.008 1078 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.50 % Rotamer: Outliers : 5.88 % Allowed : 29.41 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.27), residues: 1000 helix: 1.66 (0.21), residues: 601 sheet: -0.14 (0.80), residues: 44 loop : -1.21 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 756 TYR 0.022 0.001 TYR A 920 PHE 0.024 0.002 PHE A 960 TRP 0.014 0.001 TRP A1037 HIS 0.005 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 7248) covalent geometry : angle 0.68922 / 0.34 ( 9972) SS BOND : bond 0.00116 / 0.06 ( 3) SS BOND : angle 0.98086 / 0.53 ( 6) hydrogen bonds : bond 0.04048 / 2.84 ( 483) hydrogen bonds : angle 4.50971 / 3.36 ( 1410) link_BETA1-4 : bond 0.00576 / 0.30 ( 1) link_BETA1-4 : angle 1.04082 / 0.49 ( 3) link_NAG-ASN : bond 0.00277 / 0.14 ( 4) link_NAG-ASN : angle 1.67013 / 0.94 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1133.58 seconds wall clock time: 20 minutes 12.68 seconds (1212.68 seconds total)