Starting phenix.real_space_refine on Sat Jul 4 05:56:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kwb_62606/07_2026/9kwb_62606_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kwb_62606/07_2026/9kwb_62606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kwb_62606/07_2026/9kwb_62606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kwb_62606/07_2026/9kwb_62606.map" model { file = "/net/cci-nas-00/data/ceres_data/9kwb_62606/07_2026/9kwb_62606_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kwb_62606/07_2026/9kwb_62606_neut.cif" } resolution = 2.6 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= -0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9728 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 28 5.16 5 C 6624 2.51 5 N 1723 2.21 5 O 2105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10514 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1209, 9793 Classifications: {'peptide': 1209} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 26, 'TRANS': 1182} Chain breaks: 2 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 181 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 575 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 8, 'rna3p_pyr': 9} Link IDs: {'rna2p': 9, 'rna3p': 17} Chain: "C" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 146 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 3} Time building chain proxies: 1.77, per 1000 atoms: 0.17 Number of scatterers: 10514 At special positions: 0 Unit cell: (94.62, 110.58, 124.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 34 15.00 O 2105 8.00 N 1723 7.00 C 6624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 445.9 milliseconds 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 9 sheets defined 48.5% alpha, 10.8% beta 9 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.714A pdb=" N LYS A 6 " --> pdb=" O LYS A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 34 Processing helix chain 'A' and resid 37 through 66 removed outlier: 5.060A pdb=" N LYS A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLY A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 91 through 110 removed outlier: 3.690A pdb=" N GLU A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 119 removed outlier: 3.976A pdb=" N LEU A 118 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 119 " --> pdb=" O LYS A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 115 through 119' Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 147 through 150 removed outlier: 3.683A pdb=" N ALA A 150 " --> pdb=" O PHE A 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 150' Processing helix chain 'A' and resid 151 through 159 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 192 through 196 removed outlier: 3.963A pdb=" N ALA A 195 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 196 " --> pdb=" O VAL A 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 192 through 196' Processing helix chain 'A' and resid 198 through 209 Processing helix chain 'A' and resid 233 through 242 removed outlier: 3.563A pdb=" N ILE A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 265 removed outlier: 3.991A pdb=" N TYR A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 324 removed outlier: 4.217A pdb=" N SER A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.989A pdb=" N GLU A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.968A pdb=" N SER A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.521A pdb=" N GLU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 392 Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 409 through 431 Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 449 through 472 removed outlier: 4.328A pdb=" N ALA A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 499 removed outlier: 3.736A pdb=" N LYS A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 535 through 539 Processing helix chain 'A' and resid 564 through 569 removed outlier: 3.573A pdb=" N ILE A 569 " --> pdb=" O CYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Proline residue: A 594 - end of helix Processing helix chain 'A' and resid 609 through 619 removed outlier: 4.152A pdb=" N GLY A 619 " --> pdb=" O ILE A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 645 Processing helix chain 'A' and resid 646 through 651 Processing helix chain 'A' and resid 665 through 676 removed outlier: 3.885A pdb=" N PHE A 669 " --> pdb=" O ASP A 665 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 672 " --> pdb=" O GLY A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 697 Processing helix chain 'A' and resid 706 through 710 Processing helix chain 'A' and resid 718 through 728 removed outlier: 3.950A pdb=" N PHE A 728 " --> pdb=" O PHE A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 756 Processing helix chain 'A' and resid 786 through 790 Processing helix chain 'A' and resid 811 through 822 Processing helix chain 'A' and resid 872 through 885 Processing helix chain 'A' and resid 889 through 919 removed outlier: 3.561A pdb=" N HIS A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 954 Processing helix chain 'A' and resid 1020 through 1030 Processing helix chain 'A' and resid 1050 through 1052 No H-bonds generated for 'chain 'A' and resid 1050 through 1052' Processing helix chain 'A' and resid 1091 through 1102 Processing helix chain 'A' and resid 1111 through 1117 Processing helix chain 'A' and resid 1120 through 1136 Processing helix chain 'A' and resid 1163 through 1167 Processing helix chain 'A' and resid 1178 through 1201 removed outlier: 3.640A pdb=" N VAL A1191 " --> pdb=" O ILE A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1206 removed outlier: 3.663A pdb=" N LEU A1206 " --> pdb=" O ASP A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1226 removed outlier: 3.842A pdb=" N VAL A1226 " --> pdb=" O ALA A1222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 520 through 523 removed outlier: 4.837A pdb=" N LEU A 744 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR A 794 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR A 553 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 11.608A pdb=" N ALA A 544 " --> pdb=" O TYR A 583 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N TYR A 583 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE A 546 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 523 removed outlier: 4.837A pdb=" N LEU A 744 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA4, first strand: chain 'A' and resid 758 through 759 Processing sheet with id=AA5, first strand: chain 'A' and resid 850 through 855 removed outlier: 4.846A pdb=" N GLU A 925 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 922 " --> pdb=" O PHE A 994 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ILE A 996 " --> pdb=" O ILE A 922 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU A 924 " --> pdb=" O ILE A 996 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 858 through 863 Processing sheet with id=AA7, first strand: chain 'A' and resid 1033 through 1034 removed outlier: 3.535A pdb=" N ARG A1033 " --> pdb=" O ALA A1046 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1070 through 1072 Processing sheet with id=AA9, first strand: chain 'A' and resid 1138 through 1140 447 hydrogen bonds defined for protein. 1275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1734 1.31 - 1.44: 3144 1.44 - 1.56: 5813 1.56 - 1.68: 69 1.68 - 1.81: 47 Bond restraints: 10807 Sorted by residual: bond pdb=" CA ALA A 166 " pdb=" C ALA A 166 " ideal model delta sigma weight residual 1.533 1.510 0.023 5.60e-03 3.19e+04 1.73e+01 bond pdb=" CA LYS A 937 " pdb=" C LYS A 937 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.34e-02 5.57e+03 1.63e+01 bond pdb=" CA ALA A 920 " pdb=" C ALA A 920 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.19e-02 7.06e+03 1.62e+01 bond pdb=" CA LYS A 110 " pdb=" C LYS A 110 " ideal model delta sigma weight residual 1.522 1.572 -0.049 1.26e-02 6.30e+03 1.54e+01 bond pdb=" CA GLU A 981 " pdb=" C GLU A 981 " ideal model delta sigma weight residual 1.523 1.491 0.032 8.40e-03 1.42e+04 1.45e+01 ... (remaining 10802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 13824 2.62 - 5.23: 719 5.23 - 7.85: 148 7.85 - 10.47: 36 10.47 - 13.08: 9 Bond angle restraints: 14736 Sorted by residual: angle pdb=" N SER A 68 " pdb=" CA SER A 68 " pdb=" C SER A 68 " ideal model delta sigma weight residual 114.62 101.54 13.08 1.14e+00 7.69e-01 1.32e+02 angle pdb=" N VAL A 216 " pdb=" CA VAL A 216 " pdb=" C VAL A 216 " ideal model delta sigma weight residual 113.53 103.67 9.86 9.80e-01 1.04e+00 1.01e+02 angle pdb=" N TYR A 290 " pdb=" CA TYR A 290 " pdb=" C TYR A 290 " ideal model delta sigma weight residual 113.38 101.40 11.98 1.23e+00 6.61e-01 9.49e+01 angle pdb=" N MET A 161 " pdb=" CA MET A 161 " pdb=" C MET A 161 " ideal model delta sigma weight residual 112.90 100.87 12.03 1.31e+00 5.83e-01 8.43e+01 angle pdb=" N PHE A 315 " pdb=" CA PHE A 315 " pdb=" C PHE A 315 " ideal model delta sigma weight residual 111.36 102.98 8.38 1.09e+00 8.42e-01 5.91e+01 ... (remaining 14731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 5726 35.36 - 70.72: 751 70.72 - 106.09: 32 106.09 - 141.45: 0 141.45 - 176.81: 2 Dihedral angle restraints: 6511 sinusoidal: 2925 harmonic: 3586 Sorted by residual: dihedral pdb=" O4' U B 16 " pdb=" C1' U B 16 " pdb=" N1 U B 16 " pdb=" C2 U B 16 " ideal model delta sinusoidal sigma weight residual 232.00 56.23 175.77 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" C5' A B 14 " pdb=" C4' A B 14 " pdb=" C3' A B 14 " pdb=" O3' A B 14 " ideal model delta sinusoidal sigma weight residual 147.00 94.96 52.04 1 8.00e+00 1.56e-02 5.77e+01 dihedral pdb=" C VAL A 300 " pdb=" N VAL A 300 " pdb=" CA VAL A 300 " pdb=" CB VAL A 300 " ideal model delta harmonic sigma weight residual -122.00 -135.99 13.99 0 2.50e+00 1.60e-01 3.13e+01 ... (remaining 6508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1343 0.133 - 0.267: 248 0.267 - 0.400: 21 0.400 - 0.533: 2 0.533 - 0.667: 2 Chirality restraints: 1616 Sorted by residual: chirality pdb=" C3' A B 14 " pdb=" C4' A B 14 " pdb=" O3' A B 14 " pdb=" C2' A B 14 " both_signs ideal model delta sigma weight residual False -2.74 -2.08 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA THR A 777 " pdb=" N THR A 777 " pdb=" C THR A 777 " pdb=" CB THR A 777 " both_signs ideal model delta sigma weight residual False 2.53 1.96 0.56 2.00e-01 2.50e+01 7.92e+00 chirality pdb=" CA THR A 778 " pdb=" N THR A 778 " pdb=" C THR A 778 " pdb=" CB THR A 778 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 1613 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 607 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.60e+00 pdb=" N PRO A 608 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 608 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 608 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1175 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A1176 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A1176 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1176 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 128 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.32e+00 pdb=" N PRO A 129 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " -0.030 5.00e-02 4.00e+02 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 4093 2.88 - 3.38: 9735 3.38 - 3.89: 20605 3.89 - 4.39: 24877 4.39 - 4.90: 36616 Nonbonded interactions: 95926 Sorted by model distance: nonbonded pdb=" N LYS A 775 " pdb=" O LYS A 775 " model vdw 2.371 2.496 nonbonded pdb=" N ASN A 706 " pdb=" O ASN A 706 " model vdw 2.415 2.496 nonbonded pdb=" N LEU A 446 " pdb=" N LYS A 447 " model vdw 2.421 2.560 nonbonded pdb=" N ILE A1004 " pdb=" O ILE A1004 " model vdw 2.424 2.496 nonbonded pdb=" N TYR A 290 " pdb=" N GLY A 291 " model vdw 2.433 2.560 ... (remaining 95921 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.450 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 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 : 0.010 0.054 10807 Z= 0.728 Angle : 1.439 13.082 14736 Z= 0.961 Chirality : 0.102 0.667 1616 Planarity : 0.005 0.059 1770 Dihedral : 25.395 176.810 4203 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 1.91 % Allowed : 10.72 % Favored : 87.36 % Rotamer: Outliers : 35.76 % Allowed : 14.72 % Favored : 49.52 % Cbeta Deviations : 0.43 % 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: -3.80 (0.20), residues: 1203 helix: -2.26 (0.18), residues: 523 sheet: -1.99 (0.38), residues: 147 loop : -2.87 (0.23), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 174 TYR 0.020 0.003 TYR A 57 PHE 0.026 0.003 PHE A 304 TRP 0.014 0.002 TRP A1063 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00989 / 0.73 (10807) covalent geometry : angle 1.43883 / 0.96 (14736) hydrogen bonds : bond 0.18773 / 11.77 ( 460) hydrogen bonds : angle 7.96032 / 5.44 ( 1315) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 374 poor density : 187 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7095 (mtpt) REVERT: A 29 GLU cc_start: 0.6091 (OUTLIER) cc_final: 0.5166 (mp0) REVERT: A 35 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6665 (mtm180) REVERT: A 39 GLU cc_start: 0.6753 (pm20) cc_final: 0.6229 (mm-30) REVERT: A 70 LYS cc_start: 0.3311 (OUTLIER) cc_final: 0.2921 (pptt) REVERT: A 105 ILE cc_start: 0.4965 (OUTLIER) cc_final: 0.4710 (pt) REVERT: A 116 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6457 (tmmt) REVERT: A 125 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: A 196 ILE cc_start: 0.4293 (OUTLIER) cc_final: 0.3836 (tp) REVERT: A 204 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.5340 (mp0) REVERT: A 207 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6567 (mm-30) REVERT: A 215 ASP cc_start: 0.6245 (OUTLIER) cc_final: 0.5885 (m-30) REVERT: A 309 ASN cc_start: 0.3918 (OUTLIER) cc_final: 0.3310 (t0) REVERT: A 313 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.7011 (mm-30) REVERT: A 318 ILE cc_start: 0.6427 (OUTLIER) cc_final: 0.6212 (mt) REVERT: A 332 SER cc_start: 0.4713 (OUTLIER) cc_final: 0.4394 (p) REVERT: A 419 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6733 (OUTLIER) REVERT: A 433 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6583 (tp30) REVERT: A 476 GLU cc_start: 0.5841 (OUTLIER) cc_final: 0.5571 (tm-30) REVERT: A 552 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7112 (mttt) REVERT: A 572 ASP cc_start: 0.6085 (OUTLIER) cc_final: 0.4905 (t0) REVERT: A 600 LYS cc_start: 0.1322 (OUTLIER) cc_final: 0.1104 (mttp) REVERT: A 611 ASP cc_start: 0.3162 (OUTLIER) cc_final: 0.2838 (t0) REVERT: A 631 ASP cc_start: 0.3425 (OUTLIER) cc_final: 0.2917 (p0) REVERT: A 645 ARG cc_start: 0.4441 (OUTLIER) cc_final: 0.3971 (mmm160) REVERT: A 648 LYS cc_start: 0.5662 (OUTLIER) cc_final: 0.4816 (mtpp) REVERT: A 689 GLU cc_start: 0.6470 (mt-10) cc_final: 0.6115 (mm-30) REVERT: A 713 SER cc_start: 0.7729 (OUTLIER) cc_final: 0.7491 (m) REVERT: A 746 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8477 (tpp) REVERT: A 752 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6792 (mttp) REVERT: A 804 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6836 (tptt) REVERT: A 824 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7069 (m-30) REVERT: A 836 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7845 (mpt-90) REVERT: A 847 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7177 (mmtt) REVERT: A 867 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7019 (mpp80) REVERT: A 887 ARG cc_start: 0.5437 (OUTLIER) cc_final: 0.4797 (mtp-110) REVERT: A 888 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.7083 (mp-120) REVERT: A 898 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7095 (mt-10) REVERT: A 939 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6205 (pm20) REVERT: A 972 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6678 (tttt) REVERT: A 984 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.6789 (mtmt) REVERT: A 1062 LYS cc_start: 0.6832 (mmtm) cc_final: 0.6573 (mtmm) REVERT: A 1064 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7531 (mttp) REVERT: A 1073 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6966 (ttt-90) REVERT: A 1075 PHE cc_start: 0.6583 (p90) cc_final: 0.6116 (p90) REVERT: A 1088 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7246 (tp30) REVERT: A 1108 GLN cc_start: 0.6754 (OUTLIER) cc_final: 0.6440 (tp40) REVERT: A 1118 GLN cc_start: 0.6082 (tp40) cc_final: 0.5844 (mm-40) REVERT: A 1155 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8222 (mttt) outliers start: 374 outliers final: 71 residues processed: 478 average time/residue: 0.4778 time to fit residues: 246.1348 Evaluate side-chains 226 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 113 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 622 LYS Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 804 LYS Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 965 CYS Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1049 TYR Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1073 ARG Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1117 GLU Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1207 ASP Chi-restraints excluded: chain A residue 1224 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.1980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 ASN A 30 ASN A 33 ASN A 67 HIS A 112 ASN A 142 ASN A 160 ASN A 177 ASN A 211 ASN ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN A 370 HIS A 582 ASN A 607 ASN A 767 ASN A 772 ASN A 889 ASN A 895 ASN A 941 GLN A 955 ASN A 975 GLN A1100 ASN A1108 GLN A1136 GLN A1170 GLN A1172 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.200672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.156825 restraints weight = 10995.989| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.83 r_work: 0.3441 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10807 Z= 0.187 Angle : 0.726 8.937 14736 Z= 0.405 Chirality : 0.046 0.249 1616 Planarity : 0.005 0.060 1770 Dihedral : 18.855 170.975 2107 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.06 % Favored : 91.35 % Rotamer: Outliers : 16.44 % Allowed : 25.43 % Favored : 58.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.23), residues: 1203 helix: -0.51 (0.21), residues: 532 sheet: -1.86 (0.39), residues: 136 loop : -2.02 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 543 TYR 0.024 0.002 TYR A 57 PHE 0.042 0.002 PHE A 220 TRP 0.015 0.001 TRP A 999 HIS 0.011 0.002 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (10807) covalent geometry : angle 0.72573 / 0.41 (14736) hydrogen bonds : bond 0.05346 / 3.47 ( 460) hydrogen bonds : angle 5.64719 / 3.87 ( 1315) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 122 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6009 (mp0) REVERT: A 63 ASN cc_start: 0.7678 (m-40) cc_final: 0.7441 (t0) REVERT: A 70 LYS cc_start: 0.2972 (OUTLIER) cc_final: 0.2523 (pptt) REVERT: A 82 ARG cc_start: 0.3196 (OUTLIER) cc_final: 0.2723 (mpp-170) REVERT: A 116 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.6755 (tmmt) REVERT: A 125 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6947 (pp20) REVERT: A 184 ILE cc_start: 0.4973 (OUTLIER) cc_final: 0.4733 (mm) REVERT: A 193 VAL cc_start: 0.4200 (OUTLIER) cc_final: 0.3952 (t) REVERT: A 196 ILE cc_start: 0.4218 (OUTLIER) cc_final: 0.3754 (tt) REVERT: A 219 PHE cc_start: 0.5442 (OUTLIER) cc_final: 0.5141 (t80) REVERT: A 285 GLU cc_start: 0.4903 (OUTLIER) cc_final: 0.4370 (mm-30) REVERT: A 309 ASN cc_start: 0.4419 (OUTLIER) cc_final: 0.3984 (m-40) REVERT: A 419 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6745 (tp) REVERT: A 433 GLU cc_start: 0.6695 (tp30) cc_final: 0.6481 (tp30) REVERT: A 447 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.6945 (mtmt) REVERT: A 498 LEU cc_start: 0.8140 (mt) cc_final: 0.7929 (mt) REVERT: A 535 ASP cc_start: 0.6546 (OUTLIER) cc_final: 0.5865 (t0) REVERT: A 572 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.5991 (t0) REVERT: A 603 MET cc_start: 0.3603 (tpp) cc_final: 0.3349 (ppp) REVERT: A 611 ASP cc_start: 0.3283 (OUTLIER) cc_final: 0.3068 (t0) REVERT: A 631 ASP cc_start: 0.2814 (OUTLIER) cc_final: 0.2269 (p0) REVERT: A 683 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6436 (mm-30) REVERT: A 775 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6772 (mmtt) REVERT: A 795 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: A 804 LYS cc_start: 0.7358 (tttt) cc_final: 0.7155 (tptt) REVERT: A 824 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: A 887 ARG cc_start: 0.4999 (OUTLIER) cc_final: 0.3919 (mtm-85) REVERT: A 939 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7177 (pm20) REVERT: A 984 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7615 (mtmt) REVERT: A 1035 MET cc_start: 0.8068 (ptm) cc_final: 0.7790 (ptt) REVERT: A 1064 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8190 (mttp) REVERT: A 1073 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7972 (ttt-90) REVERT: A 1118 GLN cc_start: 0.6942 (tp40) cc_final: 0.6575 (mm-40) REVERT: A 1157 SER cc_start: 0.7523 (OUTLIER) cc_final: 0.7261 (p) outliers start: 172 outliers final: 61 residues processed: 258 average time/residue: 0.4508 time to fit residues: 126.0730 Evaluate side-chains 184 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 96 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 580 LYS Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 622 LYS Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 931 PHE Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1056 ASP Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1073 ARG Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1207 ASP Chi-restraints excluded: chain A residue 1224 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 94 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 ASN A 703 GLN A 933 ASN A 975 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.197107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.151718 restraints weight = 10914.855| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.67 r_work: 0.3379 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10807 Z= 0.215 Angle : 0.680 10.910 14736 Z= 0.375 Chirality : 0.046 0.208 1616 Planarity : 0.004 0.050 1770 Dihedral : 16.879 166.023 1972 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.89 % Favored : 90.77 % Rotamer: Outliers : 12.24 % Allowed : 28.30 % Favored : 59.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.24), residues: 1203 helix: 0.02 (0.22), residues: 524 sheet: -1.62 (0.40), residues: 137 loop : -1.55 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 836 TYR 0.022 0.002 TYR A 57 PHE 0.024 0.002 PHE A 119 TRP 0.015 0.002 TRP A 999 HIS 0.007 0.001 HIS A 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (10807) covalent geometry : angle 0.68039 / 0.37 (14736) hydrogen bonds : bond 0.05109 / 3.30 ( 460) hydrogen bonds : angle 5.31140 / 3.62 ( 1315) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 102 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6049 (mp0) REVERT: A 63 ASN cc_start: 0.7723 (m-40) cc_final: 0.7476 (t0) REVERT: A 70 LYS cc_start: 0.3075 (OUTLIER) cc_final: 0.2255 (mmmt) REVERT: A 101 LEU cc_start: 0.3597 (OUTLIER) cc_final: 0.3323 (tp) REVERT: A 116 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.6790 (tmmt) REVERT: A 193 VAL cc_start: 0.3980 (OUTLIER) cc_final: 0.3771 (t) REVERT: A 196 ILE cc_start: 0.4158 (OUTLIER) cc_final: 0.3624 (tp) REVERT: A 204 GLU cc_start: 0.5512 (OUTLIER) cc_final: 0.4904 (mp0) REVERT: A 240 ILE cc_start: 0.6182 (OUTLIER) cc_final: 0.5751 (pp) REVERT: A 255 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6404 (mt) REVERT: A 285 GLU cc_start: 0.5075 (OUTLIER) cc_final: 0.4586 (mm-30) REVERT: A 433 GLU cc_start: 0.6946 (tp30) cc_final: 0.6588 (tp30) REVERT: A 434 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7144 (tppt) REVERT: A 447 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7028 (mtmt) REVERT: A 498 LEU cc_start: 0.8189 (mt) cc_final: 0.7709 (mp) REVERT: A 535 ASP cc_start: 0.6460 (OUTLIER) cc_final: 0.5810 (t0) REVERT: A 572 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6026 (t0) REVERT: A 603 MET cc_start: 0.3607 (tpp) cc_final: 0.3319 (ppp) REVERT: A 631 ASP cc_start: 0.2843 (OUTLIER) cc_final: 0.2306 (p0) REVERT: A 689 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6777 (mm-30) REVERT: A 775 LYS cc_start: 0.7035 (OUTLIER) cc_final: 0.6796 (mmtt) REVERT: A 824 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7275 (m-30) REVERT: A 887 ARG cc_start: 0.5240 (OUTLIER) cc_final: 0.4127 (mtm-85) REVERT: A 939 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7185 (pm20) REVERT: A 984 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7608 (mtmt) REVERT: A 1035 MET cc_start: 0.8115 (ptm) cc_final: 0.7843 (ptt) REVERT: A 1064 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8123 (mttp) REVERT: A 1104 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7560 (mp) outliers start: 128 outliers final: 53 residues processed: 208 average time/residue: 0.4409 time to fit residues: 99.8652 Evaluate side-chains 166 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 90 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 931 PHE Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1056 ASP Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1144 ARG Chi-restraints excluded: chain A residue 1207 ASP Chi-restraints excluded: chain A residue 1224 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 74 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 56 optimal weight: 0.0060 chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 GLN A1136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.196147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.150068 restraints weight = 10892.982| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.57 r_work: 0.3379 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10807 Z= 0.234 Angle : 0.659 8.663 14736 Z= 0.364 Chirality : 0.046 0.186 1616 Planarity : 0.004 0.049 1770 Dihedral : 16.147 164.861 1927 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.98 % Favored : 91.69 % Rotamer: Outliers : 10.42 % Allowed : 29.73 % Favored : 59.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.24), residues: 1203 helix: 0.13 (0.22), residues: 523 sheet: -1.49 (0.40), residues: 137 loop : -1.39 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 174 TYR 0.023 0.002 TYR A 57 PHE 0.026 0.002 PHE A 131 TRP 0.016 0.002 TRP A 999 HIS 0.008 0.001 HIS A 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (10807) covalent geometry : angle 0.65948 / 0.36 (14736) hydrogen bonds : bond 0.04913 / 3.20 ( 460) hydrogen bonds : angle 5.23923 / 3.56 ( 1315) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 97 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: A 63 ASN cc_start: 0.7845 (m-40) cc_final: 0.7599 (t0) REVERT: A 64 ASP cc_start: 0.7271 (m-30) cc_final: 0.7040 (m-30) REVERT: A 70 LYS cc_start: 0.3288 (OUTLIER) cc_final: 0.2324 (mmmt) REVERT: A 125 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6346 (mp0) REVERT: A 204 GLU cc_start: 0.5533 (OUTLIER) cc_final: 0.4936 (mp0) REVERT: A 240 ILE cc_start: 0.6423 (OUTLIER) cc_final: 0.6074 (OUTLIER) REVERT: A 285 GLU cc_start: 0.4932 (OUTLIER) cc_final: 0.4427 (mm-30) REVERT: A 433 GLU cc_start: 0.7100 (tp30) cc_final: 0.6676 (tp30) REVERT: A 434 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7183 (tppt) REVERT: A 498 LEU cc_start: 0.8302 (mt) cc_final: 0.7823 (mp) REVERT: A 535 ASP cc_start: 0.6618 (OUTLIER) cc_final: 0.5806 (t70) REVERT: A 572 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.5938 (t0) REVERT: A 603 MET cc_start: 0.3606 (tpp) cc_final: 0.3234 (ppp) REVERT: A 631 ASP cc_start: 0.2928 (OUTLIER) cc_final: 0.2345 (p0) REVERT: A 689 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6977 (mm-30) REVERT: A 775 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6900 (mmtt) REVERT: A 824 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7337 (m-30) REVERT: A 887 ARG cc_start: 0.5367 (OUTLIER) cc_final: 0.3975 (mtm-85) REVERT: A 889 ASN cc_start: 0.6863 (OUTLIER) cc_final: 0.6540 (m110) REVERT: A 939 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7433 (pm20) REVERT: A 984 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7717 (mtmt) REVERT: A 1035 MET cc_start: 0.8238 (ptm) cc_final: 0.7982 (ptt) REVERT: A 1064 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8272 (mttp) REVERT: A 1118 GLN cc_start: 0.7343 (mm110) cc_final: 0.6632 (mm-40) outliers start: 109 outliers final: 57 residues processed: 186 average time/residue: 0.4356 time to fit residues: 88.2822 Evaluate side-chains 165 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 92 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 931 PHE Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1056 ASP Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1144 ARG Chi-restraints excluded: chain A residue 1207 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 90 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 116 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 ASN A 975 GLN A1118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.199577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.153588 restraints weight = 10823.066| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.42 r_work: 0.3440 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10807 Z= 0.137 Angle : 0.571 6.066 14736 Z= 0.317 Chirality : 0.042 0.261 1616 Planarity : 0.004 0.048 1770 Dihedral : 15.842 169.884 1916 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.65 % Favored : 92.10 % Rotamer: Outliers : 8.89 % Allowed : 31.64 % Favored : 59.46 % 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: -0.80 (0.24), residues: 1203 helix: 0.46 (0.22), residues: 528 sheet: -1.30 (0.44), residues: 116 loop : -1.30 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 305 TYR 0.018 0.001 TYR A 57 PHE 0.032 0.002 PHE A 219 TRP 0.024 0.001 TRP A 999 HIS 0.004 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (10807) covalent geometry : angle 0.57145 / 0.32 (14736) hydrogen bonds : bond 0.04131 / 2.70 ( 460) hydrogen bonds : angle 5.00110 / 3.40 ( 1315) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 101 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6138 (mp0) REVERT: A 63 ASN cc_start: 0.7743 (m-40) cc_final: 0.7493 (t0) REVERT: A 64 ASP cc_start: 0.7185 (m-30) cc_final: 0.6957 (m-30) REVERT: A 70 LYS cc_start: 0.3151 (OUTLIER) cc_final: 0.2177 (mmmt) REVERT: A 125 GLU cc_start: 0.7527 (mm-30) cc_final: 0.6336 (mp0) REVERT: A 204 GLU cc_start: 0.5544 (OUTLIER) cc_final: 0.4917 (mp0) REVERT: A 369 ILE cc_start: 0.6600 (OUTLIER) cc_final: 0.6286 (mp) REVERT: A 433 GLU cc_start: 0.7134 (tp30) cc_final: 0.6755 (tp30) REVERT: A 498 LEU cc_start: 0.8211 (mt) cc_final: 0.7728 (mp) REVERT: A 535 ASP cc_start: 0.6522 (OUTLIER) cc_final: 0.5646 (t70) REVERT: A 572 ASP cc_start: 0.6927 (OUTLIER) cc_final: 0.5946 (t0) REVERT: A 603 MET cc_start: 0.3572 (tpp) cc_final: 0.3207 (ppp) REVERT: A 605 TYR cc_start: 0.5887 (OUTLIER) cc_final: 0.5352 (m-80) REVERT: A 631 ASP cc_start: 0.2966 (OUTLIER) cc_final: 0.2372 (p0) REVERT: A 689 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6864 (mm-30) REVERT: A 824 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7321 (m-30) REVERT: A 887 ARG cc_start: 0.5498 (OUTLIER) cc_final: 0.4008 (mtm-85) REVERT: A 889 ASN cc_start: 0.6721 (OUTLIER) cc_final: 0.6349 (m110) REVERT: A 939 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7232 (pm20) REVERT: A 1035 MET cc_start: 0.8121 (ptm) cc_final: 0.7834 (ptt) REVERT: A 1064 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8106 (mttp) outliers start: 93 outliers final: 46 residues processed: 173 average time/residue: 0.4587 time to fit residues: 86.1310 Evaluate side-chains 151 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 91 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 931 PHE Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1056 ASP Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1144 ARG Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1207 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 104 optimal weight: 0.2980 chunk 43 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 975 GLN ** A1118 GLN ** 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 = 0.4299 r_free = 0.4299 target = 0.199488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.153385 restraints weight = 10927.816| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.49 r_work: 0.3434 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10807 Z= 0.137 Angle : 0.560 6.071 14736 Z= 0.310 Chirality : 0.041 0.173 1616 Planarity : 0.004 0.050 1770 Dihedral : 15.491 168.847 1897 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.65 % Favored : 92.10 % Rotamer: Outliers : 8.80 % Allowed : 31.93 % Favored : 59.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.62 (0.24), residues: 1203 helix: 0.56 (0.22), residues: 536 sheet: -1.02 (0.41), residues: 138 loop : -1.21 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 305 TYR 0.015 0.001 TYR A 57 PHE 0.022 0.002 PHE A 119 TRP 0.027 0.001 TRP A 999 HIS 0.004 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (10807) covalent geometry : angle 0.56022 / 0.31 (14736) hydrogen bonds : bond 0.03970 / 2.58 ( 460) hydrogen bonds : angle 4.85642 / 3.30 ( 1315) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 99 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6287 (mp0) REVERT: A 63 ASN cc_start: 0.7789 (m-40) cc_final: 0.7542 (t0) REVERT: A 64 ASP cc_start: 0.7197 (m-30) cc_final: 0.6985 (m-30) REVERT: A 70 LYS cc_start: 0.3308 (OUTLIER) cc_final: 0.2321 (mmmt) REVERT: A 93 GLU cc_start: 0.2905 (OUTLIER) cc_final: 0.2040 (mp0) REVERT: A 109 PHE cc_start: 0.4100 (OUTLIER) cc_final: 0.3739 (m-80) REVERT: A 122 ASP cc_start: 0.8466 (m-30) cc_final: 0.8112 (m-30) REVERT: A 125 GLU cc_start: 0.7523 (mm-30) cc_final: 0.6467 (mp0) REVERT: A 159 GLU cc_start: 0.6345 (tt0) cc_final: 0.5716 (tm-30) REVERT: A 204 GLU cc_start: 0.5559 (OUTLIER) cc_final: 0.4902 (mp0) REVERT: A 369 ILE cc_start: 0.6618 (OUTLIER) cc_final: 0.6272 (mp) REVERT: A 433 GLU cc_start: 0.7240 (tp30) cc_final: 0.6845 (tp30) REVERT: A 498 LEU cc_start: 0.8172 (mt) cc_final: 0.7667 (mp) REVERT: A 535 ASP cc_start: 0.6491 (OUTLIER) cc_final: 0.5663 (t70) REVERT: A 572 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.6050 (t0) REVERT: A 603 MET cc_start: 0.3567 (OUTLIER) cc_final: 0.3145 (ppp) REVERT: A 605 TYR cc_start: 0.5919 (OUTLIER) cc_final: 0.5342 (m-80) REVERT: A 631 ASP cc_start: 0.3107 (OUTLIER) cc_final: 0.2422 (p0) REVERT: A 689 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6916 (mm-30) REVERT: A 692 LYS cc_start: 0.7816 (tttm) cc_final: 0.7608 (ttpt) REVERT: A 782 ASP cc_start: 0.8470 (m-30) cc_final: 0.8261 (m-30) REVERT: A 795 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: A 824 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7325 (m-30) REVERT: A 887 ARG cc_start: 0.5695 (OUTLIER) cc_final: 0.4553 (ptm-80) REVERT: A 889 ASN cc_start: 0.6797 (OUTLIER) cc_final: 0.6459 (m110) REVERT: A 939 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7265 (pm20) REVERT: A 984 LYS cc_start: 0.8356 (mptt) cc_final: 0.7700 (mtmt) REVERT: A 1035 MET cc_start: 0.8131 (ptm) cc_final: 0.7899 (ptt) REVERT: A 1064 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8060 (mttp) REVERT: A 1087 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8109 (pt0) outliers start: 92 outliers final: 44 residues processed: 177 average time/residue: 0.4596 time to fit residues: 88.4971 Evaluate side-chains 155 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 92 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1056 ASP Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1144 ARG Chi-restraints excluded: chain A residue 1207 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 35 optimal weight: 0.0670 chunk 66 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 975 GLN ** A1118 GLN ** 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 = 0.4277 r_free = 0.4277 target = 0.197158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.150760 restraints weight = 10785.126| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.44 r_work: 0.3393 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10807 Z= 0.196 Angle : 0.600 5.910 14736 Z= 0.330 Chirality : 0.044 0.207 1616 Planarity : 0.004 0.051 1770 Dihedral : 15.353 164.835 1894 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.15 % Favored : 91.69 % Rotamer: Outliers : 8.70 % Allowed : 32.31 % Favored : 58.99 % 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: -0.70 (0.24), residues: 1203 helix: 0.48 (0.22), residues: 535 sheet: -0.99 (0.41), residues: 138 loop : -1.25 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 305 TYR 0.021 0.002 TYR A 57 PHE 0.023 0.002 PHE A 119 TRP 0.010 0.001 TRP A 999 HIS 0.007 0.001 HIS A 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (10807) covalent geometry : angle 0.60013 / 0.33 (14736) hydrogen bonds : bond 0.04348 / 2.84 ( 460) hydrogen bonds : angle 4.91809 / 3.34 ( 1315) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 95 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6306 (mp0) REVERT: A 63 ASN cc_start: 0.7847 (m-40) cc_final: 0.7618 (t0) REVERT: A 70 LYS cc_start: 0.3330 (OUTLIER) cc_final: 0.2362 (mmmt) REVERT: A 109 PHE cc_start: 0.4151 (OUTLIER) cc_final: 0.3631 (m-80) REVERT: A 122 ASP cc_start: 0.8434 (m-30) cc_final: 0.8084 (m-30) REVERT: A 125 GLU cc_start: 0.7459 (mm-30) cc_final: 0.6446 (mp0) REVERT: A 358 ILE cc_start: 0.6735 (OUTLIER) cc_final: 0.6455 (tp) REVERT: A 369 ILE cc_start: 0.6634 (OUTLIER) cc_final: 0.6276 (mp) REVERT: A 433 GLU cc_start: 0.7278 (tp30) cc_final: 0.6880 (tp30) REVERT: A 476 GLU cc_start: 0.4732 (OUTLIER) cc_final: 0.4255 (tp30) REVERT: A 498 LEU cc_start: 0.8243 (mt) cc_final: 0.7740 (mp) REVERT: A 535 ASP cc_start: 0.6488 (OUTLIER) cc_final: 0.5643 (t70) REVERT: A 572 ASP cc_start: 0.7036 (OUTLIER) cc_final: 0.6032 (t0) REVERT: A 603 MET cc_start: 0.3584 (OUTLIER) cc_final: 0.3112 (ppp) REVERT: A 605 TYR cc_start: 0.5957 (OUTLIER) cc_final: 0.5376 (m-80) REVERT: A 613 GLN cc_start: 0.2913 (OUTLIER) cc_final: 0.2652 (tp-100) REVERT: A 631 ASP cc_start: 0.3116 (OUTLIER) cc_final: 0.2447 (p0) REVERT: A 692 LYS cc_start: 0.7812 (tttm) cc_final: 0.7585 (ttpt) REVERT: A 782 ASP cc_start: 0.8503 (m-30) cc_final: 0.8296 (m-30) REVERT: A 795 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: A 824 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7298 (m-30) REVERT: A 887 ARG cc_start: 0.5789 (OUTLIER) cc_final: 0.4557 (ptm-80) REVERT: A 889 ASN cc_start: 0.6808 (OUTLIER) cc_final: 0.6553 (m-40) REVERT: A 932 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7868 (mttp) REVERT: A 939 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7437 (pm20) REVERT: A 984 LYS cc_start: 0.8315 (mptt) cc_final: 0.7677 (mtmt) REVERT: A 1035 MET cc_start: 0.8168 (ptm) cc_final: 0.7926 (ptt) REVERT: A 1064 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8163 (mttp) outliers start: 91 outliers final: 49 residues processed: 173 average time/residue: 0.4690 time to fit residues: 88.0891 Evaluate side-chains 157 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 89 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 932 LYS Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1056 ASP Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1144 ARG Chi-restraints excluded: chain A residue 1207 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 975 GLN A1118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.196639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.151245 restraints weight = 10773.961| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.55 r_work: 0.3372 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10807 Z= 0.200 Angle : 0.604 6.232 14736 Z= 0.332 Chirality : 0.044 0.182 1616 Planarity : 0.004 0.050 1770 Dihedral : 15.274 165.471 1891 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.81 % Favored : 92.02 % Rotamer: Outliers : 8.41 % Allowed : 32.79 % Favored : 58.80 % 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: -0.71 (0.24), residues: 1203 helix: 0.39 (0.22), residues: 543 sheet: -0.99 (0.41), residues: 138 loop : -1.18 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 305 TYR 0.021 0.002 TYR A 57 PHE 0.035 0.002 PHE A 131 TRP 0.013 0.001 TRP A 999 HIS 0.007 0.001 HIS A 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (10807) covalent geometry : angle 0.60431 / 0.33 (14736) hydrogen bonds : bond 0.04338 / 2.83 ( 460) hydrogen bonds : angle 4.90920 / 3.33 ( 1315) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 97 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6286 (mp0) REVERT: A 70 LYS cc_start: 0.3196 (OUTLIER) cc_final: 0.2295 (mmmt) REVERT: A 109 PHE cc_start: 0.4150 (OUTLIER) cc_final: 0.3561 (m-80) REVERT: A 116 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.6855 (tmmt) REVERT: A 122 ASP cc_start: 0.8422 (m-30) cc_final: 0.8112 (m-30) REVERT: A 125 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6405 (mp0) REVERT: A 221 GLU cc_start: 0.1925 (OUTLIER) cc_final: 0.1312 (pm20) REVERT: A 369 ILE cc_start: 0.6645 (OUTLIER) cc_final: 0.6282 (mp) REVERT: A 433 GLU cc_start: 0.7323 (tp30) cc_final: 0.6952 (tp30) REVERT: A 476 GLU cc_start: 0.4715 (OUTLIER) cc_final: 0.4216 (tp30) REVERT: A 484 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.5832 (tp30) REVERT: A 498 LEU cc_start: 0.8133 (mt) cc_final: 0.7614 (mp) REVERT: A 535 ASP cc_start: 0.6347 (OUTLIER) cc_final: 0.5649 (t70) REVERT: A 572 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6199 (t0) REVERT: A 603 MET cc_start: 0.3602 (OUTLIER) cc_final: 0.3148 (ppp) REVERT: A 605 TYR cc_start: 0.5874 (OUTLIER) cc_final: 0.5299 (m-80) REVERT: A 613 GLN cc_start: 0.2838 (OUTLIER) cc_final: 0.2590 (tp-100) REVERT: A 631 ASP cc_start: 0.3169 (OUTLIER) cc_final: 0.2365 (p0) REVERT: A 692 LYS cc_start: 0.7851 (tttm) cc_final: 0.7595 (ttpt) REVERT: A 795 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: A 824 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7210 (m-30) REVERT: A 887 ARG cc_start: 0.5753 (OUTLIER) cc_final: 0.4610 (ptm-80) REVERT: A 889 ASN cc_start: 0.6860 (OUTLIER) cc_final: 0.6643 (m-40) REVERT: A 932 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7892 (mttp) REVERT: A 984 LYS cc_start: 0.8247 (mptt) cc_final: 0.7630 (mtmt) REVERT: A 1035 MET cc_start: 0.8044 (ptm) cc_final: 0.7791 (ptt) REVERT: A 1064 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8097 (mttp) REVERT: A 1087 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7988 (pt0) outliers start: 88 outliers final: 43 residues processed: 173 average time/residue: 0.4323 time to fit residues: 81.3918 Evaluate side-chains 157 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 93 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 932 LYS Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1056 ASP Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1144 ARG Chi-restraints excluded: chain A residue 1207 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 114 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 975 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.198192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.152695 restraints weight = 10898.759| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.69 r_work: 0.3394 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10807 Z= 0.155 Angle : 0.576 7.771 14736 Z= 0.316 Chirality : 0.042 0.177 1616 Planarity : 0.004 0.050 1770 Dihedral : 15.145 167.085 1887 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.73 % Favored : 92.10 % Rotamer: Outliers : 7.36 % Allowed : 33.37 % Favored : 59.27 % 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: -0.58 (0.24), residues: 1203 helix: 0.55 (0.22), residues: 540 sheet: -1.02 (0.45), residues: 115 loop : -1.15 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 305 TYR 0.018 0.001 TYR A 549 PHE 0.030 0.002 PHE A 131 TRP 0.014 0.001 TRP A 999 HIS 0.005 0.001 HIS A 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (10807) covalent geometry : angle 0.57642 / 0.32 (14736) hydrogen bonds : bond 0.04022 / 2.62 ( 460) hydrogen bonds : angle 4.82313 / 3.28 ( 1315) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 98 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6199 (mp0) REVERT: A 70 LYS cc_start: 0.3107 (OUTLIER) cc_final: 0.2133 (mmmt) REVERT: A 109 PHE cc_start: 0.4109 (OUTLIER) cc_final: 0.3526 (m-80) REVERT: A 116 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.6821 (tmmt) REVERT: A 122 ASP cc_start: 0.8428 (m-30) cc_final: 0.8127 (m-30) REVERT: A 125 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6477 (mp0) REVERT: A 159 GLU cc_start: 0.6041 (tt0) cc_final: 0.5462 (tm-30) REVERT: A 221 GLU cc_start: 0.1829 (OUTLIER) cc_final: 0.1369 (pm20) REVERT: A 369 ILE cc_start: 0.6646 (OUTLIER) cc_final: 0.6295 (mp) REVERT: A 424 GLU cc_start: 0.7079 (tt0) cc_final: 0.6663 (tm-30) REVERT: A 433 GLU cc_start: 0.7336 (tp30) cc_final: 0.6972 (tp30) REVERT: A 476 GLU cc_start: 0.4670 (OUTLIER) cc_final: 0.4212 (tp30) REVERT: A 484 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.5832 (tp30) REVERT: A 498 LEU cc_start: 0.8083 (mt) cc_final: 0.7554 (mp) REVERT: A 535 ASP cc_start: 0.6253 (OUTLIER) cc_final: 0.5547 (t70) REVERT: A 572 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6142 (t0) REVERT: A 603 MET cc_start: 0.3571 (OUTLIER) cc_final: 0.3143 (ppp) REVERT: A 605 TYR cc_start: 0.5850 (OUTLIER) cc_final: 0.5304 (m-80) REVERT: A 613 GLN cc_start: 0.2782 (OUTLIER) cc_final: 0.2547 (tp-100) REVERT: A 631 ASP cc_start: 0.3110 (OUTLIER) cc_final: 0.2328 (p0) REVERT: A 692 LYS cc_start: 0.7813 (tttm) cc_final: 0.7572 (ttpt) REVERT: A 752 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7308 (mttp) REVERT: A 795 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: A 824 ASP cc_start: 0.7511 (p0) cc_final: 0.7184 (m-30) REVERT: A 887 ARG cc_start: 0.5704 (OUTLIER) cc_final: 0.4585 (ptm-80) REVERT: A 932 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7867 (mttp) REVERT: A 984 LYS cc_start: 0.8259 (mptt) cc_final: 0.7627 (mtmt) REVERT: A 1035 MET cc_start: 0.7997 (ptm) cc_final: 0.7749 (ptt) REVERT: A 1064 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8001 (mttp) outliers start: 77 outliers final: 40 residues processed: 164 average time/residue: 0.4546 time to fit residues: 80.9554 Evaluate side-chains 151 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 92 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 932 LYS Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1056 ASP Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1144 ARG Chi-restraints excluded: chain A residue 1207 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 71 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 43 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 16 optimal weight: 0.0040 chunk 117 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN A 311 ASN A 975 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.200432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.155518 restraints weight = 10785.044| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.66 r_work: 0.3435 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10807 Z= 0.118 Angle : 0.549 9.799 14736 Z= 0.301 Chirality : 0.041 0.210 1616 Planarity : 0.003 0.049 1770 Dihedral : 15.082 170.423 1885 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.32 % Favored : 92.52 % Rotamer: Outliers : 5.83 % Allowed : 34.89 % Favored : 59.27 % 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: -0.34 (0.25), residues: 1203 helix: 0.81 (0.22), residues: 536 sheet: -1.04 (0.45), residues: 115 loop : -1.05 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 305 TYR 0.016 0.001 TYR A 57 PHE 0.031 0.001 PHE A 131 TRP 0.034 0.001 TRP A 999 HIS 0.004 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (10807) covalent geometry : angle 0.54906 / 0.30 (14736) hydrogen bonds : bond 0.03658 / 2.39 ( 460) hydrogen bonds : angle 4.66908 / 3.18 ( 1315) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 101 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.7019 (mt) REVERT: A 70 LYS cc_start: 0.3072 (OUTLIER) cc_final: 0.2039 (mmmt) REVERT: A 109 PHE cc_start: 0.4088 (OUTLIER) cc_final: 0.3549 (m-80) REVERT: A 122 ASP cc_start: 0.8411 (m-30) cc_final: 0.8034 (m-30) REVERT: A 125 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6521 (mp0) REVERT: A 131 PHE cc_start: 0.7541 (t80) cc_final: 0.7273 (t80) REVERT: A 159 GLU cc_start: 0.5916 (tt0) cc_final: 0.5359 (tm-30) REVERT: A 187 MET cc_start: 0.2384 (mtt) cc_final: 0.2043 (mtt) REVERT: A 369 ILE cc_start: 0.6662 (OUTLIER) cc_final: 0.6369 (mm) REVERT: A 424 GLU cc_start: 0.7046 (tt0) cc_final: 0.6653 (tm-30) REVERT: A 433 GLU cc_start: 0.7407 (tp30) cc_final: 0.7063 (tp30) REVERT: A 476 GLU cc_start: 0.4615 (OUTLIER) cc_final: 0.4183 (tp30) REVERT: A 484 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.5868 (tp30) REVERT: A 535 ASP cc_start: 0.6293 (OUTLIER) cc_final: 0.5646 (t70) REVERT: A 572 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6244 (t0) REVERT: A 603 MET cc_start: 0.3516 (OUTLIER) cc_final: 0.3082 (ppp) REVERT: A 605 TYR cc_start: 0.5851 (OUTLIER) cc_final: 0.5300 (m-80) REVERT: A 613 GLN cc_start: 0.2853 (OUTLIER) cc_final: 0.2566 (tp-100) REVERT: A 631 ASP cc_start: 0.3116 (OUTLIER) cc_final: 0.2505 (p0) REVERT: A 692 LYS cc_start: 0.7821 (tttm) cc_final: 0.7603 (ttpt) REVERT: A 752 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7460 (mttp) REVERT: A 824 ASP cc_start: 0.7501 (p0) cc_final: 0.7173 (m-30) REVERT: A 887 ARG cc_start: 0.5495 (OUTLIER) cc_final: 0.4609 (ptm-80) REVERT: A 932 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7850 (mttp) REVERT: A 1035 MET cc_start: 0.7916 (ptm) cc_final: 0.7668 (ptt) REVERT: A 1064 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7921 (mttp) outliers start: 61 outliers final: 34 residues processed: 153 average time/residue: 0.4360 time to fit residues: 72.7889 Evaluate side-chains 148 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 98 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 932 LYS Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1056 ASP Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1157 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 73 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 68 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN A 975 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.196561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.150696 restraints weight = 10892.668| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.56 r_work: 0.3376 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10807 Z= 0.212 Angle : 0.623 11.189 14736 Z= 0.339 Chirality : 0.044 0.188 1616 Planarity : 0.004 0.049 1770 Dihedral : 14.788 164.393 1873 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.90 % Favored : 91.94 % Rotamer: Outliers : 5.54 % Allowed : 35.28 % Favored : 59.18 % 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: -0.52 (0.24), residues: 1203 helix: 0.56 (0.22), residues: 545 sheet: -0.93 (0.41), residues: 138 loop : -1.09 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 305 TYR 0.023 0.002 TYR A 549 PHE 0.030 0.002 PHE A 131 TRP 0.030 0.002 TRP A 999 HIS 0.007 0.001 HIS A 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (10807) covalent geometry : angle 0.62272 / 0.34 (14736) hydrogen bonds : bond 0.04361 / 2.82 ( 460) hydrogen bonds : angle 4.82914 / 3.28 ( 1315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4352.28 seconds wall clock time: 74 minutes 37.65 seconds (4477.65 seconds total)