Starting phenix.real_space_refine on Fri Aug 7 02:20:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kwb_62606/08_2026/9kwb_62606_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kwb_62606/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9kwb_62606/08_2026/9kwb_62606_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kwb_62606/08_2026/9kwb_62606_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kwb_62606/08_2026/9kwb_62606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kwb_62606/08_2026/9kwb_62606.map" } 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): 0.17s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 2.41, per 1000 atoms: 0.23 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: 0.96 Conformation dependent library (CDL) restraints added in 586.2 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: 1.58 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: 2.50 Time building geometry restraints manager: 1.31 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: 13837 2.62 - 5.23: 706 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: 1356 0.133 - 0.267: 235 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: 12.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.900 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.490 ------------------------------------------------------------------------------- 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= 0.731 Angle : 1.434 13.082 14736 Z= 0.958 Chirality : 0.101 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 0.00990 / 0.73 (10807) covalent geometry : angle 1.43375 / 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 : 0.354 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: 0.7492 (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: 0.7094 (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: 0.6115 (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: 0.5271 time to fit residues: 271.5944 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 : 0.299 ------------------------------------------------------------------------------- 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: 0.0980 chunk 117 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 ASN A 30 ASN A 33 ASN 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.201285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.156659 restraints weight = 11009.343| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.58 r_work: 0.3485 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10807 Z= 0.177 Angle : 0.730 9.722 14736 Z= 0.405 Chirality : 0.048 0.438 1616 Planarity : 0.005 0.070 1770 Dihedral : 18.797 171.149 2107 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.90 % Favored : 91.44 % Rotamer: Outliers : 16.44 % Allowed : 25.33 % Favored : 58.22 % 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: -2.00 (0.23), residues: 1203 helix: -0.47 (0.21), residues: 532 sheet: -1.87 (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 174 TYR 0.024 0.002 TYR A 57 PHE 0.037 0.002 PHE A 220 TRP 0.015 0.001 TRP A 999 HIS 0.014 0.002 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (10807) covalent geometry : angle 0.73049 / 0.41 (14736) hydrogen bonds : bond 0.05323 / 3.46 ( 460) hydrogen bonds : angle 5.64196 / 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 296 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 124 time to evaluate : 0.384 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: A 29 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6027 (mp0) REVERT: A 63 ASN cc_start: 0.7840 (m-40) cc_final: 0.7583 (t0) REVERT: A 70 LYS cc_start: 0.3113 (OUTLIER) cc_final: 0.2582 (pptt) REVERT: A 116 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.6730 (tmmt) REVERT: A 125 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6907 (pp20) REVERT: A 193 VAL cc_start: 0.4268 (OUTLIER) cc_final: 0.4018 (t) REVERT: A 196 ILE cc_start: 0.4256 (OUTLIER) cc_final: 0.3750 (tt) REVERT: A 219 PHE cc_start: 0.5488 (OUTLIER) cc_final: 0.5214 (t80) REVERT: A 285 GLU cc_start: 0.4894 (OUTLIER) cc_final: 0.4341 (mm-30) REVERT: A 309 ASN cc_start: 0.4414 (OUTLIER) cc_final: 0.3945 (m-40) REVERT: A 419 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6768 (tp) REVERT: A 433 GLU cc_start: 0.6678 (tp30) cc_final: 0.6448 (tp30) REVERT: A 447 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7079 (mtmt) REVERT: A 498 LEU cc_start: 0.8202 (mt) cc_final: 0.8001 (mt) REVERT: A 535 ASP cc_start: 0.6685 (OUTLIER) cc_final: 0.5913 (t0) REVERT: A 552 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7938 (mttt) REVERT: A 572 ASP cc_start: 0.6950 (OUTLIER) cc_final: 0.5916 (t0) REVERT: A 603 MET cc_start: 0.3600 (tpp) cc_final: 0.3334 (ppp) REVERT: A 611 ASP cc_start: 0.3299 (OUTLIER) cc_final: 0.3084 (t0) REVERT: A 631 ASP cc_start: 0.2825 (OUTLIER) cc_final: 0.2277 (p0) REVERT: A 683 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6351 (mm-30) REVERT: A 689 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6537 (mm-30) REVERT: A 775 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6868 (mmtt) REVERT: A 778 THR cc_start: 0.6501 (t) cc_final: 0.6285 (m) REVERT: A 795 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: A 804 LYS cc_start: 0.7467 (tttt) cc_final: 0.7256 (tptt) REVERT: A 824 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7407 (m-30) REVERT: A 887 ARG cc_start: 0.5022 (OUTLIER) cc_final: 0.3849 (mtm-85) REVERT: A 939 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7254 (pm20) REVERT: A 984 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7630 (mtmt) REVERT: A 1035 MET cc_start: 0.8137 (ptm) cc_final: 0.7856 (ptt) REVERT: A 1064 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8214 (mttp) REVERT: A 1073 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.8052 (ttt-90) REVERT: A 1118 GLN cc_start: 0.6913 (tp40) cc_final: 0.6552 (mm-40) REVERT: A 1157 SER cc_start: 0.7588 (OUTLIER) cc_final: 0.7294 (p) outliers start: 172 outliers final: 60 residues processed: 260 average time/residue: 0.5245 time to fit residues: 148.0420 Evaluate side-chains 188 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 102 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 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 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 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 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 552 LYS 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 967 THR 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: 2.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 116 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.196430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.150735 restraints weight = 10925.599| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.58 r_work: 0.3387 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10807 Z= 0.234 Angle : 0.710 10.499 14736 Z= 0.386 Chirality : 0.048 0.239 1616 Planarity : 0.005 0.050 1770 Dihedral : 16.841 165.462 1973 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.81 % Favored : 90.77 % Rotamer: Outliers : 12.14 % Allowed : 28.39 % 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: -1.39 (0.24), residues: 1203 helix: 0.01 (0.22), residues: 518 sheet: -1.63 (0.40), residues: 137 loop : -1.60 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 174 TYR 0.023 0.002 TYR A 57 PHE 0.023 0.002 PHE A 119 TRP 0.014 0.002 TRP A 999 HIS 0.008 0.001 HIS A 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 (10807) covalent geometry : angle 0.70978 / 0.39 (14736) hydrogen bonds : bond 0.05269 / 3.41 ( 460) hydrogen bonds : angle 5.35442 / 3.65 ( 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 227 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 100 time to evaluate : 0.363 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: 0.7143 (OUTLIER) cc_final: 0.6130 (mp0) REVERT: A 63 ASN cc_start: 0.7913 (m-40) cc_final: 0.7613 (t0) REVERT: A 70 LYS cc_start: 0.3188 (OUTLIER) cc_final: 0.2524 (pmtt) REVERT: A 71 LEU cc_start: 0.4935 (OUTLIER) cc_final: 0.4685 (tt) REVERT: A 101 LEU cc_start: 0.3827 (OUTLIER) cc_final: 0.3522 (tp) REVERT: A 116 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.6800 (tmmt) REVERT: A 125 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6897 (pp20) REVERT: A 193 VAL cc_start: 0.4104 (OUTLIER) cc_final: 0.3902 (t) REVERT: A 196 ILE cc_start: 0.4157 (OUTLIER) cc_final: 0.3593 (tp) REVERT: A 204 GLU cc_start: 0.5499 (OUTLIER) cc_final: 0.4900 (mp0) REVERT: A 240 ILE cc_start: 0.6374 (OUTLIER) cc_final: 0.5978 (pp) REVERT: A 255 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6485 (mt) REVERT: A 285 GLU cc_start: 0.5017 (OUTLIER) cc_final: 0.4078 (mm-30) REVERT: A 433 GLU cc_start: 0.6932 (tp30) cc_final: 0.6577 (tp30) REVERT: A 434 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7093 (tppt) REVERT: A 498 LEU cc_start: 0.8333 (mt) cc_final: 0.7861 (mp) REVERT: A 535 ASP cc_start: 0.6621 (OUTLIER) cc_final: 0.5884 (t0) REVERT: A 552 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7987 (mttt) REVERT: A 572 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.5938 (t0) REVERT: A 603 MET cc_start: 0.3625 (tpp) cc_final: 0.3313 (ppp) REVERT: A 631 ASP cc_start: 0.2840 (OUTLIER) cc_final: 0.2314 (p0) REVERT: A 683 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6398 (mm-30) REVERT: A 689 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6591 (tp30) REVERT: A 775 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6814 (mmtt) REVERT: A 824 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7329 (m-30) REVERT: A 887 ARG cc_start: 0.5311 (OUTLIER) cc_final: 0.4098 (mtm-85) REVERT: A 939 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7361 (pm20) REVERT: A 984 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7674 (mtmt) REVERT: A 1035 MET cc_start: 0.8238 (ptm) cc_final: 0.7986 (ptt) REVERT: A 1064 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8283 (mttp) REVERT: A 1104 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7627 (mp) REVERT: A 1157 SER cc_start: 0.7662 (p) cc_final: 0.7444 (p) outliers start: 127 outliers final: 54 residues processed: 205 average time/residue: 0.4905 time to fit residues: 109.6364 Evaluate side-chains 172 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 93 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 71 LEU 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 125 GLU 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 194 ASP 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 301 LEU 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 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 535 ASP 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 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 631 ASP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 683 GLU 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 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 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: 0.0970 chunk 34 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.197679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.152750 restraints weight = 10904.856| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.69 r_work: 0.3384 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10807 Z= 0.173 Angle : 0.618 6.971 14736 Z= 0.340 Chirality : 0.044 0.200 1616 Planarity : 0.004 0.049 1770 Dihedral : 16.272 167.469 1940 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.56 % Favored : 92.10 % Rotamer: Outliers : 9.66 % Allowed : 30.78 % Favored : 59.56 % 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: -1.09 (0.24), residues: 1203 helix: 0.21 (0.22), residues: 529 sheet: -1.37 (0.39), residues: 144 loop : -1.44 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 174 TYR 0.020 0.002 TYR A 57 PHE 0.027 0.002 PHE A 131 TRP 0.017 0.001 TRP A 999 HIS 0.005 0.001 HIS A 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (10807) covalent geometry : angle 0.61795 / 0.34 (14736) hydrogen bonds : bond 0.04612 / 3.01 ( 460) hydrogen bonds : angle 5.17427 / 3.53 ( 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 199 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 98 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6044 (mp0) REVERT: A 63 ASN cc_start: 0.7667 (m-40) cc_final: 0.7432 (t0) REVERT: A 64 ASP cc_start: 0.7081 (m-30) cc_final: 0.6844 (m-30) REVERT: A 70 LYS cc_start: 0.3095 (OUTLIER) cc_final: 0.2170 (mmmt) REVERT: A 71 LEU cc_start: 0.4760 (OUTLIER) cc_final: 0.4419 (tt) REVERT: A 93 GLU cc_start: 0.2752 (OUTLIER) cc_final: 0.2112 (mp0) REVERT: A 94 LEU cc_start: 0.4446 (OUTLIER) cc_final: 0.4043 (mm) REVERT: A 116 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.6789 (tmmt) REVERT: A 131 PHE cc_start: 0.7689 (t80) cc_final: 0.7487 (t80) REVERT: A 178 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7366 (mt-10) REVERT: A 196 ILE cc_start: 0.4145 (OUTLIER) cc_final: 0.3622 (tp) REVERT: A 204 GLU cc_start: 0.5503 (OUTLIER) cc_final: 0.4930 (mp0) REVERT: A 240 ILE cc_start: 0.6189 (OUTLIER) cc_final: 0.5835 (pt) REVERT: A 285 GLU cc_start: 0.4985 (OUTLIER) cc_final: 0.4295 (mm-30) REVERT: A 433 GLU cc_start: 0.7030 (tp30) cc_final: 0.6659 (tp30) REVERT: A 434 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7200 (tppt) REVERT: A 498 LEU cc_start: 0.8159 (mt) cc_final: 0.7665 (mp) REVERT: A 535 ASP cc_start: 0.6419 (OUTLIER) cc_final: 0.5707 (t70) REVERT: A 552 LYS cc_start: 0.8106 (mmpt) cc_final: 0.7877 (mttt) REVERT: A 572 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.5986 (t0) REVERT: A 603 MET cc_start: 0.3672 (tpp) cc_final: 0.3296 (ppp) REVERT: A 631 ASP cc_start: 0.2881 (OUTLIER) cc_final: 0.2297 (p0) REVERT: A 683 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6153 (mm-30) REVERT: A 689 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6613 (tp30) REVERT: A 775 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6432 (mmtt) REVERT: A 824 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7244 (m-30) REVERT: A 887 ARG cc_start: 0.5257 (OUTLIER) cc_final: 0.4062 (mtm-85) REVERT: A 939 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7215 (pm20) REVERT: A 984 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7637 (mtmt) REVERT: A 1035 MET cc_start: 0.8090 (ptm) cc_final: 0.7824 (ptt) REVERT: A 1064 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8106 (mttp) outliers start: 101 outliers final: 49 residues processed: 180 average time/residue: 0.4563 time to fit residues: 89.6186 Evaluate side-chains 161 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 90 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 71 LEU Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 94 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 178 GLU 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 304 PHE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 333 SER 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 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 612 ILE 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 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 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 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 1134 MET Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1142 THR 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: 0.6980 chunk 106 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 64 optimal weight: 0.0030 chunk 52 optimal weight: 3.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.4306 r_free = 0.4306 target = 0.200298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.155203 restraints weight = 10841.236| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.54 r_work: 0.3449 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10807 Z= 0.132 Angle : 0.575 8.918 14736 Z= 0.316 Chirality : 0.042 0.305 1616 Planarity : 0.004 0.049 1770 Dihedral : 15.844 170.802 1919 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.65 % Favored : 92.10 % Rotamer: Outliers : 8.70 % Allowed : 31.74 % Favored : 59.56 % 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: -0.78 (0.24), residues: 1203 helix: 0.49 (0.22), residues: 534 sheet: -1.33 (0.43), residues: 116 loop : -1.31 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 305 TYR 0.019 0.001 TYR A 237 PHE 0.033 0.002 PHE A 219 TRP 0.024 0.001 TRP A 999 HIS 0.005 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (10807) covalent geometry : angle 0.57538 / 0.32 (14736) hydrogen bonds : bond 0.04063 / 2.66 ( 460) hydrogen bonds : angle 4.96835 / 3.39 ( 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 192 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 101 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6182 (mp0) REVERT: A 63 ASN cc_start: 0.7769 (m-40) cc_final: 0.7551 (t0) REVERT: A 64 ASP cc_start: 0.7229 (m-30) cc_final: 0.7008 (m-30) REVERT: A 70 LYS cc_start: 0.3231 (OUTLIER) cc_final: 0.2340 (mmmt) REVERT: A 204 GLU cc_start: 0.5520 (OUTLIER) cc_final: 0.4929 (mp0) REVERT: A 369 ILE cc_start: 0.6606 (OUTLIER) cc_final: 0.6303 (mp) REVERT: A 433 GLU cc_start: 0.7104 (tp30) cc_final: 0.6738 (tp30) REVERT: A 498 LEU cc_start: 0.8240 (mt) cc_final: 0.7770 (mp) REVERT: A 535 ASP cc_start: 0.6473 (OUTLIER) cc_final: 0.5632 (t70) REVERT: A 552 LYS cc_start: 0.8222 (mmpt) cc_final: 0.7974 (mttt) REVERT: A 572 ASP cc_start: 0.6910 (OUTLIER) cc_final: 0.5966 (t0) REVERT: A 582 ASN cc_start: 0.7048 (OUTLIER) cc_final: 0.6578 (t0) REVERT: A 603 MET cc_start: 0.3624 (tpp) cc_final: 0.3236 (ppp) REVERT: A 631 ASP cc_start: 0.2954 (OUTLIER) cc_final: 0.2340 (p0) REVERT: A 689 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6555 (mm-30) REVERT: A 782 ASP cc_start: 0.8470 (m-30) cc_final: 0.8257 (m-30) REVERT: A 824 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7325 (m-30) REVERT: A 887 ARG cc_start: 0.5258 (OUTLIER) cc_final: 0.3907 (mtm-85) REVERT: A 889 ASN cc_start: 0.6728 (OUTLIER) cc_final: 0.6373 (m110) REVERT: A 939 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7172 (pm20) REVERT: A 984 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7661 (mtmt) REVERT: A 1035 MET cc_start: 0.8108 (ptm) cc_final: 0.7836 (ptt) REVERT: A 1064 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8089 (mttp) outliers start: 91 outliers final: 43 residues processed: 174 average time/residue: 0.5127 time to fit residues: 97.1269 Evaluate side-chains 146 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 89 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 71 LEU 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 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 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 303 VAL 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 464 LYS Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ASP 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 582 ASN Chi-restraints excluded: chain A residue 592 MET 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 701 MET Chi-restraints excluded: chain A residue 739 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 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 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 1089 VAL Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1142 THR 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: 10.0000 chunk 37 optimal weight: 10.0000 chunk 104 optimal weight: 0.0370 chunk 43 optimal weight: 0.6980 chunk 75 optimal weight: 0.0000 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 53 optimal weight: 0.0170 overall best weight: 0.2700 ------------------------------------------------------------------------------- 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 = 0.4324 r_free = 0.4324 target = 0.202379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.157147 restraints weight = 10965.075| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.58 r_work: 0.3484 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10807 Z= 0.112 Angle : 0.546 7.829 14736 Z= 0.300 Chirality : 0.041 0.212 1616 Planarity : 0.003 0.050 1770 Dihedral : 15.499 173.519 1900 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.98 % Favored : 92.77 % Rotamer: Outliers : 8.03 % Allowed : 32.41 % Favored : 59.56 % 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: -0.52 (0.25), residues: 1203 helix: 0.70 (0.23), residues: 542 sheet: -1.14 (0.44), residues: 115 loop : -1.20 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 182 TYR 0.014 0.001 TYR A 237 PHE 0.027 0.001 PHE A 131 TRP 0.032 0.001 TRP A 999 HIS 0.004 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (10807) covalent geometry : angle 0.54595 / 0.30 (14736) hydrogen bonds : bond 0.03688 / 2.41 ( 460) hydrogen bonds : angle 4.74800 / 3.24 ( 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 185 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 101 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6245 (mp0) REVERT: A 63 ASN cc_start: 0.7793 (m-40) cc_final: 0.7550 (t0) REVERT: A 64 ASP cc_start: 0.7201 (m-30) cc_final: 0.6997 (m-30) REVERT: A 70 LYS cc_start: 0.3320 (OUTLIER) cc_final: 0.2561 (mmmt) REVERT: A 93 GLU cc_start: 0.2810 (OUTLIER) cc_final: 0.2043 (mp0) REVERT: A 94 LEU cc_start: 0.4348 (OUTLIER) cc_final: 0.4038 (mm) REVERT: A 109 PHE cc_start: 0.4059 (OUTLIER) cc_final: 0.3707 (m-80) REVERT: A 196 ILE cc_start: 0.4167 (OUTLIER) cc_final: 0.3607 (tp) REVERT: A 219 PHE cc_start: 0.5769 (OUTLIER) cc_final: 0.5555 (t80) REVERT: A 369 ILE cc_start: 0.6632 (OUTLIER) cc_final: 0.6291 (mm) REVERT: A 433 GLU cc_start: 0.7144 (tp30) cc_final: 0.6774 (tp30) REVERT: A 484 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.5915 (tp30) REVERT: A 498 LEU cc_start: 0.8177 (mt) cc_final: 0.7696 (mp) REVERT: A 501 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7402 (t0) REVERT: A 535 ASP cc_start: 0.6447 (OUTLIER) cc_final: 0.5659 (t70) REVERT: A 552 LYS cc_start: 0.8176 (mmpt) cc_final: 0.7959 (mttt) REVERT: A 572 ASP cc_start: 0.6899 (OUTLIER) cc_final: 0.6019 (t0) REVERT: A 603 MET cc_start: 0.3620 (tpp) cc_final: 0.3166 (ppp) REVERT: A 605 TYR cc_start: 0.5858 (OUTLIER) cc_final: 0.5314 (m-80) REVERT: A 631 ASP cc_start: 0.3049 (OUTLIER) cc_final: 0.2354 (p0) REVERT: A 689 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6512 (mm-30) REVERT: A 774 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7535 (tttp) REVERT: A 824 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7310 (m-30) REVERT: A 887 ARG cc_start: 0.5137 (OUTLIER) cc_final: 0.3770 (mtm-85) REVERT: A 889 ASN cc_start: 0.6632 (OUTLIER) cc_final: 0.6350 (m-40) REVERT: A 939 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7053 (pm20) REVERT: A 984 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7659 (mtmt) REVERT: A 1035 MET cc_start: 0.8077 (ptm) cc_final: 0.7871 (ptt) REVERT: A 1064 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8058 (mttp) outliers start: 84 outliers final: 37 residues processed: 171 average time/residue: 0.5151 time to fit residues: 95.9590 Evaluate side-chains 149 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 91 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 71 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 94 LEU 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 190 PHE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 219 PHE 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 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 304 PHE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 464 LYS 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 501 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 605 TYR 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 774 LYS 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 967 THR 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 1089 VAL Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1142 THR 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: 2.9990 chunk 65 optimal weight: 0.5980 chunk 35 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 111 optimal weight: 0.4980 chunk 84 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.200132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.154182 restraints weight = 10829.943| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.47 r_work: 0.3450 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10807 Z= 0.142 Angle : 0.566 7.531 14736 Z= 0.309 Chirality : 0.042 0.232 1616 Planarity : 0.003 0.049 1770 Dihedral : 15.289 169.685 1892 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.56 % Favored : 92.27 % Rotamer: Outliers : 7.65 % Allowed : 33.65 % Favored : 58.70 % 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: -0.51 (0.25), residues: 1203 helix: 0.67 (0.22), residues: 544 sheet: -1.11 (0.44), residues: 115 loop : -1.16 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 182 TYR 0.019 0.001 TYR A 57 PHE 0.020 0.002 PHE A 119 TRP 0.032 0.001 TRP A 999 HIS 0.005 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (10807) covalent geometry : angle 0.56572 / 0.31 (14736) hydrogen bonds : bond 0.03924 / 2.56 ( 460) hydrogen bonds : angle 4.71506 / 3.22 ( 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 178 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 98 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6321 (mp0) REVERT: A 63 ASN cc_start: 0.7812 (m-40) cc_final: 0.7543 (t0) REVERT: A 70 LYS cc_start: 0.3363 (OUTLIER) cc_final: 0.2400 (mmmt) REVERT: A 109 PHE cc_start: 0.3985 (OUTLIER) cc_final: 0.3553 (m-80) REVERT: A 121 LYS cc_start: 0.7357 (ptpp) cc_final: 0.6651 (pttm) REVERT: A 159 GLU cc_start: 0.6378 (tt0) cc_final: 0.5697 (tm-30) REVERT: A 369 ILE cc_start: 0.6660 (OUTLIER) cc_final: 0.6329 (mm) REVERT: A 424 GLU cc_start: 0.7080 (tt0) cc_final: 0.6650 (tm-30) REVERT: A 433 GLU cc_start: 0.7246 (tp30) cc_final: 0.6869 (tp30) REVERT: A 498 LEU cc_start: 0.8196 (mt) cc_final: 0.7692 (mp) REVERT: A 501 ASP cc_start: 0.7692 (m-30) cc_final: 0.7399 (t0) REVERT: A 535 ASP cc_start: 0.6438 (OUTLIER) cc_final: 0.5641 (t70) REVERT: A 552 LYS cc_start: 0.8199 (mmpt) cc_final: 0.7981 (mttt) REVERT: A 572 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6070 (t0) REVERT: A 603 MET cc_start: 0.3577 (tpp) cc_final: 0.3107 (ppp) REVERT: A 605 TYR cc_start: 0.5880 (OUTLIER) cc_final: 0.5305 (m-80) REVERT: A 613 GLN cc_start: 0.2832 (OUTLIER) cc_final: 0.2542 (tp-100) REVERT: A 631 ASP cc_start: 0.3022 (OUTLIER) cc_final: 0.2318 (p0) REVERT: A 689 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6641 (tp30) REVERT: A 692 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7793 (tmmt) REVERT: A 774 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7720 (tttp) REVERT: A 795 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: A 824 ASP cc_start: 0.7623 (p0) cc_final: 0.7318 (m-30) REVERT: A 887 ARG cc_start: 0.5235 (OUTLIER) cc_final: 0.3876 (ptt-90) REVERT: A 889 ASN cc_start: 0.6781 (OUTLIER) cc_final: 0.6536 (m-40) REVERT: A 932 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7853 (mttp) REVERT: A 939 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7164 (pm20) REVERT: A 984 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7665 (mtmt) REVERT: A 1035 MET cc_start: 0.8122 (ptm) cc_final: 0.7897 (ptt) REVERT: A 1064 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8021 (mttp) outliers start: 80 outliers final: 37 residues processed: 165 average time/residue: 0.4855 time to fit residues: 87.3497 Evaluate side-chains 147 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 92 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 71 LEU 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 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 225 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 262 TYR 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 325 PHE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 385 ARG 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 613 GLN Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 774 LYS Chi-restraints excluded: chain A residue 795 GLU 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 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 1089 VAL Chi-restraints excluded: chain A residue 1142 THR 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: 7.9990 chunk 39 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 115 optimal weight: 0.0020 chunk 25 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 overall best weight: 2.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4253 r_free = 0.4253 target = 0.194800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.149291 restraints weight = 10796.695| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.69 r_work: 0.3329 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 10807 Z= 0.293 Angle : 0.733 9.059 14736 Z= 0.396 Chirality : 0.050 0.327 1616 Planarity : 0.005 0.050 1770 Dihedral : 15.203 161.830 1884 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.48 % Favored : 91.35 % Rotamer: Outliers : 7.46 % Allowed : 33.84 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.24), residues: 1203 helix: 0.32 (0.22), residues: 530 sheet: -1.09 (0.43), residues: 127 loop : -1.30 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 887 TYR 0.025 0.002 TYR A 57 PHE 0.028 0.003 PHE A 131 TRP 0.012 0.002 TRP A 999 HIS 0.012 0.002 HIS A 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.29 (10807) covalent geometry : angle 0.73332 / 0.40 (14736) hydrogen bonds : bond 0.05108 / 3.32 ( 460) hydrogen bonds : angle 5.07010 / 3.44 ( 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 175 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 97 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6338 (mp0) REVERT: A 63 ASN cc_start: 0.7796 (m-40) cc_final: 0.7517 (t0) REVERT: A 70 LYS cc_start: 0.3325 (OUTLIER) cc_final: 0.2428 (mmmt) REVERT: A 71 LEU cc_start: 0.4594 (OUTLIER) cc_final: 0.3896 (tp) REVERT: A 109 PHE cc_start: 0.4062 (OUTLIER) cc_final: 0.3490 (m-80) REVERT: A 187 MET cc_start: 0.2609 (mtt) cc_final: 0.2284 (mtt) REVERT: A 369 ILE cc_start: 0.6614 (OUTLIER) cc_final: 0.6265 (mp) REVERT: A 433 GLU cc_start: 0.7310 (tp30) cc_final: 0.6920 (tp30) REVERT: A 498 LEU cc_start: 0.8155 (mt) cc_final: 0.7645 (mp) REVERT: A 535 ASP cc_start: 0.6418 (OUTLIER) cc_final: 0.5693 (t70) REVERT: A 552 LYS cc_start: 0.8139 (mmpt) cc_final: 0.7866 (mttt) REVERT: A 572 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6155 (t0) REVERT: A 603 MET cc_start: 0.3641 (tpp) cc_final: 0.3112 (ppp) REVERT: A 605 TYR cc_start: 0.5960 (OUTLIER) cc_final: 0.5354 (m-80) REVERT: A 613 GLN cc_start: 0.2982 (OUTLIER) cc_final: 0.2709 (tp-100) REVERT: A 631 ASP cc_start: 0.3150 (OUTLIER) cc_final: 0.2470 (p0) REVERT: A 689 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6494 (mm-30) REVERT: A 692 LYS cc_start: 0.8088 (tmmt) cc_final: 0.7821 (ttpm) REVERT: A 782 ASP cc_start: 0.8434 (m-30) cc_final: 0.8228 (m-30) REVERT: A 824 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7252 (m-30) REVERT: A 887 ARG cc_start: 0.5500 (OUTLIER) cc_final: 0.4524 (ptm-80) REVERT: A 889 ASN cc_start: 0.6869 (OUTLIER) cc_final: 0.6593 (m-40) REVERT: A 932 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7978 (mttp) REVERT: A 939 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7503 (pm20) REVERT: A 984 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7629 (mtmt) REVERT: A 1035 MET cc_start: 0.8145 (ptm) cc_final: 0.7883 (ptt) REVERT: A 1064 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8110 (mttp) outliers start: 78 outliers final: 41 residues processed: 162 average time/residue: 0.5403 time to fit residues: 95.0536 Evaluate side-chains 149 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 91 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 71 LEU 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 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 225 PHE Chi-restraints excluded: chain A residue 229 LEU 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 285 GLU 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 369 ILE Chi-restraints excluded: chain A residue 377 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 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 586 LEU Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 592 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 739 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 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 1131 MET Chi-restraints excluded: chain A residue 1134 MET 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: 0.0470 chunk 32 optimal weight: 9.9990 chunk 54 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.199670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.154001 restraints weight = 10906.704| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.51 r_work: 0.3436 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10807 Z= 0.135 Angle : 0.597 7.672 14736 Z= 0.327 Chirality : 0.042 0.240 1616 Planarity : 0.004 0.049 1770 Dihedral : 15.102 169.450 1883 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.98 % Favored : 92.85 % Rotamer: Outliers : 5.93 % Allowed : 35.28 % 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: -0.58 (0.24), residues: 1203 helix: 0.59 (0.22), residues: 541 sheet: -1.12 (0.45), residues: 111 loop : -1.19 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 82 TYR 0.018 0.001 TYR A 57 PHE 0.032 0.002 PHE A 131 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 0.00290 / 0.14 (10807) covalent geometry : angle 0.59651 / 0.33 (14736) hydrogen bonds : bond 0.03949 / 2.60 ( 460) hydrogen bonds : angle 4.80150 / 3.27 ( 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 160 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 98 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6258 (mp0) REVERT: A 63 ASN cc_start: 0.7820 (m-40) cc_final: 0.7567 (t0) REVERT: A 70 LYS cc_start: 0.3454 (OUTLIER) cc_final: 0.2456 (mmmt) REVERT: A 71 LEU cc_start: 0.4591 (OUTLIER) cc_final: 0.3895 (tp) REVERT: A 109 PHE cc_start: 0.4226 (OUTLIER) cc_final: 0.3650 (m-80) REVERT: A 159 GLU cc_start: 0.6202 (tt0) cc_final: 0.5605 (tm-30) REVERT: A 187 MET cc_start: 0.2710 (mtt) cc_final: 0.2448 (mtt) REVERT: A 369 ILE cc_start: 0.6668 (OUTLIER) cc_final: 0.6350 (mm) REVERT: A 424 GLU cc_start: 0.7111 (tt0) cc_final: 0.6693 (tm-30) REVERT: A 433 GLU cc_start: 0.7307 (tp30) cc_final: 0.6946 (tp30) REVERT: A 498 LEU cc_start: 0.8198 (mt) cc_final: 0.7686 (mp) REVERT: A 535 ASP cc_start: 0.6455 (OUTLIER) cc_final: 0.5672 (t70) REVERT: A 552 LYS cc_start: 0.8227 (mmpt) cc_final: 0.7967 (mttt) REVERT: A 572 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6192 (t0) REVERT: A 603 MET cc_start: 0.3531 (tpp) cc_final: 0.3086 (ppp) REVERT: A 631 ASP cc_start: 0.3057 (OUTLIER) cc_final: 0.2349 (p0) REVERT: A 689 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6667 (tp30) REVERT: A 692 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7902 (tttm) REVERT: A 782 ASP cc_start: 0.8477 (m-30) cc_final: 0.8272 (m-30) REVERT: A 824 ASP cc_start: 0.7657 (p0) cc_final: 0.7280 (m-30) REVERT: A 887 ARG cc_start: 0.5619 (OUTLIER) cc_final: 0.4495 (ptm-80) REVERT: A 939 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7320 (pm20) REVERT: A 984 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7701 (mtmt) REVERT: A 1035 MET cc_start: 0.8147 (ptm) cc_final: 0.7915 (ptt) REVERT: A 1064 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8037 (mttp) outliers start: 62 outliers final: 31 residues processed: 150 average time/residue: 0.5016 time to fit residues: 82.0613 Evaluate side-chains 136 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 92 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 71 LEU 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 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 283 ASP Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 377 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 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 586 LEU Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 739 SER 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 935 ARG 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 1131 MET 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: 2.9990 chunk 94 optimal weight: 0.8980 chunk 43 optimal weight: 0.0030 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 16 optimal weight: 0.0370 chunk 117 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.4668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.201490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.156497 restraints weight = 10788.575| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.51 r_work: 0.3461 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10807 Z= 0.124 Angle : 0.578 10.448 14736 Z= 0.314 Chirality : 0.042 0.240 1616 Planarity : 0.004 0.049 1770 Dihedral : 14.973 171.820 1883 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.98 % Favored : 92.85 % Rotamer: Outliers : 4.78 % Allowed : 36.42 % 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: -0.35 (0.25), residues: 1203 helix: 0.79 (0.22), residues: 545 sheet: -1.05 (0.45), residues: 115 loop : -1.06 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 305 TYR 0.016 0.001 TYR A 57 PHE 0.031 0.001 PHE A 131 TRP 0.022 0.001 TRP A 999 HIS 0.005 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (10807) covalent geometry : angle 0.57800 / 0.31 (14736) hydrogen bonds : bond 0.03707 / 2.41 ( 460) hydrogen bonds : angle 4.59322 / 3.13 ( 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 150 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 100 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.7866 (m-40) cc_final: 0.7513 (t0) REVERT: A 70 LYS cc_start: 0.3437 (OUTLIER) cc_final: 0.2447 (mmmt) REVERT: A 71 LEU cc_start: 0.4465 (OUTLIER) cc_final: 0.3798 (tp) REVERT: A 109 PHE cc_start: 0.4071 (OUTLIER) cc_final: 0.3561 (m-80) REVERT: A 121 LYS cc_start: 0.7387 (ptpp) cc_final: 0.7003 (tttt) REVERT: A 125 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7051 (pp20) REVERT: A 131 PHE cc_start: 0.7546 (t80) cc_final: 0.7299 (t80) REVERT: A 187 MET cc_start: 0.2385 (mtt) cc_final: 0.2138 (mtt) REVERT: A 369 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6386 (mm) REVERT: A 424 GLU cc_start: 0.7102 (tt0) cc_final: 0.6695 (tm-30) REVERT: A 433 GLU cc_start: 0.7398 (tp30) cc_final: 0.7008 (tp30) REVERT: A 501 ASP cc_start: 0.7856 (m-30) cc_final: 0.7323 (t0) REVERT: A 535 ASP cc_start: 0.6443 (OUTLIER) cc_final: 0.5711 (t70) REVERT: A 537 ASP cc_start: 0.7658 (m-30) cc_final: 0.6859 (t0) REVERT: A 552 LYS cc_start: 0.8189 (mmpt) cc_final: 0.7961 (mttt) REVERT: A 572 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6104 (t0) REVERT: A 603 MET cc_start: 0.3551 (OUTLIER) cc_final: 0.3066 (ppp) REVERT: A 631 ASP cc_start: 0.3164 (OUTLIER) cc_final: 0.2478 (p0) REVERT: A 689 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6626 (tp30) REVERT: A 692 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7821 (ttpm) REVERT: A 782 ASP cc_start: 0.8443 (m-30) cc_final: 0.8232 (m-30) REVERT: A 824 ASP cc_start: 0.7684 (p0) cc_final: 0.7298 (m-30) REVERT: A 887 ARG cc_start: 0.5473 (OUTLIER) cc_final: 0.4446 (ptm-80) REVERT: A 939 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7106 (pm20) REVERT: A 1064 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8054 (mttp) outliers start: 50 outliers final: 23 residues processed: 142 average time/residue: 0.5136 time to fit residues: 81.0575 Evaluate side-chains 132 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 204 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 283 ASP Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 377 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 535 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 603 MET Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 935 ARG 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 1144 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 73 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 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 = 0.4307 r_free = 0.4307 target = 0.200373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.155088 restraints weight = 10874.420| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.55 r_work: 0.3439 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4931 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= 0.142 Angle : 0.587 11.815 14736 Z= 0.317 Chirality : 0.042 0.250 1616 Planarity : 0.004 0.049 1770 Dihedral : 14.714 169.473 1872 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.07 % Favored : 92.77 % Rotamer: Outliers : 4.68 % Allowed : 36.62 % Favored : 58.70 % 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: -0.38 (0.24), residues: 1203 helix: 0.74 (0.22), residues: 545 sheet: -1.03 (0.45), residues: 115 loop : -1.06 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 836 TYR 0.018 0.001 TYR A 237 PHE 0.029 0.002 PHE A 131 TRP 0.019 0.001 TRP A 999 HIS 0.004 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (10807) covalent geometry : angle 0.58742 / 0.32 (14736) hydrogen bonds : bond 0.03799 / 2.48 ( 460) hydrogen bonds : angle 4.62718 / 3.16 ( 1315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4973.82 seconds wall clock time: 85 minutes 13.68 seconds (5113.68 seconds total)