Starting phenix.real_space_refine on Thu Sep 18 17:41:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kwb_62606/09_2025/9kwb_62606_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kwb_62606/09_2025/9kwb_62606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kwb_62606/09_2025/9kwb_62606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kwb_62606/09_2025/9kwb_62606.map" model { file = "/net/cci-nas-00/data/ceres_data/9kwb_62606/09_2025/9kwb_62606_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kwb_62606/09_2025/9kwb_62606_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9728 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 28 5.16 5 C 6624 2.51 5 N 1723 2.21 5 O 2105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 2.45, 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: 0.86 Conformation dependent library (CDL) restraints added in 419.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.02 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: 2.14 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1734 1.31 - 1.44: 3144 1.44 - 1.56: 5813 1.56 - 1.68: 69 1.68 - 1.81: 47 Bond restraints: 10807 Sorted by residual: bond pdb=" CA ALA A 166 " pdb=" C ALA A 166 " ideal model delta sigma weight residual 1.533 1.510 0.023 5.60e-03 3.19e+04 1.73e+01 bond pdb=" CA LYS A 937 " pdb=" C LYS A 937 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.34e-02 5.57e+03 1.63e+01 bond pdb=" CA ALA A 920 " pdb=" C ALA A 920 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.19e-02 7.06e+03 1.62e+01 bond pdb=" CA LYS A 110 " pdb=" C LYS A 110 " ideal model delta sigma weight residual 1.522 1.572 -0.049 1.26e-02 6.30e+03 1.54e+01 bond pdb=" CA GLU A 981 " pdb=" C GLU A 981 " ideal model delta sigma weight residual 1.523 1.491 0.032 8.40e-03 1.42e+04 1.45e+01 ... (remaining 10802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 13824 2.62 - 5.23: 719 5.23 - 7.85: 148 7.85 - 10.47: 36 10.47 - 13.08: 9 Bond angle restraints: 14736 Sorted by residual: angle pdb=" N SER A 68 " pdb=" CA SER A 68 " pdb=" C SER A 68 " ideal model delta sigma weight residual 114.62 101.54 13.08 1.14e+00 7.69e-01 1.32e+02 angle pdb=" N VAL A 216 " pdb=" CA VAL A 216 " pdb=" C VAL A 216 " ideal model delta sigma weight residual 113.53 103.67 9.86 9.80e-01 1.04e+00 1.01e+02 angle pdb=" N TYR A 290 " pdb=" CA TYR A 290 " pdb=" C TYR A 290 " ideal model delta sigma weight residual 113.38 101.40 11.98 1.23e+00 6.61e-01 9.49e+01 angle pdb=" N MET A 161 " pdb=" CA MET A 161 " pdb=" C MET A 161 " ideal model delta sigma weight residual 112.90 100.87 12.03 1.31e+00 5.83e-01 8.43e+01 angle pdb=" N PHE A 315 " pdb=" CA PHE A 315 " pdb=" C PHE A 315 " ideal model delta sigma weight residual 111.36 102.98 8.38 1.09e+00 8.42e-01 5.91e+01 ... (remaining 14731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 5726 35.36 - 70.72: 751 70.72 - 106.09: 32 106.09 - 141.45: 0 141.45 - 176.81: 2 Dihedral angle restraints: 6511 sinusoidal: 2925 harmonic: 3586 Sorted by residual: dihedral pdb=" O4' U B 16 " pdb=" C1' U B 16 " pdb=" N1 U B 16 " pdb=" C2 U B 16 " ideal model delta sinusoidal sigma weight residual 232.00 56.23 175.77 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" C5' A B 14 " pdb=" C4' A B 14 " pdb=" C3' A B 14 " pdb=" O3' A B 14 " ideal model delta sinusoidal sigma weight residual 147.00 94.96 52.04 1 8.00e+00 1.56e-02 5.77e+01 dihedral pdb=" C VAL A 300 " pdb=" N VAL A 300 " pdb=" CA VAL A 300 " pdb=" CB VAL A 300 " ideal model delta harmonic sigma weight residual -122.00 -135.99 13.99 0 2.50e+00 1.60e-01 3.13e+01 ... (remaining 6508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1343 0.133 - 0.267: 248 0.267 - 0.400: 21 0.400 - 0.533: 2 0.533 - 0.667: 2 Chirality restraints: 1616 Sorted by residual: chirality pdb=" C3' A B 14 " pdb=" C4' A B 14 " pdb=" O3' A B 14 " pdb=" C2' A B 14 " both_signs ideal model delta sigma weight residual False -2.74 -2.08 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA THR A 777 " pdb=" N THR A 777 " pdb=" C THR A 777 " pdb=" CB THR A 777 " both_signs ideal model delta sigma weight residual False 2.53 1.96 0.56 2.00e-01 2.50e+01 7.92e+00 chirality pdb=" CA THR A 778 " pdb=" N THR A 778 " pdb=" C THR A 778 " pdb=" CB THR A 778 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 1613 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 607 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.60e+00 pdb=" N PRO A 608 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 608 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 608 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1175 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A1176 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A1176 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1176 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 128 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.32e+00 pdb=" N PRO A 129 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " -0.030 5.00e-02 4.00e+02 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 4093 2.88 - 3.38: 9735 3.38 - 3.89: 20605 3.89 - 4.39: 24877 4.39 - 4.90: 36616 Nonbonded interactions: 95926 Sorted by model distance: nonbonded pdb=" N LYS A 775 " pdb=" O LYS A 775 " model vdw 2.371 2.496 nonbonded pdb=" N ASN A 706 " pdb=" O ASN A 706 " model vdw 2.415 2.496 nonbonded pdb=" N LEU A 446 " pdb=" N LYS A 447 " model vdw 2.421 2.560 nonbonded pdb=" N ILE A1004 " pdb=" O ILE A1004 " model vdw 2.424 2.496 nonbonded pdb=" N TYR A 290 " pdb=" N GLY A 291 " model vdw 2.433 2.560 ... (remaining 95921 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.600 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.620 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 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= 0.727 Angle : 1.439 13.082 14736 Z= 0.960 Chirality : 0.102 0.667 1616 Planarity : 0.005 0.059 1770 Dihedral : 25.395 176.810 4203 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 1.91 % Allowed : 10.72 % Favored : 87.36 % Rotamer: Outliers : 35.76 % Allowed : 14.72 % Favored : 49.52 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00989 (10807) covalent geometry : angle 1.43883 (14736) hydrogen bonds : bond 0.18773 ( 460) hydrogen bonds : angle 7.96032 ( 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 : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7095 (mtpt) REVERT: A 29 GLU cc_start: 0.6091 (OUTLIER) cc_final: 0.5166 (mp0) REVERT: A 35 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6665 (mtm180) REVERT: A 39 GLU cc_start: 0.6753 (pm20) cc_final: 0.6229 (mm-30) REVERT: A 70 LYS cc_start: 0.3311 (OUTLIER) cc_final: 0.2921 (pptt) REVERT: A 105 ILE cc_start: 0.4965 (OUTLIER) cc_final: 0.4710 (pt) REVERT: A 116 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6457 (tmmt) REVERT: A 125 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: A 196 ILE cc_start: 0.4293 (OUTLIER) cc_final: 0.3836 (tp) REVERT: A 204 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.5340 (mp0) REVERT: A 207 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6567 (mm-30) REVERT: A 215 ASP cc_start: 0.6245 (OUTLIER) cc_final: 0.5885 (m-30) REVERT: A 309 ASN cc_start: 0.3918 (OUTLIER) cc_final: 0.3310 (t0) REVERT: A 313 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.7011 (mm-30) REVERT: A 318 ILE cc_start: 0.6427 (OUTLIER) cc_final: 0.6212 (mt) REVERT: A 332 SER cc_start: 0.4713 (OUTLIER) cc_final: 0.4394 (p) REVERT: A 419 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6733 (OUTLIER) REVERT: A 433 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6583 (tp30) REVERT: A 476 GLU cc_start: 0.5841 (OUTLIER) cc_final: 0.5571 (tm-30) REVERT: A 552 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7112 (mttt) REVERT: A 572 ASP cc_start: 0.6085 (OUTLIER) cc_final: 0.4905 (t0) REVERT: A 600 LYS cc_start: 0.1322 (OUTLIER) cc_final: 0.1104 (mttp) REVERT: A 611 ASP cc_start: 0.3162 (OUTLIER) cc_final: 0.2838 (t0) REVERT: A 631 ASP cc_start: 0.3425 (OUTLIER) cc_final: 0.2917 (p0) REVERT: A 645 ARG cc_start: 0.4441 (OUTLIER) cc_final: 0.3971 (mmm160) REVERT: A 648 LYS cc_start: 0.5662 (OUTLIER) cc_final: 0.4816 (mtpp) REVERT: A 689 GLU cc_start: 0.6470 (mt-10) cc_final: 0.6115 (mm-30) REVERT: A 713 SER cc_start: 0.7729 (OUTLIER) cc_final: 0.7491 (m) REVERT: A 746 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8477 (tpp) REVERT: A 752 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6792 (mttp) REVERT: A 804 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6836 (tptt) REVERT: A 824 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7069 (m-30) REVERT: A 836 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7845 (mpt-90) REVERT: A 847 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7177 (mmtt) REVERT: A 867 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7019 (mpp80) REVERT: A 887 ARG cc_start: 0.5437 (OUTLIER) cc_final: 0.4797 (mtp-110) REVERT: A 888 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.7083 (mp-120) REVERT: A 898 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7095 (mt-10) REVERT: A 939 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6205 (pm20) REVERT: A 972 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6678 (tttt) REVERT: A 984 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.6789 (mtmt) REVERT: A 1062 LYS cc_start: 0.6832 (mmtm) cc_final: 0.6573 (mtmm) REVERT: A 1064 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7531 (mttp) REVERT: A 1073 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6966 (ttt-90) REVERT: A 1075 PHE cc_start: 0.6583 (p90) cc_final: 0.6116 (p90) REVERT: A 1088 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7246 (tp30) REVERT: A 1108 GLN cc_start: 0.6754 (OUTLIER) cc_final: 0.6440 (tp40) REVERT: A 1118 GLN cc_start: 0.6082 (tp40) cc_final: 0.5844 (mm-40) REVERT: A 1155 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8222 (mttt) outliers start: 374 outliers final: 71 residues processed: 478 average time/residue: 0.5646 time to fit residues: 289.6287 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 : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 622 LYS Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 804 LYS Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 965 CYS Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1049 TYR Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1073 ARG Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1117 GLU Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1207 ASP Chi-restraints excluded: chain A residue 1224 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.1980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN A 30 ASN A 33 ASN A 67 HIS ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 607 ASN A 703 GLN A 767 ASN A 772 ASN A 895 ASN A 941 GLN A 955 ASN A 975 GLN A1100 ASN A1108 GLN A1136 GLN A1139 ASN 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 = 0.4337 r_free = 0.4337 target = 0.202011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.157763 restraints weight = 11027.781| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.51 r_work: 0.3513 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10807 Z= 0.163 Angle : 0.687 10.788 14736 Z= 0.373 Chirality : 0.045 0.193 1616 Planarity : 0.005 0.053 1770 Dihedral : 18.094 166.479 2107 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.90 % Favored : 91.69 % Rotamer: Outliers : 13.29 % Allowed : 28.11 % Favored : 58.60 % 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 aren not related in a simple way. whole: -1.80 (0.23), residues: 1203 helix: -0.31 (0.21), residues: 529 sheet: -1.74 (0.43), residues: 122 loop : -1.92 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 174 TYR 0.023 0.002 TYR A 237 PHE 0.035 0.002 PHE A 220 TRP 0.017 0.001 TRP A 999 HIS 0.013 0.002 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00352 (10807) covalent geometry : angle 0.68723 (14736) hydrogen bonds : bond 0.04706 ( 460) hydrogen bonds : angle 5.37811 ( 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 263 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 124 time to evaluate : 0.426 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: A 29 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6131 (mp0) REVERT: A 64 ASP cc_start: 0.7318 (m-30) cc_final: 0.7024 (m-30) REVERT: A 70 LYS cc_start: 0.3257 (OUTLIER) cc_final: 0.2495 (mmmt) REVERT: A 116 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.6792 (tmmt) REVERT: A 125 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: A 193 VAL cc_start: 0.3996 (OUTLIER) cc_final: 0.3747 (t) REVERT: A 196 ILE cc_start: 0.4169 (OUTLIER) cc_final: 0.3739 (tp) REVERT: A 215 ASP cc_start: 0.4963 (OUTLIER) cc_final: 0.4485 (m-30) REVERT: A 240 ILE cc_start: 0.6281 (OUTLIER) cc_final: 0.5830 (pp) REVERT: A 241 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7243 (mm) REVERT: A 255 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6338 (mp) REVERT: A 285 GLU cc_start: 0.4960 (OUTLIER) cc_final: 0.4559 (mm-30) REVERT: A 385 ARG cc_start: 0.6700 (ttp80) cc_final: 0.6497 (mtp85) REVERT: A 433 GLU cc_start: 0.6785 (tp30) cc_final: 0.6446 (tp30) REVERT: A 498 LEU cc_start: 0.8242 (mt) cc_final: 0.7837 (mp) REVERT: A 535 ASP cc_start: 0.6676 (OUTLIER) cc_final: 0.6013 (t0) REVERT: A 539 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6719 (tt0) REVERT: A 572 ASP cc_start: 0.6987 (OUTLIER) cc_final: 0.6048 (t0) REVERT: A 603 MET cc_start: 0.3604 (tpp) cc_final: 0.3258 (ppp) REVERT: A 631 ASP cc_start: 0.2848 (OUTLIER) cc_final: 0.2285 (p0) REVERT: A 683 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6335 (mm-30) REVERT: A 689 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6612 (tp30) REVERT: A 775 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6779 (mmtt) REVERT: A 778 THR cc_start: 0.6371 (t) cc_final: 0.6083 (m) REVERT: A 824 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7385 (m-30) REVERT: A 887 ARG cc_start: 0.5254 (OUTLIER) cc_final: 0.4073 (mtm-85) REVERT: A 939 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: A 984 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7680 (mtmt) REVERT: A 1035 MET cc_start: 0.8138 (ptm) cc_final: 0.7905 (ptt) REVERT: A 1064 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8200 (mttp) REVERT: A 1118 GLN cc_start: 0.6993 (tp40) cc_final: 0.6475 (mm-40) REVERT: A 1157 SER cc_start: 0.7652 (p) cc_final: 0.7439 (p) outliers start: 139 outliers final: 52 residues processed: 235 average time/residue: 0.6053 time to fit residues: 152.8986 Evaluate side-chains 166 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 93 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 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 215 ASP 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 240 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 259 ILE 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 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 312 SER Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 595 LYS 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 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 1142 THR 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: 0.6980 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 177 ASN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN 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 = 0.4255 r_free = 0.4255 target = 0.194770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.148269 restraints weight = 10892.881| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.53 r_work: 0.3364 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10807 Z= 0.271 Angle : 0.702 7.488 14736 Z= 0.381 Chirality : 0.047 0.202 1616 Planarity : 0.005 0.052 1770 Dihedral : 16.307 158.898 1945 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.65 % Favored : 90.94 % Rotamer: Outliers : 11.28 % Allowed : 29.16 % 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 aren not related in a simple way. whole: -1.41 (0.24), residues: 1203 helix: -0.07 (0.21), residues: 524 sheet: -1.62 (0.40), residues: 133 loop : -1.57 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 836 TYR 0.024 0.002 TYR A 57 PHE 0.023 0.002 PHE A 131 TRP 0.011 0.002 TRP A1086 HIS 0.010 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00606 (10807) covalent geometry : angle 0.70197 (14736) hydrogen bonds : bond 0.05147 ( 460) hydrogen bonds : angle 5.28997 ( 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 225 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 107 time to evaluate : 0.426 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: 0.7286 (OUTLIER) cc_final: 0.6266 (mp0) REVERT: A 63 ASN cc_start: 0.8020 (t0) cc_final: 0.7807 (t0) REVERT: A 64 ASP cc_start: 0.7383 (m-30) cc_final: 0.7130 (m-30) REVERT: A 70 LYS cc_start: 0.3272 (OUTLIER) cc_final: 0.2274 (mmmt) REVERT: A 93 GLU cc_start: 0.2745 (OUTLIER) cc_final: 0.1996 (mp0) REVERT: A 94 LEU cc_start: 0.4361 (OUTLIER) cc_final: 0.3994 (mm) REVERT: A 109 PHE cc_start: 0.4279 (OUTLIER) cc_final: 0.3940 (m-80) REVERT: A 193 VAL cc_start: 0.3836 (OUTLIER) cc_final: 0.3636 (t) REVERT: A 204 GLU cc_start: 0.5421 (OUTLIER) cc_final: 0.4870 (mp0) REVERT: A 219 PHE cc_start: 0.5710 (OUTLIER) cc_final: 0.5429 (t80) REVERT: A 240 ILE cc_start: 0.6364 (OUTLIER) cc_final: 0.5926 (pt) REVERT: A 255 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6444 (mt) REVERT: A 313 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6892 (mm-30) REVERT: A 433 GLU cc_start: 0.7102 (tp30) cc_final: 0.6718 (tp30) REVERT: A 498 LEU cc_start: 0.8266 (mt) cc_final: 0.7796 (mp) REVERT: A 535 ASP cc_start: 0.6695 (OUTLIER) cc_final: 0.5793 (t70) REVERT: A 572 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6010 (t0) REVERT: A 603 MET cc_start: 0.3668 (OUTLIER) cc_final: 0.3264 (ppp) REVERT: A 631 ASP cc_start: 0.3002 (OUTLIER) cc_final: 0.2474 (p0) REVERT: A 683 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6050 (mm-30) REVERT: A 689 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6543 (mm-30) REVERT: A 824 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7364 (m-30) REVERT: A 887 ARG cc_start: 0.5478 (OUTLIER) cc_final: 0.4053 (mtm-85) REVERT: A 889 ASN cc_start: 0.6874 (OUTLIER) cc_final: 0.6486 (m110) REVERT: A 939 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7468 (pm20) REVERT: A 984 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7703 (mtmt) REVERT: A 1035 MET cc_start: 0.8269 (ptm) cc_final: 0.7980 (ptt) REVERT: A 1064 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8332 (mttp) outliers start: 118 outliers final: 55 residues processed: 204 average time/residue: 0.5786 time to fit residues: 127.4707 Evaluate side-chains 171 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 94 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 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 133 ASP 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 203 GLN Chi-restraints excluded: chain A residue 204 GLU 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 240 ILE Chi-restraints excluded: chain A residue 253 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 294 TYR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 380 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 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 603 MET Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 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 1140 SER Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1144 ARG Chi-restraints excluded: chain A residue 1207 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 74 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 56 optimal weight: 0.0010 chunk 34 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 889 ASN A 975 GLN A1118 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.197918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.152121 restraints weight = 10870.291| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.66 r_work: 0.3402 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10807 Z= 0.159 Angle : 0.592 7.709 14736 Z= 0.320 Chirality : 0.042 0.179 1616 Planarity : 0.004 0.050 1770 Dihedral : 15.752 163.447 1919 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.07 % Favored : 92.68 % Rotamer: Outliers : 9.66 % Allowed : 29.92 % Favored : 60.42 % 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 aren not related in a simple way. whole: -0.98 (0.24), residues: 1203 helix: 0.33 (0.22), residues: 537 sheet: -1.42 (0.44), residues: 112 loop : -1.43 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 385 TYR 0.024 0.001 TYR A 237 PHE 0.026 0.002 PHE A 131 TRP 0.015 0.001 TRP A 999 HIS 0.005 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00350 (10807) covalent geometry : angle 0.59154 (14736) hydrogen bonds : bond 0.04141 ( 460) hydrogen bonds : angle 4.96163 ( 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 208 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 107 time to evaluate : 0.414 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: A 29 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6254 (mp0) REVERT: A 63 ASN cc_start: 0.8010 (t0) cc_final: 0.7709 (t0) REVERT: A 64 ASP cc_start: 0.7120 (m-30) cc_final: 0.6862 (m-30) REVERT: A 70 LYS cc_start: 0.3171 (OUTLIER) cc_final: 0.2274 (mmmt) REVERT: A 71 LEU cc_start: 0.4644 (OUTLIER) cc_final: 0.3988 (tt) REVERT: A 89 LYS cc_start: 0.4376 (OUTLIER) cc_final: 0.4141 (ptpt) REVERT: A 219 PHE cc_start: 0.5482 (OUTLIER) cc_final: 0.5279 (t80) REVERT: A 240 ILE cc_start: 0.6213 (OUTLIER) cc_final: 0.5853 (pt) REVERT: A 369 ILE cc_start: 0.6591 (OUTLIER) cc_final: 0.6258 (mp) REVERT: A 385 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.6385 (mtp85) REVERT: A 433 GLU cc_start: 0.7188 (tp30) cc_final: 0.6843 (tp30) REVERT: A 498 LEU cc_start: 0.8110 (mt) cc_final: 0.7615 (mp) REVERT: A 535 ASP cc_start: 0.6409 (OUTLIER) cc_final: 0.5616 (t70) REVERT: A 572 ASP cc_start: 0.6940 (OUTLIER) cc_final: 0.6128 (t0) REVERT: A 603 MET cc_start: 0.3506 (tpp) cc_final: 0.3212 (ppp) REVERT: A 631 ASP cc_start: 0.3025 (OUTLIER) cc_final: 0.2397 (p0) REVERT: A 683 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.5876 (pp20) REVERT: A 689 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6471 (mm-30) REVERT: A 824 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7230 (m-30) REVERT: A 887 ARG cc_start: 0.5822 (OUTLIER) cc_final: 0.4305 (ptt-90) REVERT: A 939 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7250 (pm20) REVERT: A 1035 MET cc_start: 0.8012 (ptm) cc_final: 0.7767 (ptt) REVERT: A 1064 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8054 (mttp) outliers start: 101 outliers final: 43 residues processed: 190 average time/residue: 0.6099 time to fit residues: 124.6736 Evaluate side-chains 156 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 97 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 89 LYS Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 204 GLU 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 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 303 VAL Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 369 ILE 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 535 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 580 LYS Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 592 MET 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 683 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 1047 LEU Chi-restraints excluded: chain A residue 1056 ASP Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1144 ARG Chi-restraints excluded: chain A residue 1207 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 90 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 975 GLN A1118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.199819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.154585 restraints weight = 10811.154| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.65 r_work: 0.3422 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10807 Z= 0.133 Angle : 0.561 5.859 14736 Z= 0.302 Chirality : 0.041 0.175 1616 Planarity : 0.004 0.050 1770 Dihedral : 15.343 163.436 1904 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.23 % Favored : 92.52 % Rotamer: Outliers : 7.93 % Allowed : 32.31 % Favored : 59.75 % 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 aren not related in a simple way. whole: -0.72 (0.24), residues: 1203 helix: 0.50 (0.22), residues: 549 sheet: -1.24 (0.44), residues: 115 loop : -1.29 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 385 TYR 0.018 0.001 TYR A 57 PHE 0.027 0.002 PHE A 131 TRP 0.021 0.001 TRP A 999 HIS 0.004 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00289 (10807) covalent geometry : angle 0.56128 (14736) hydrogen bonds : bond 0.03763 ( 460) hydrogen bonds : angle 4.75880 ( 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 191 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 108 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6248 (mp0) REVERT: A 63 ASN cc_start: 0.8045 (t0) cc_final: 0.7741 (t0) REVERT: A 64 ASP cc_start: 0.7116 (m-30) cc_final: 0.6844 (m-30) REVERT: A 70 LYS cc_start: 0.3151 (OUTLIER) cc_final: 0.2155 (mmmt) REVERT: A 71 LEU cc_start: 0.4427 (OUTLIER) cc_final: 0.3783 (tt) REVERT: A 125 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: A 159 GLU cc_start: 0.6168 (tt0) cc_final: 0.5571 (tm-30) REVERT: A 219 PHE cc_start: 0.5620 (OUTLIER) cc_final: 0.5325 (t80) REVERT: A 221 GLU cc_start: 0.1968 (OUTLIER) cc_final: 0.1408 (pm20) REVERT: A 278 LYS cc_start: 0.5322 (OUTLIER) cc_final: 0.3869 (mmmt) REVERT: A 369 ILE cc_start: 0.6628 (OUTLIER) cc_final: 0.6300 (mm) REVERT: A 424 GLU cc_start: 0.7068 (tt0) cc_final: 0.6664 (tm-30) REVERT: A 433 GLU cc_start: 0.7241 (tp30) cc_final: 0.6929 (tp30) REVERT: A 484 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.5923 (tp30) REVERT: A 498 LEU cc_start: 0.8055 (mt) cc_final: 0.7555 (mp) REVERT: A 501 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7221 (t0) REVERT: A 535 ASP cc_start: 0.6328 (OUTLIER) cc_final: 0.5512 (t70) REVERT: A 572 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6160 (t0) REVERT: A 603 MET cc_start: 0.3549 (tpp) cc_final: 0.3192 (ppp) REVERT: A 613 GLN cc_start: 0.2815 (OUTLIER) cc_final: 0.2522 (tp-100) REVERT: A 631 ASP cc_start: 0.3021 (OUTLIER) cc_final: 0.2228 (p0) REVERT: A 683 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6315 (mm-30) REVERT: A 689 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6412 (mm-30) REVERT: A 692 LYS cc_start: 0.7832 (ttpm) cc_final: 0.7616 (ttpt) REVERT: A 696 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7245 (mt-10) REVERT: A 795 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: A 824 ASP cc_start: 0.7518 (p0) cc_final: 0.7216 (m-30) REVERT: A 887 ARG cc_start: 0.5675 (OUTLIER) cc_final: 0.4696 (ptm-80) REVERT: A 939 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7144 (pm20) REVERT: A 984 LYS cc_start: 0.8260 (mptt) cc_final: 0.7632 (mtmt) REVERT: A 1035 MET cc_start: 0.7973 (ptm) cc_final: 0.7715 (ptt) REVERT: A 1064 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7995 (mttp) outliers start: 83 outliers final: 37 residues processed: 177 average time/residue: 0.5495 time to fit residues: 105.3389 Evaluate side-chains 154 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 98 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 89 LYS Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 125 GLU 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 253 LYS Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 369 ILE 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 484 GLU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 501 ASP 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 590 ASN 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 683 GLU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1056 ASP Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1140 SER 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: 3.9990 chunk 43 optimal weight: 0.0270 chunk 75 optimal weight: 0.0870 chunk 55 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 975 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.198212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.152604 restraints weight = 10895.095| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.63 r_work: 0.3398 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10807 Z= 0.166 Angle : 0.587 6.308 14736 Z= 0.315 Chirality : 0.042 0.185 1616 Planarity : 0.004 0.048 1770 Dihedral : 15.017 161.765 1888 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.23 % Favored : 92.52 % Rotamer: Outliers : 8.60 % Allowed : 31.84 % 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 aren not related in a simple way. whole: -0.67 (0.24), residues: 1203 helix: 0.55 (0.22), residues: 548 sheet: -1.20 (0.44), residues: 115 loop : -1.27 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 305 TYR 0.017 0.001 TYR A 57 PHE 0.026 0.002 PHE A 131 TRP 0.021 0.001 TRP A 999 HIS 0.005 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00367 (10807) covalent geometry : angle 0.58678 (14736) hydrogen bonds : bond 0.03954 ( 460) hydrogen bonds : angle 4.77172 ( 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 188 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 98 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6227 (mp0) REVERT: A 64 ASP cc_start: 0.7140 (m-30) cc_final: 0.6898 (m-30) REVERT: A 70 LYS cc_start: 0.3254 (OUTLIER) cc_final: 0.2402 (mmmt) REVERT: A 71 LEU cc_start: 0.4414 (OUTLIER) cc_final: 0.3764 (tt) REVERT: A 159 GLU cc_start: 0.6178 (tt0) cc_final: 0.5601 (tm-30) REVERT: A 219 PHE cc_start: 0.5571 (OUTLIER) cc_final: 0.5121 (t80) REVERT: A 369 ILE cc_start: 0.6618 (OUTLIER) cc_final: 0.6302 (mm) REVERT: A 385 ARG cc_start: 0.6566 (OUTLIER) cc_final: 0.6354 (mtp85) REVERT: A 424 GLU cc_start: 0.7052 (tt0) cc_final: 0.6643 (tm-30) REVERT: A 433 GLU cc_start: 0.7374 (tp30) cc_final: 0.7037 (tp30) REVERT: A 484 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.5995 (tp30) REVERT: A 501 ASP cc_start: 0.7536 (m-30) cc_final: 0.7234 (t0) REVERT: A 535 ASP cc_start: 0.6279 (OUTLIER) cc_final: 0.5438 (t70) REVERT: A 572 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6211 (t0) REVERT: A 603 MET cc_start: 0.3602 (tpp) cc_final: 0.3157 (ppp) REVERT: A 613 GLN cc_start: 0.2879 (OUTLIER) cc_final: 0.2631 (tp-100) REVERT: A 631 ASP cc_start: 0.3109 (OUTLIER) cc_final: 0.2429 (p0) REVERT: A 683 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6378 (mm-30) REVERT: A 689 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6457 (mm-30) REVERT: A 795 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: A 824 ASP cc_start: 0.7521 (p0) cc_final: 0.7188 (m-30) REVERT: A 887 ARG cc_start: 0.5675 (OUTLIER) cc_final: 0.4657 (ptm-80) REVERT: A 939 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7270 (pm20) REVERT: A 1035 MET cc_start: 0.7996 (ptm) cc_final: 0.7749 (ptt) REVERT: A 1064 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7980 (mttp) outliers start: 90 outliers final: 44 residues processed: 176 average time/residue: 0.5270 time to fit residues: 100.6406 Evaluate side-chains 154 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 94 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 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 253 LYS Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 312 SER 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 484 GLU 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 590 ASN Chi-restraints excluded: chain A residue 592 MET 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 683 GLU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1089 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 975 GLN ** A1118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN A1139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.195626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.149063 restraints weight = 10773.972| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.49 r_work: 0.3392 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10807 Z= 0.269 Angle : 0.681 7.343 14736 Z= 0.363 Chirality : 0.047 0.207 1616 Planarity : 0.005 0.048 1770 Dihedral : 15.147 158.373 1888 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.48 % Favored : 91.35 % Rotamer: Outliers : 8.89 % Allowed : 31.07 % Favored : 60.04 % 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 aren not related in a simple way. whole: -0.94 (0.24), residues: 1203 helix: 0.28 (0.22), residues: 538 sheet: -1.17 (0.42), residues: 126 loop : -1.37 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 385 TYR 0.024 0.002 TYR A 549 PHE 0.030 0.002 PHE A 119 TRP 0.013 0.002 TRP A 999 HIS 0.008 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00614 (10807) covalent geometry : angle 0.68124 (14736) hydrogen bonds : bond 0.04735 ( 460) hydrogen bonds : angle 5.06322 ( 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 193 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 100 time to evaluate : 0.411 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: 0.7432 (OUTLIER) cc_final: 0.6397 (mp0) REVERT: A 64 ASP cc_start: 0.7304 (m-30) cc_final: 0.7067 (m-30) REVERT: A 70 LYS cc_start: 0.3327 (OUTLIER) cc_final: 0.2228 (mmmt) REVERT: A 182 ARG cc_start: 0.7144 (mtp180) cc_final: 0.6857 (mtp180) REVERT: A 219 PHE cc_start: 0.5757 (OUTLIER) cc_final: 0.5424 (t80) REVERT: A 221 GLU cc_start: 0.1915 (OUTLIER) cc_final: 0.1243 (pm20) REVERT: A 369 ILE cc_start: 0.6679 (OUTLIER) cc_final: 0.6259 (mp) REVERT: A 433 GLU cc_start: 0.7406 (tp30) cc_final: 0.7068 (tp30) REVERT: A 572 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6265 (t0) REVERT: A 603 MET cc_start: 0.3639 (tpp) cc_final: 0.3268 (ppp) REVERT: A 631 ASP cc_start: 0.3170 (OUTLIER) cc_final: 0.2576 (p0) REVERT: A 683 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.5810 (pp20) REVERT: A 689 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6554 (mm-30) REVERT: A 824 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7275 (m-30) REVERT: A 887 ARG cc_start: 0.5718 (OUTLIER) cc_final: 0.4436 (ptm-80) REVERT: A 984 LYS cc_start: 0.8331 (mptt) cc_final: 0.7717 (mtmt) REVERT: A 1035 MET cc_start: 0.8231 (ptm) cc_final: 0.7970 (ptt) REVERT: A 1064 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8268 (mttp) outliers start: 93 outliers final: 51 residues processed: 180 average time/residue: 0.5741 time to fit residues: 111.7302 Evaluate side-chains 151 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 89 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 85 THR Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 358 ILE 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 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 590 ASN Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 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 1047 LEU Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1144 ARG Chi-restraints excluded: chain A residue 1157 SER 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: 4.9990 chunk 73 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4304 r_free = 0.4304 target = 0.198684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.152669 restraints weight = 10781.683| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.46 r_work: 0.3439 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10807 Z= 0.168 Angle : 0.601 9.684 14736 Z= 0.321 Chirality : 0.043 0.183 1616 Planarity : 0.004 0.047 1770 Dihedral : 14.861 161.929 1883 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.23 % Favored : 92.60 % Rotamer: Outliers : 6.41 % Allowed : 33.46 % Favored : 60.13 % 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 aren not related in a simple way. whole: -0.70 (0.24), residues: 1203 helix: 0.48 (0.22), residues: 544 sheet: -1.13 (0.45), residues: 111 loop : -1.26 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 385 TYR 0.017 0.001 TYR A 549 PHE 0.029 0.002 PHE A 119 TRP 0.024 0.001 TRP A 999 HIS 0.005 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00377 (10807) covalent geometry : angle 0.60084 (14736) hydrogen bonds : bond 0.04014 ( 460) hydrogen bonds : angle 4.84679 ( 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 168 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 101 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.3248 (OUTLIER) cc_final: 0.2231 (mmmt) REVERT: A 159 GLU cc_start: 0.6108 (tt0) cc_final: 0.5610 (tm-30) REVERT: A 182 ARG cc_start: 0.7208 (mtp180) cc_final: 0.6900 (mtp180) REVERT: A 221 GLU cc_start: 0.1967 (OUTLIER) cc_final: 0.1386 (pm20) REVERT: A 433 GLU cc_start: 0.7407 (tp30) cc_final: 0.7080 (tp30) REVERT: A 535 ASP cc_start: 0.6397 (OUTLIER) cc_final: 0.5522 (t70) REVERT: A 572 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6283 (t0) REVERT: A 603 MET cc_start: 0.3675 (tpp) cc_final: 0.3269 (ppp) REVERT: A 631 ASP cc_start: 0.3220 (OUTLIER) cc_final: 0.2588 (p0) REVERT: A 683 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6362 (mm-30) REVERT: A 689 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6543 (mm-30) REVERT: A 696 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7408 (mt-10) REVERT: A 795 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: A 824 ASP cc_start: 0.7746 (p0) cc_final: 0.7302 (m-30) REVERT: A 887 ARG cc_start: 0.5700 (OUTLIER) cc_final: 0.4557 (ptm-80) REVERT: A 938 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8303 (m) REVERT: A 1035 MET cc_start: 0.8128 (ptm) cc_final: 0.7887 (ptt) REVERT: A 1064 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8143 (mttp) outliers start: 67 outliers final: 37 residues processed: 154 average time/residue: 0.4941 time to fit residues: 83.0693 Evaluate side-chains 142 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 95 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 358 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 537 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1047 LEU 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 1207 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 51 optimal weight: 0.0020 chunk 32 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 0.0050 chunk 114 optimal weight: 0.9980 chunk 76 optimal weight: 0.0870 chunk 55 optimal weight: 0.9980 chunk 58 optimal weight: 0.0770 chunk 57 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.2338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4362 r_free = 0.4362 target = 0.204761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.160255 restraints weight = 10980.950| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.43 r_work: 0.3544 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 10807 Z= 0.108 Angle : 0.556 9.350 14736 Z= 0.296 Chirality : 0.040 0.163 1616 Planarity : 0.003 0.046 1770 Dihedral : 14.445 166.753 1879 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.73 % Favored : 93.10 % Rotamer: Outliers : 4.21 % Allowed : 35.76 % Favored : 60.04 % 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 aren not related in a simple way. whole: -0.30 (0.25), residues: 1203 helix: 0.89 (0.23), residues: 548 sheet: -1.17 (0.43), residues: 124 loop : -1.08 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 385 TYR 0.015 0.001 TYR A1018 PHE 0.029 0.001 PHE A 131 TRP 0.029 0.001 TRP A 999 HIS 0.003 0.001 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.00234 (10807) covalent geometry : angle 0.55646 (14736) hydrogen bonds : bond 0.03354 ( 460) hydrogen bonds : angle 4.54047 ( 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 147 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 103 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7087 (m-30) cc_final: 0.6881 (m-30) REVERT: A 70 LYS cc_start: 0.3153 (OUTLIER) cc_final: 0.2171 (mmmt) REVERT: A 121 LYS cc_start: 0.7224 (ptpp) cc_final: 0.6882 (tttt) REVERT: A 125 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7148 (pp20) REVERT: A 159 GLU cc_start: 0.5755 (tt0) cc_final: 0.5261 (tm-30) REVERT: A 433 GLU cc_start: 0.7343 (tp30) cc_final: 0.7057 (tp30) REVERT: A 505 ASP cc_start: 0.8027 (m-30) cc_final: 0.7698 (m-30) REVERT: A 535 ASP cc_start: 0.6398 (OUTLIER) cc_final: 0.5611 (t70) REVERT: A 537 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.6761 (t70) REVERT: A 572 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6328 (t0) REVERT: A 603 MET cc_start: 0.3668 (tpp) cc_final: 0.3283 (ppp) REVERT: A 631 ASP cc_start: 0.3390 (OUTLIER) cc_final: 0.2665 (p0) REVERT: A 683 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6400 (mm-30) REVERT: A 689 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6511 (mm-30) REVERT: A 824 ASP cc_start: 0.7743 (p0) cc_final: 0.7300 (m-30) REVERT: A 887 ARG cc_start: 0.5459 (OUTLIER) cc_final: 0.4468 (ptm-80) REVERT: A 984 LYS cc_start: 0.8344 (mptt) cc_final: 0.7792 (mtmt) REVERT: A 1039 GLU cc_start: 0.7180 (mp0) cc_final: 0.6873 (mp0) REVERT: A 1064 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7988 (mttp) outliers start: 44 outliers final: 19 residues processed: 137 average time/residue: 0.5184 time to fit residues: 77.1549 Evaluate side-chains 126 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 89 LYS 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 241 ILE Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 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 631 ASP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1134 MET 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: 1.9990 chunk 43 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 117 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 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 = 0.4310 r_free = 0.4310 target = 0.199246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.153521 restraints weight = 10746.295| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.59 r_work: 0.3433 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10807 Z= 0.179 Angle : 0.619 9.508 14736 Z= 0.329 Chirality : 0.043 0.188 1616 Planarity : 0.004 0.047 1770 Dihedral : 14.266 160.879 1869 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.65 % Favored : 92.19 % Rotamer: Outliers : 3.82 % Allowed : 36.04 % Favored : 60.13 % 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 aren not related in a simple way. whole: -0.45 (0.24), residues: 1203 helix: 0.71 (0.22), residues: 546 sheet: -1.02 (0.41), residues: 138 loop : -1.12 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 385 TYR 0.022 0.002 TYR A 549 PHE 0.040 0.002 PHE A 131 TRP 0.030 0.002 TRP A 999 HIS 0.006 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00403 (10807) covalent geometry : angle 0.61885 (14736) hydrogen bonds : bond 0.03944 ( 460) hydrogen bonds : angle 4.72040 ( 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 139 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7097 (m-30) cc_final: 0.6896 (m-30) REVERT: A 70 LYS cc_start: 0.3266 (OUTLIER) cc_final: 0.2306 (mmmt) REVERT: A 121 LYS cc_start: 0.7259 (ptpp) cc_final: 0.6849 (tttm) REVERT: A 125 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7095 (pp20) REVERT: A 131 PHE cc_start: 0.7317 (t80) cc_final: 0.7060 (t80) REVERT: A 159 GLU cc_start: 0.5953 (tt0) cc_final: 0.5625 (tm-30) REVERT: A 182 ARG cc_start: 0.7152 (mtp180) cc_final: 0.6831 (mtp180) REVERT: A 433 GLU cc_start: 0.7441 (tp30) cc_final: 0.7144 (tp30) REVERT: A 505 ASP cc_start: 0.8168 (m-30) cc_final: 0.7888 (m-30) REVERT: A 535 ASP cc_start: 0.6416 (OUTLIER) cc_final: 0.5551 (t70) REVERT: A 537 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.6816 (t0) REVERT: A 572 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6231 (t0) REVERT: A 603 MET cc_start: 0.3852 (tpp) cc_final: 0.3405 (ppp) REVERT: A 631 ASP cc_start: 0.3428 (OUTLIER) cc_final: 0.2648 (p0) REVERT: A 683 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6338 (mm-30) REVERT: A 824 ASP cc_start: 0.7791 (p0) cc_final: 0.7281 (m-30) REVERT: A 887 ARG cc_start: 0.5419 (OUTLIER) cc_final: 0.4367 (ptm-80) REVERT: A 984 LYS cc_start: 0.8276 (mptt) cc_final: 0.7689 (mtmt) REVERT: A 1039 GLU cc_start: 0.7292 (mp0) cc_final: 0.6963 (mp0) REVERT: A 1064 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8084 (mttp) outliers start: 40 outliers final: 21 residues processed: 131 average time/residue: 0.5368 time to fit residues: 76.2303 Evaluate side-chains 124 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 89 LYS 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 241 ILE Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 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 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 887 ARG Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1134 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 73 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 975 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.199818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.154663 restraints weight = 10863.886| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.61 r_work: 0.3429 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10807 Z= 0.159 Angle : 0.600 10.806 14736 Z= 0.318 Chirality : 0.042 0.179 1616 Planarity : 0.004 0.046 1770 Dihedral : 14.253 162.321 1869 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.23 % Favored : 92.60 % Rotamer: Outliers : 3.25 % Allowed : 36.81 % Favored : 59.94 % 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 aren not related in a simple way. whole: -0.47 (0.25), residues: 1203 helix: 0.63 (0.22), residues: 554 sheet: -1.03 (0.46), residues: 111 loop : -1.09 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 385 TYR 0.021 0.001 TYR A 549 PHE 0.035 0.002 PHE A 131 TRP 0.034 0.002 TRP A 999 HIS 0.005 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00356 (10807) covalent geometry : angle 0.60015 (14736) hydrogen bonds : bond 0.03801 ( 460) hydrogen bonds : angle 4.70856 ( 1315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5078.34 seconds wall clock time: 87 minutes 2.60 seconds (5222.60 seconds total)