Starting phenix.real_space_refine on Wed Aug 5 14:05:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfj_40443/08_2026/8sfj_40443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfj_40443/08_2026/8sfj_40443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sfj_40443/08_2026/8sfj_40443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfj_40443/08_2026/8sfj_40443.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfj_40443/08_2026/8sfj_40443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfj_40443/08_2026/8sfj_40443.cif" } resolution = 3.6 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= -0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 96 5.49 5 S 20 5.16 5 C 6225 2.51 5 N 1740 2.21 5 O 2126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10207 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 8202 Classifications: {'peptide': 1001} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 959} Chain breaks: 4 Chain: "B" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 611 Classifications: {'RNA': 29} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 11, 'rna3p_pyr': 12} Link IDs: {'rna2p': 6, 'rna3p': 22} Chain: "C" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 696 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "D" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 698 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Time building chain proxies: 2.30, per 1000 atoms: 0.23 Number of scatterers: 10207 At special positions: 0 Unit cell: (83.3, 98.294, 149.94, 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 20 16.00 P 96 15.00 O 2126 8.00 N 1740 7.00 C 6225 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: 0.89 Conformation dependent library (CDL) restraints added in 188.5 milliseconds 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1900 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 49.8% alpha, 13.5% beta 34 base pairs and 65 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.578A pdb=" N PHE A 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 35 through 67 removed outlier: 3.727A pdb=" N GLU A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 88 through 111 Processing helix chain 'A' and resid 118 through 132 Processing helix chain 'A' and resid 133 through 138 removed outlier: 7.052A pdb=" N GLU A 136 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 137 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 146 removed outlier: 3.914A pdb=" N LYS A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 181 Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 215 removed outlier: 4.311A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 230 removed outlier: 4.243A pdb=" N GLU A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.635A pdb=" N LEU A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 289 through 297 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.776A pdb=" N TYR A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.751A pdb=" N ALA A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 687 Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.599A pdb=" N TYR A 704 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 removed outlier: 3.615A pdb=" N TYR A 710 " --> pdb=" O ASP A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.696A pdb=" N PHE A 769 " --> pdb=" O TRP A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 940 through 949 removed outlier: 4.044A pdb=" N ASN A 946 " --> pdb=" O LYS A 942 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 949 " --> pdb=" O ASP A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 987 removed outlier: 4.055A pdb=" N HIS A 977 " --> pdb=" O SER A 973 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 998 Processing helix chain 'A' and resid 1008 through 1025 removed outlier: 3.809A pdb=" N TYR A1012 " --> pdb=" O GLU A1008 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1100 Processing helix chain 'A' and resid 1177 through 1187 Processing helix chain 'A' and resid 1198 through 1206 removed outlier: 4.360A pdb=" N LYS A1202 " --> pdb=" O ASN A1198 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN A1206 " --> pdb=" O LYS A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1224 Processing helix chain 'A' and resid 1252 through 1254 No H-bonds generated for 'chain 'A' and resid 1252 through 1254' Processing helix chain 'A' and resid 1261 through 1284 Processing helix chain 'A' and resid 1294 through 1307 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.660A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 11.319A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.660A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AA4, first strand: chain 'A' and resid 926 through 931 removed outlier: 6.435A pdb=" N VAL A 919 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN A 929 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 917 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N SER A 931 " --> pdb=" O ILE A 915 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE A 915 " --> pdb=" O SER A 931 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 905 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N GLU A 993 " --> pdb=" O ILE A 905 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N ILE A 907 " --> pdb=" O GLU A 993 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A 990 " --> pdb=" O PHE A1063 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL A1065 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A 992 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1103 through 1106 removed outlier: 4.037A pdb=" N PHE A1103 " --> pdb=" O HIS A1116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1145 through 1147 Processing sheet with id=AA7, first strand: chain 'A' and resid 1159 through 1161 Processing sheet with id=AA8, first strand: chain 'A' and resid 1164 through 1165 Processing sheet with id=AA9, first strand: chain 'A' and resid 1226 through 1229 removed outlier: 4.241A pdb=" N PHE A1249 " --> pdb=" O SER A1239 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 65 stacking parallelities Total time for adding SS restraints: 2.32 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: 1.21 - 1.33: 2262 1.33 - 1.46: 2968 1.46 - 1.58: 5185 1.58 - 1.70: 191 1.70 - 1.82: 34 Bond restraints: 10640 Sorted by residual: bond pdb=" C1' DT D 16 " pdb=" N1 DT D 16 " ideal model delta sigma weight residual 1.468 1.552 -0.084 1.40e-02 5.10e+03 3.61e+01 bond pdb=" C1' DT C 13 " pdb=" N1 DT C 13 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.57e+01 bond pdb=" N1 DT D 16 " pdb=" C2 DT D 16 " ideal model delta sigma weight residual 1.376 1.405 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C3' DT C 20 " pdb=" C2' DT C 20 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.80e+00 bond pdb=" C3' DC C 17 " pdb=" C2' DC C 17 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.13e+00 ... (remaining 10635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 14558 3.82 - 7.64: 174 7.64 - 11.46: 62 11.46 - 15.28: 9 15.28 - 19.10: 3 Bond angle restraints: 14806 Sorted by residual: angle pdb=" CA PRO A1256 " pdb=" N PRO A1256 " pdb=" CD PRO A1256 " ideal model delta sigma weight residual 112.00 101.40 10.60 1.40e+00 5.10e-01 5.74e+01 angle pdb=" O3' DG D 17 " pdb=" P DA D 18 " pdb=" OP1 DA D 18 " ideal model delta sigma weight residual 108.00 127.10 -19.10 3.00e+00 1.11e-01 4.05e+01 angle pdb=" CA GLN A 987 " pdb=" CB GLN A 987 " pdb=" CG GLN A 987 " ideal model delta sigma weight residual 114.10 126.82 -12.72 2.00e+00 2.50e-01 4.05e+01 angle pdb=" CB MET A 604 " pdb=" CG MET A 604 " pdb=" SD MET A 604 " ideal model delta sigma weight residual 112.70 130.23 -17.53 3.00e+00 1.11e-01 3.41e+01 angle pdb=" CA ASN A1291 " pdb=" CB ASN A1291 " pdb=" CG ASN A1291 " ideal model delta sigma weight residual 112.60 118.39 -5.79 1.00e+00 1.00e+00 3.35e+01 ... (remaining 14801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.11: 5554 31.11 - 62.21: 624 62.21 - 93.32: 52 93.32 - 124.42: 1 124.42 - 155.53: 3 Dihedral angle restraints: 6234 sinusoidal: 3291 harmonic: 2943 Sorted by residual: dihedral pdb=" O4' C B 11 " pdb=" C1' C B 11 " pdb=" N1 C B 11 " pdb=" C2 C B 11 " ideal model delta sinusoidal sigma weight residual 200.00 44.47 155.53 1 1.50e+01 4.44e-03 8.15e+01 dihedral pdb=" O4' U B 12 " pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sinusoidal sigma weight residual 200.00 56.96 143.04 1 1.50e+01 4.44e-03 7.68e+01 dihedral pdb=" CA PRO A 700 " pdb=" C PRO A 700 " pdb=" N SER A 701 " pdb=" CA SER A 701 " ideal model delta harmonic sigma weight residual -180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 6231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1534 0.122 - 0.244: 91 0.244 - 0.366: 1 0.366 - 0.488: 14 0.488 - 0.611: 1 Chirality restraints: 1641 Sorted by residual: chirality pdb=" P DA D 18 " pdb=" OP1 DA D 18 " pdb=" OP2 DA D 18 " pdb=" O5' DA D 18 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.61 2.00e-01 2.50e+01 9.32e+00 chirality pdb=" P DA D 14 " pdb=" OP1 DA D 14 " pdb=" OP2 DA D 14 " pdb=" O5' DA D 14 " both_signs ideal model delta sigma weight residual True 2.34 -2.81 -0.47 2.00e-01 2.50e+01 5.59e+00 chirality pdb=" P DA C 28 " pdb=" OP1 DA C 28 " pdb=" OP2 DA C 28 " pdb=" O5' DA C 28 " both_signs ideal model delta sigma weight residual True 2.34 -2.81 -0.47 2.00e-01 2.50e+01 5.55e+00 ... (remaining 1638 not shown) Planarity restraints: 1559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1255 " 0.115 5.00e-02 4.00e+02 1.67e-01 4.48e+01 pdb=" N PRO A1256 " -0.289 5.00e-02 4.00e+02 pdb=" CA PRO A1256 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO A1256 " 0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A1065 " -0.097 5.00e-02 4.00e+02 1.44e-01 3.33e+01 pdb=" N PRO A1066 " 0.250 5.00e-02 4.00e+02 pdb=" CA PRO A1066 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO A1066 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1085 " 0.028 2.00e-02 2.50e+03 2.76e-02 1.91e+01 pdb=" CG TRP A1085 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP A1085 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A1085 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1085 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A1085 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1085 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1085 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1085 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A1085 " 0.004 2.00e-02 2.50e+03 ... (remaining 1556 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 608 2.73 - 3.27: 9840 3.27 - 3.81: 18235 3.81 - 4.36: 21820 4.36 - 4.90: 34103 Nonbonded interactions: 84606 Sorted by model distance: nonbonded pdb=" OG SER A 931 " pdb=" OD1 ASN A 933 " model vdw 2.182 3.040 nonbonded pdb=" OG1 THR A 610 " pdb=" OE1 GLN A 611 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR A 8 " pdb=" O PRO A1042 " model vdw 2.292 3.040 nonbonded pdb=" O THR A 167 " pdb=" OG SER A 170 " model vdw 2.292 3.040 nonbonded pdb=" NZ LYS A 59 " pdb=" OD1 ASP A 312 " model vdw 2.295 3.120 ... (remaining 84601 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.520 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 10640 Z= 0.370 Angle : 1.229 19.101 14806 Z= 0.728 Chirality : 0.071 0.611 1641 Planarity : 0.009 0.167 1559 Dihedral : 22.090 155.528 4334 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.22 % Allowed : 24.97 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.26), residues: 991 helix: -0.35 (0.23), residues: 444 sheet: -0.39 (0.41), residues: 140 loop : -0.08 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1003 TYR 0.050 0.003 TYR A1236 PHE 0.047 0.003 PHE A 619 TRP 0.071 0.004 TRP A1085 HIS 0.034 0.002 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.37 (10640) covalent geometry : angle 1.22857 / 0.73 (14806) hydrogen bonds : bond 0.12190 / 7.86 ( 474) hydrogen bonds : angle 6.28194 / 4.49 ( 1284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1055 MET cc_start: 0.7436 (ppp) cc_final: 0.6393 (ppp) outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 0.0844 time to fit residues: 7.7552 Evaluate side-chains 45 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1080 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 HIS A 547 ASN A 620 GLN ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 ASN A 936 GLN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1275 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.042939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.029645 restraints weight = 76327.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.030702 restraints weight = 39322.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.031381 restraints weight = 26618.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.031782 restraints weight = 21074.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.032060 restraints weight = 18420.364| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10640 Z= 0.282 Angle : 0.738 12.801 14806 Z= 0.403 Chirality : 0.046 0.257 1641 Planarity : 0.005 0.086 1559 Dihedral : 23.245 153.858 2280 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.25 % Allowed : 20.38 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.27), residues: 991 helix: 0.52 (0.25), residues: 447 sheet: -0.25 (0.43), residues: 136 loop : 0.10 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 947 TYR 0.020 0.002 TYR A1173 PHE 0.024 0.002 PHE A1101 TRP 0.022 0.002 TRP A1085 HIS 0.016 0.002 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.28 (10640) covalent geometry : angle 0.73835 / 0.40 (14806) hydrogen bonds : bond 0.04687 / 3.06 ( 474) hydrogen bonds : angle 5.08310 / 3.67 ( 1284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 43 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 633 ILE cc_start: 0.9698 (OUTLIER) cc_final: 0.9458 (pt) REVERT: A 782 ASN cc_start: 0.9229 (m-40) cc_final: 0.8280 (m110) REVERT: A 908 ASP cc_start: 0.8352 (t0) cc_final: 0.8093 (t0) REVERT: A 1018 MET cc_start: 0.9048 (mtm) cc_final: 0.8761 (mtm) REVERT: A 1280 HIS cc_start: 0.9335 (OUTLIER) cc_final: 0.8756 (t-90) outliers start: 29 outliers final: 14 residues processed: 70 average time/residue: 0.0836 time to fit residues: 9.3511 Evaluate side-chains 57 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1280 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1091 HIS A1279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.043932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.030553 restraints weight = 74734.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.031631 restraints weight = 38465.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.032342 restraints weight = 25970.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.032778 restraints weight = 20462.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.033022 restraints weight = 17758.836| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10640 Z= 0.143 Angle : 0.637 11.535 14806 Z= 0.347 Chirality : 0.043 0.295 1641 Planarity : 0.004 0.066 1559 Dihedral : 23.196 153.146 2280 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.24 % Allowed : 21.05 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.27), residues: 991 helix: 0.81 (0.25), residues: 449 sheet: -0.11 (0.44), residues: 136 loop : 0.19 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1194 TYR 0.019 0.001 TYR A 764 PHE 0.009 0.001 PHE A 999 TRP 0.016 0.001 TRP A1085 HIS 0.013 0.001 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (10640) covalent geometry : angle 0.63732 / 0.35 (14806) hydrogen bonds : bond 0.03724 / 2.44 ( 474) hydrogen bonds : angle 4.67440 / 3.35 ( 1284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 537 MET cc_start: 0.9299 (ptm) cc_final: 0.8994 (ptp) REVERT: A 782 ASN cc_start: 0.9225 (m-40) cc_final: 0.8259 (m110) REVERT: A 938 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8664 (t80) REVERT: A 1018 MET cc_start: 0.8893 (mtm) cc_final: 0.8661 (mtm) REVERT: A 1280 HIS cc_start: 0.9316 (OUTLIER) cc_final: 0.8709 (t-90) outliers start: 20 outliers final: 14 residues processed: 63 average time/residue: 0.0775 time to fit residues: 7.6191 Evaluate side-chains 57 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 938 PHE Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1280 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 chunk 58 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 HIS ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.043717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.030339 restraints weight = 75705.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.031405 restraints weight = 39311.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.032088 restraints weight = 26715.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.032501 restraints weight = 21202.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.032733 restraints weight = 18511.727| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10640 Z= 0.169 Angle : 0.621 10.872 14806 Z= 0.340 Chirality : 0.043 0.260 1641 Planarity : 0.004 0.059 1559 Dihedral : 23.187 153.339 2280 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.48 % Allowed : 19.71 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.28), residues: 991 helix: 1.03 (0.25), residues: 450 sheet: -0.06 (0.44), residues: 139 loop : 0.25 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.020 0.001 TYR A 764 PHE 0.009 0.001 PHE A1249 TRP 0.013 0.001 TRP A1085 HIS 0.011 0.001 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (10640) covalent geometry : angle 0.62056 / 0.34 (14806) hydrogen bonds : bond 0.03830 / 2.52 ( 474) hydrogen bonds : angle 4.52084 / 3.25 ( 1284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 44 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 MET cc_start: 0.9329 (ptm) cc_final: 0.9112 (ptp) REVERT: A 782 ASN cc_start: 0.9249 (m-40) cc_final: 0.8705 (t0) REVERT: A 938 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8639 (t80) REVERT: A 1116 HIS cc_start: 0.9336 (OUTLIER) cc_final: 0.8624 (t-90) REVERT: A 1280 HIS cc_start: 0.9298 (OUTLIER) cc_final: 0.8695 (t-90) outliers start: 40 outliers final: 22 residues processed: 78 average time/residue: 0.0790 time to fit residues: 9.6381 Evaluate side-chains 67 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 42 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 938 PHE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1090 ASN Chi-restraints excluded: chain A residue 1116 HIS Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1280 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 47 optimal weight: 0.3980 chunk 59 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.043298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.029924 restraints weight = 76489.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.030985 restraints weight = 40046.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.031651 restraints weight = 27286.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.032064 restraints weight = 21817.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.032208 restraints weight = 19027.566| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10640 Z= 0.204 Angle : 0.634 13.335 14806 Z= 0.345 Chirality : 0.043 0.268 1641 Planarity : 0.004 0.056 1559 Dihedral : 23.234 154.062 2280 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.92 % Allowed : 20.04 % Favored : 76.04 % 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 are not related in a simple way. whole: 0.85 (0.28), residues: 991 helix: 1.17 (0.25), residues: 450 sheet: -0.23 (0.42), residues: 147 loop : 0.37 (0.35), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 912 TYR 0.014 0.002 TYR A 61 PHE 0.011 0.001 PHE A 999 TRP 0.012 0.001 TRP A1085 HIS 0.008 0.001 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.20 (10640) covalent geometry : angle 0.63428 / 0.35 (14806) hydrogen bonds : bond 0.03957 / 2.63 ( 474) hydrogen bonds : angle 4.45807 / 3.20 ( 1284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 39 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 307 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7836 (ttpp) REVERT: A 908 ASP cc_start: 0.8503 (t0) cc_final: 0.8166 (t0) REVERT: A 938 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8661 (t80) REVERT: A 1018 MET cc_start: 0.9127 (mtm) cc_final: 0.8745 (mtm) REVERT: A 1116 HIS cc_start: 0.9369 (OUTLIER) cc_final: 0.8676 (t-90) REVERT: A 1133 MET cc_start: 0.9228 (pmm) cc_final: 0.8831 (pmm) REVERT: A 1280 HIS cc_start: 0.9311 (OUTLIER) cc_final: 0.8720 (t-90) outliers start: 35 outliers final: 23 residues processed: 70 average time/residue: 0.0785 time to fit residues: 8.5615 Evaluate side-chains 64 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 37 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 938 PHE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1090 ASN Chi-restraints excluded: chain A residue 1116 HIS Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1280 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 105 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.042483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.029256 restraints weight = 76000.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.030302 restraints weight = 39339.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.030964 restraints weight = 26650.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.031349 restraints weight = 21099.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.031631 restraints weight = 18418.463| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10640 Z= 0.207 Angle : 0.628 11.108 14806 Z= 0.343 Chirality : 0.043 0.271 1641 Planarity : 0.004 0.054 1559 Dihedral : 23.302 154.731 2280 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.37 % Allowed : 20.60 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.28), residues: 991 helix: 1.23 (0.25), residues: 449 sheet: -0.35 (0.41), residues: 147 loop : 0.46 (0.36), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 912 TYR 0.015 0.002 TYR A 61 PHE 0.015 0.001 PHE A 557 TRP 0.012 0.001 TRP A1085 HIS 0.008 0.001 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.21 (10640) covalent geometry : angle 0.62765 / 0.34 (14806) hydrogen bonds : bond 0.03987 / 2.64 ( 474) hydrogen bonds : angle 4.43942 / 3.19 ( 1284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 38 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9337 (tp) REVERT: A 307 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7954 (ttpp) REVERT: A 593 MET cc_start: 0.9482 (ppp) cc_final: 0.9176 (ppp) REVERT: A 908 ASP cc_start: 0.8550 (t0) cc_final: 0.8274 (t0) REVERT: A 938 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8606 (t80) REVERT: A 1018 MET cc_start: 0.9085 (mtm) cc_final: 0.8804 (mtm) REVERT: A 1116 HIS cc_start: 0.9336 (OUTLIER) cc_final: 0.8646 (t-90) REVERT: A 1133 MET cc_start: 0.9201 (pmm) cc_final: 0.8857 (pmm) REVERT: A 1280 HIS cc_start: 0.9263 (OUTLIER) cc_final: 0.8686 (t-90) outliers start: 39 outliers final: 27 residues processed: 71 average time/residue: 0.0798 time to fit residues: 8.8213 Evaluate side-chains 69 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 37 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 938 PHE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1090 ASN Chi-restraints excluded: chain A residue 1116 HIS Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1280 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 13 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 69 optimal weight: 0.0060 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.043225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.029920 restraints weight = 73379.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.030974 restraints weight = 38176.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.031648 restraints weight = 26019.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.032040 restraints weight = 20623.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.032298 restraints weight = 18019.749| |-----------------------------------------------------------------------------| r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10640 Z= 0.130 Angle : 0.611 15.323 14806 Z= 0.329 Chirality : 0.042 0.263 1641 Planarity : 0.004 0.053 1559 Dihedral : 23.265 154.439 2280 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.14 % Allowed : 22.28 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.28), residues: 991 helix: 1.27 (0.25), residues: 450 sheet: -0.21 (0.42), residues: 147 loop : 0.46 (0.36), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1121 TYR 0.014 0.001 TYR A 61 PHE 0.027 0.001 PHE A 557 TRP 0.013 0.001 TRP A1085 HIS 0.007 0.001 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (10640) covalent geometry : angle 0.61110 / 0.33 (14806) hydrogen bonds : bond 0.03531 / 2.33 ( 474) hydrogen bonds : angle 4.31814 / 3.10 ( 1284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 39 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9334 (tp) REVERT: A 307 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7888 (ttpp) REVERT: A 593 MET cc_start: 0.9512 (ppp) cc_final: 0.9200 (ppp) REVERT: A 908 ASP cc_start: 0.8465 (t0) cc_final: 0.8087 (t0) REVERT: A 938 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8622 (t80) REVERT: A 1018 MET cc_start: 0.9065 (mtm) cc_final: 0.8745 (mtm) REVERT: A 1116 HIS cc_start: 0.9327 (OUTLIER) cc_final: 0.8639 (t-90) REVERT: A 1133 MET cc_start: 0.9207 (pmm) cc_final: 0.8888 (pmm) REVERT: A 1280 HIS cc_start: 0.9268 (OUTLIER) cc_final: 0.8687 (t-90) outliers start: 28 outliers final: 22 residues processed: 64 average time/residue: 0.0861 time to fit residues: 8.3745 Evaluate side-chains 64 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 37 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 938 PHE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1090 ASN Chi-restraints excluded: chain A residue 1116 HIS Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1280 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 60 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 105 optimal weight: 30.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.043135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.029837 restraints weight = 73438.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.030902 restraints weight = 38167.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.031581 restraints weight = 25924.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.031969 restraints weight = 20539.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.032251 restraints weight = 17970.123| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10640 Z= 0.133 Angle : 0.605 14.751 14806 Z= 0.326 Chirality : 0.042 0.262 1641 Planarity : 0.004 0.052 1559 Dihedral : 23.237 154.240 2280 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.58 % Allowed : 22.06 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.28), residues: 991 helix: 1.34 (0.25), residues: 450 sheet: -0.24 (0.42), residues: 149 loop : 0.47 (0.36), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1194 TYR 0.017 0.001 TYR A1012 PHE 0.028 0.001 PHE A 557 TRP 0.012 0.001 TRP A1085 HIS 0.007 0.001 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (10640) covalent geometry : angle 0.60534 / 0.33 (14806) hydrogen bonds : bond 0.03442 / 2.26 ( 474) hydrogen bonds : angle 4.27440 / 3.06 ( 1284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 39 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9328 (tp) REVERT: A 307 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7879 (ttpp) REVERT: A 593 MET cc_start: 0.9527 (ppp) cc_final: 0.9200 (ppp) REVERT: A 908 ASP cc_start: 0.8419 (t0) cc_final: 0.8087 (t0) REVERT: A 938 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8632 (t80) REVERT: A 1018 MET cc_start: 0.9060 (mtm) cc_final: 0.8710 (mtm) REVERT: A 1116 HIS cc_start: 0.9334 (OUTLIER) cc_final: 0.8649 (t-90) REVERT: A 1133 MET cc_start: 0.9221 (pmm) cc_final: 0.8918 (pmm) REVERT: A 1280 HIS cc_start: 0.9276 (OUTLIER) cc_final: 0.8697 (t-90) outliers start: 32 outliers final: 22 residues processed: 67 average time/residue: 0.0852 time to fit residues: 8.9075 Evaluate side-chains 65 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 38 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 938 PHE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1090 ASN Chi-restraints excluded: chain A residue 1116 HIS Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1280 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 chunk 92 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 0.0070 chunk 64 optimal weight: 0.0980 chunk 18 optimal weight: 8.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.043541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.030225 restraints weight = 72747.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.031289 restraints weight = 37720.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.031989 restraints weight = 25529.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.032386 restraints weight = 20096.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.032670 restraints weight = 17558.163| |-----------------------------------------------------------------------------| r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10640 Z= 0.115 Angle : 0.610 15.457 14806 Z= 0.325 Chirality : 0.042 0.256 1641 Planarity : 0.004 0.052 1559 Dihedral : 23.195 153.806 2279 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.14 % Allowed : 22.73 % Favored : 74.13 % 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 are not related in a simple way. whole: 1.05 (0.28), residues: 991 helix: 1.38 (0.25), residues: 450 sheet: -0.20 (0.42), residues: 149 loop : 0.44 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.016 0.001 TYR A1012 PHE 0.024 0.001 PHE A 557 TRP 0.013 0.001 TRP A1085 HIS 0.006 0.001 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 (10640) covalent geometry : angle 0.61011 / 0.32 (14806) hydrogen bonds : bond 0.03260 / 2.13 ( 474) hydrogen bonds : angle 4.20462 / 3.00 ( 1284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 42 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9342 (tp) REVERT: A 307 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7850 (ttpp) REVERT: A 593 MET cc_start: 0.9540 (ppp) cc_final: 0.9241 (ppp) REVERT: A 908 ASP cc_start: 0.8389 (t0) cc_final: 0.8085 (t0) REVERT: A 938 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8634 (t80) REVERT: A 1116 HIS cc_start: 0.9331 (OUTLIER) cc_final: 0.8648 (t-90) REVERT: A 1133 MET cc_start: 0.9222 (pmm) cc_final: 0.8903 (pmm) REVERT: A 1199 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9376 (mm) REVERT: A 1280 HIS cc_start: 0.9288 (OUTLIER) cc_final: 0.8713 (t-90) outliers start: 28 outliers final: 19 residues processed: 68 average time/residue: 0.0854 time to fit residues: 8.9508 Evaluate side-chains 65 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 40 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 938 PHE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1090 ASN Chi-restraints excluded: chain A residue 1116 HIS Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1280 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.042617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.029397 restraints weight = 74212.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.030436 restraints weight = 38909.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.031099 restraints weight = 26649.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.031484 restraints weight = 21170.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.031762 restraints weight = 18515.647| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10640 Z= 0.223 Angle : 0.641 13.485 14806 Z= 0.344 Chirality : 0.043 0.274 1641 Planarity : 0.004 0.052 1559 Dihedral : 23.247 154.375 2279 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.91 % Allowed : 22.96 % Favored : 74.13 % 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 are not related in a simple way. whole: 1.05 (0.28), residues: 991 helix: 1.37 (0.25), residues: 449 sheet: -0.23 (0.42), residues: 147 loop : 0.48 (0.36), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 912 TYR 0.017 0.002 TYR A 764 PHE 0.024 0.001 PHE A 557 TRP 0.008 0.001 TRP A1085 HIS 0.006 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.22 (10640) covalent geometry : angle 0.64130 / 0.34 (14806) hydrogen bonds : bond 0.03880 / 2.55 ( 474) hydrogen bonds : angle 4.34669 / 3.11 ( 1284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 38 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 307 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7908 (ttpp) REVERT: A 593 MET cc_start: 0.9527 (ppp) cc_final: 0.9297 (ppp) REVERT: A 908 ASP cc_start: 0.8448 (t0) cc_final: 0.8118 (t0) REVERT: A 938 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8610 (t80) REVERT: A 1133 MET cc_start: 0.9218 (pmm) cc_final: 0.8946 (pmm) REVERT: A 1199 ILE cc_start: 0.9584 (OUTLIER) cc_final: 0.9371 (mm) REVERT: A 1280 HIS cc_start: 0.9274 (OUTLIER) cc_final: 0.8712 (t-90) outliers start: 26 outliers final: 20 residues processed: 63 average time/residue: 0.0844 time to fit residues: 8.2037 Evaluate side-chains 62 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 38 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 938 PHE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1090 ASN Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1280 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 77 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.042305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.029223 restraints weight = 75362.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.030279 restraints weight = 39152.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.030931 restraints weight = 26579.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.031340 restraints weight = 21076.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.031493 restraints weight = 18384.380| |-----------------------------------------------------------------------------| r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10640 Z= 0.199 Angle : 0.639 13.794 14806 Z= 0.343 Chirality : 0.043 0.275 1641 Planarity : 0.004 0.051 1559 Dihedral : 23.330 154.774 2279 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.14 % Allowed : 22.84 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.28), residues: 991 helix: 1.26 (0.25), residues: 449 sheet: -0.30 (0.42), residues: 149 loop : 0.51 (0.36), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1121 TYR 0.017 0.002 TYR A 764 PHE 0.022 0.001 PHE A 557 TRP 0.012 0.001 TRP A1085 HIS 0.006 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.20 (10640) covalent geometry : angle 0.63937 / 0.34 (14806) hydrogen bonds : bond 0.03818 / 2.51 ( 474) hydrogen bonds : angle 4.35165 / 3.12 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1546.44 seconds wall clock time: 27 minutes 32.17 seconds (1652.17 seconds total)