Starting phenix.real_space_refine on Thu Jul 2 20:33:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfj_40443/07_2026/8sfj_40443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfj_40443/07_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_40443/07_2026/8sfj_40443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfj_40443/07_2026/8sfj_40443.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfj_40443/07_2026/8sfj_40443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfj_40443/07_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-dev-6108/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: 1.97, per 1000 atoms: 0.19 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: 0.79 Conformation dependent library (CDL) restraints added in 288.2 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: 1.27 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: 1.98 Time building geometry restraints manager: 1.00 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: 14560 3.82 - 7.64: 172 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: 1556 0.122 - 0.244: 69 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: 3.230 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: 10.480 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.260 ------------------------------------------------------------------------------- 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= 0.369 Angle : 1.214 19.101 14806 Z= 0.711 Chirality : 0.070 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 0.00582 / 0.37 (10640) covalent geometry : angle 1.21449 / 0.71 (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 : 0.362 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: 0.0983 time to fit residues: 8.7810 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 : 0.354 ------------------------------------------------------------------------------- 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 = 0.043162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.029923 restraints weight = 76025.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.030960 restraints weight = 39388.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031636 restraints weight = 26687.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.032046 restraints weight = 21229.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.032206 restraints weight = 18476.640| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1347 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= 0.280 Angle : 0.737 13.154 14806 Z= 0.403 Chirality : 0.046 0.261 1641 Planarity : 0.006 0.088 1559 Dihedral : 23.298 153.824 2280 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.47 % Allowed : 20.16 % 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: 0.22 (0.27), residues: 991 helix: 0.49 (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 0.004 0.001 ARG A1194 TYR 0.020 0.002 TYR A1173 PHE 0.024 0.002 PHE A1101 TRP 0.024 0.002 TRP A1085 HIS 0.016 0.001 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.28 (10640) covalent geometry : angle 0.73671 / 0.40 (14806) hydrogen bonds : bond 0.04778 / 3.11 ( 474) hydrogen bonds : angle 5.09018 / 3.68 ( 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 74 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 43 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 633 ILE cc_start: 0.9697 (OUTLIER) cc_final: 0.9456 (pt) REVERT: A 782 ASN cc_start: 0.9235 (m-40) cc_final: 0.8722 (t0) REVERT: A 908 ASP cc_start: 0.8349 (t0) cc_final: 0.8085 (t0) REVERT: A 1018 MET cc_start: 0.9051 (mtm) cc_final: 0.8766 (mtm) REVERT: A 1280 HIS cc_start: 0.9328 (OUTLIER) cc_final: 0.8744 (t-90) outliers start: 31 outliers final: 16 residues processed: 72 average time/residue: 0.0739 time to fit residues: 8.1709 Evaluate side-chains 59 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 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 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 1210 HIS 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: 6.9990 chunk 73 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 80 optimal weight: 0.0570 overall best weight: 1.3100 ------------------------------------------------------------------------------- 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** A1091 HIS ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.044146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.030748 restraints weight = 74362.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.031838 restraints weight = 38048.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.032547 restraints weight = 25631.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.032969 restraints weight = 20179.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.033247 restraints weight = 17585.749| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1412 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 : 0.637 11.444 14806 Z= 0.346 Chirality : 0.043 0.248 1641 Planarity : 0.004 0.066 1559 Dihedral : 23.245 152.874 2280 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.90 % Allowed : 20.94 % Favored : 77.16 % 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: 0.82 (0.25), residues: 450 sheet: -0.11 (0.44), residues: 136 loop : 0.17 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1094 TYR 0.020 0.001 TYR A 764 PHE 0.008 0.001 PHE A1249 TRP 0.017 0.001 TRP A1085 HIS 0.013 0.001 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (10640) covalent geometry : angle 0.63663 / 0.35 (14806) hydrogen bonds : bond 0.03648 / 2.38 ( 474) hydrogen bonds : angle 4.63557 / 3.32 ( 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 61 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 ASN cc_start: 0.8657 (m110) cc_final: 0.8455 (m110) REVERT: A 537 MET cc_start: 0.9298 (ptm) cc_final: 0.8984 (ptp) REVERT: A 782 ASN cc_start: 0.9218 (m-40) cc_final: 0.8246 (m110) REVERT: A 938 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8673 (t80) REVERT: A 1018 MET cc_start: 0.8900 (mtm) cc_final: 0.8663 (mtm) REVERT: A 1280 HIS cc_start: 0.9321 (OUTLIER) cc_final: 0.8712 (t-90) outliers start: 17 outliers final: 11 residues processed: 60 average time/residue: 0.0860 time to fit residues: 7.9726 Evaluate side-chains 55 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 118 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 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: 0.6980 chunk 86 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- 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 = 0.3217 r_free = 0.3217 target = 0.043721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.030343 restraints weight = 75750.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.031417 restraints weight = 39155.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.032072 restraints weight = 26561.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.032526 restraints weight = 21206.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.032775 restraints weight = 18361.616| |-----------------------------------------------------------------------------| r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10640 Z= 0.175 Angle : 0.617 10.685 14806 Z= 0.339 Chirality : 0.043 0.262 1641 Planarity : 0.004 0.060 1559 Dihedral : 23.245 153.259 2280 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.14 % Allowed : 19.71 % Favored : 76.15 % 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: 0.75 (0.28), residues: 991 helix: 1.06 (0.25), residues: 450 sheet: -0.17 (0.42), residues: 147 loop : 0.30 (0.35), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1194 TYR 0.019 0.001 TYR A 764 PHE 0.010 0.001 PHE A1249 TRP 0.013 0.001 TRP A1085 HIS 0.012 0.001 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (10640) covalent geometry : angle 0.61745 / 0.34 (14806) hydrogen bonds : bond 0.03872 / 2.55 ( 474) hydrogen bonds : angle 4.50952 / 3.23 ( 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 81 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 44 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 537 MET cc_start: 0.9331 (ptm) cc_final: 0.9104 (ptp) REVERT: A 782 ASN cc_start: 0.9249 (m-40) cc_final: 0.8704 (t0) REVERT: A 938 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8652 (t80) REVERT: A 1116 HIS cc_start: 0.9345 (OUTLIER) cc_final: 0.8632 (t-90) REVERT: A 1280 HIS cc_start: 0.9305 (OUTLIER) cc_final: 0.8700 (t-90) outliers start: 37 outliers final: 22 residues processed: 76 average time/residue: 0.0772 time to fit residues: 8.9793 Evaluate side-chains 66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 41 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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: 10.0000 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3187 r_free = 0.3187 target = 0.042159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.028955 restraints weight = 76202.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.029989 restraints weight = 39588.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.030645 restraints weight = 26942.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.031044 restraints weight = 21340.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.031271 restraints weight = 18626.796| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10640 Z= 0.245 Angle : 0.654 13.155 14806 Z= 0.358 Chirality : 0.043 0.273 1641 Planarity : 0.004 0.056 1559 Dihedral : 23.349 154.554 2280 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.26 % Allowed : 20.04 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.28), residues: 991 helix: 1.10 (0.25), residues: 449 sheet: -0.31 (0.41), residues: 147 loop : 0.34 (0.35), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 176 TYR 0.017 0.002 TYR A1012 PHE 0.013 0.002 PHE A1052 TRP 0.013 0.001 TRP A1085 HIS 0.009 0.001 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.25 (10640) covalent geometry : angle 0.65404 / 0.36 (14806) hydrogen bonds : bond 0.04366 / 2.89 ( 474) hydrogen bonds : angle 4.55063 / 3.29 ( 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 77 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 39 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7917 (tmmt) REVERT: A 782 ASN cc_start: 0.9282 (m-40) cc_final: 0.8771 (t0) REVERT: A 908 ASP cc_start: 0.8387 (t0) cc_final: 0.7892 (t0) REVERT: A 938 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8625 (t80) REVERT: A 1018 MET cc_start: 0.9201 (mtm) cc_final: 0.8820 (mtm) REVERT: A 1116 HIS cc_start: 0.9348 (OUTLIER) cc_final: 0.8640 (t70) REVERT: A 1133 MET cc_start: 0.9231 (pmm) cc_final: 0.8826 (pmm) REVERT: A 1280 HIS cc_start: 0.9247 (OUTLIER) cc_final: 0.8658 (t-90) outliers start: 38 outliers final: 26 residues processed: 73 average time/residue: 0.0763 time to fit residues: 8.6422 Evaluate side-chains 69 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 39 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 75 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 132 LEU 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 1225 MET 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: 3.9990 chunk 22 optimal weight: 7.9990 chunk 105 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.042913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.029645 restraints weight = 75129.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.030700 restraints weight = 38730.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.031376 restraints weight = 26185.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.031773 restraints weight = 20641.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.032060 restraints weight = 17982.264| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10640 Z= 0.147 Angle : 0.604 12.723 14806 Z= 0.329 Chirality : 0.042 0.265 1641 Planarity : 0.004 0.054 1559 Dihedral : 23.335 154.344 2280 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.47 % Allowed : 21.39 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.28), residues: 991 helix: 1.23 (0.25), residues: 450 sheet: -0.30 (0.41), residues: 147 loop : 0.45 (0.36), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.016 0.001 TYR A 764 PHE 0.016 0.001 PHE A 557 TRP 0.014 0.001 TRP A1085 HIS 0.008 0.001 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (10640) covalent geometry : angle 0.60420 / 0.33 (14806) hydrogen bonds : bond 0.03585 / 2.36 ( 474) hydrogen bonds : angle 4.34978 / 3.11 ( 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 71 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 40 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7894 (tmmt) REVERT: A 593 MET cc_start: 0.9504 (ppp) cc_final: 0.9210 (ppp) REVERT: A 782 ASN cc_start: 0.9255 (m-40) cc_final: 0.8713 (t0) REVERT: A 908 ASP cc_start: 0.8526 (t0) cc_final: 0.8234 (t0) REVERT: A 938 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8616 (t80) REVERT: A 1018 MET cc_start: 0.9080 (mtm) cc_final: 0.8777 (mtm) REVERT: A 1116 HIS cc_start: 0.9341 (OUTLIER) cc_final: 0.8642 (t-90) REVERT: A 1133 MET cc_start: 0.9214 (pmm) cc_final: 0.8850 (pmm) REVERT: A 1280 HIS cc_start: 0.9267 (OUTLIER) cc_final: 0.8686 (t-90) outliers start: 31 outliers final: 22 residues processed: 67 average time/residue: 0.0813 time to fit residues: 8.3876 Evaluate side-chains 66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 132 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 186 SER 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 69 optimal weight: 0.0470 overall best weight: 1.5682 ------------------------------------------------------------------------------- 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 = 0.3208 r_free = 0.3208 target = 0.043214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.029899 restraints weight = 73869.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.030962 restraints weight = 38575.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.031647 restraints weight = 26254.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.032032 restraints weight = 20786.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.032303 restraints weight = 18204.771| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2199 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= 0.132 Angle : 0.601 15.819 14806 Z= 0.323 Chirality : 0.042 0.261 1641 Planarity : 0.004 0.055 1559 Dihedral : 23.277 154.018 2280 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.25 % Allowed : 21.50 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.28), residues: 991 helix: 1.36 (0.25), residues: 450 sheet: -0.30 (0.41), residues: 149 loop : 0.47 (0.36), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1121 TYR 0.018 0.001 TYR A1012 PHE 0.026 0.001 PHE A 557 TRP 0.013 0.001 TRP A1085 HIS 0.008 0.001 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (10640) covalent geometry : angle 0.60053 / 0.32 (14806) hydrogen bonds : bond 0.03345 / 2.19 ( 474) hydrogen bonds : angle 4.24459 / 3.03 ( 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 70 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 41 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7802 (tmmt) REVERT: A 593 MET cc_start: 0.9532 (ppp) cc_final: 0.9322 (ppp) REVERT: A 782 ASN cc_start: 0.9244 (m-40) cc_final: 0.8664 (t0) REVERT: A 908 ASP cc_start: 0.8405 (t0) cc_final: 0.8017 (t0) REVERT: A 938 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8610 (t80) REVERT: A 1018 MET cc_start: 0.9054 (mtm) cc_final: 0.8701 (mtm) REVERT: A 1116 HIS cc_start: 0.9363 (OUTLIER) cc_final: 0.8658 (t-90) REVERT: A 1133 MET cc_start: 0.9209 (pmm) cc_final: 0.8906 (pmm) REVERT: A 1280 HIS cc_start: 0.9310 (OUTLIER) cc_final: 0.8731 (t-90) outliers start: 29 outliers final: 21 residues processed: 67 average time/residue: 0.0791 time to fit residues: 8.1550 Evaluate side-chains 62 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 37 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 75 ASN Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 132 LEU 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 755 HIS Chi-restraints excluded: chain A residue 779 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 60 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.0670 chunk 62 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 105 optimal weight: 30.0000 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 178 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.042883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.029641 restraints weight = 73843.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.030687 restraints weight = 38614.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.031349 restraints weight = 26304.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.031742 restraints weight = 20928.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.032009 restraints weight = 18305.775| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10640 Z= 0.163 Angle : 0.599 14.197 14806 Z= 0.325 Chirality : 0.042 0.267 1641 Planarity : 0.004 0.054 1559 Dihedral : 23.290 154.190 2279 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.81 % Allowed : 21.72 % Favored : 74.47 % 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: 1.38 (0.25), residues: 450 sheet: -0.34 (0.41), residues: 149 loop : 0.47 (0.36), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 176 TYR 0.013 0.001 TYR A 61 PHE 0.022 0.001 PHE A 557 TRP 0.010 0.001 TRP A1085 HIS 0.007 0.001 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (10640) covalent geometry : angle 0.59851 / 0.32 (14806) hydrogen bonds : bond 0.03546 / 2.32 ( 474) hydrogen bonds : angle 4.26825 / 3.07 ( 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 73 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 39 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7835 (tmmt) REVERT: A 593 MET cc_start: 0.9532 (ppp) cc_final: 0.9196 (ppp) REVERT: A 782 ASN cc_start: 0.9265 (m-40) cc_final: 0.8712 (t0) REVERT: A 908 ASP cc_start: 0.8428 (t0) cc_final: 0.8078 (t0) REVERT: A 938 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8613 (t80) REVERT: A 1116 HIS cc_start: 0.9370 (OUTLIER) cc_final: 0.8673 (t-90) REVERT: A 1133 MET cc_start: 0.9202 (pmm) cc_final: 0.8896 (pmm) REVERT: A 1280 HIS cc_start: 0.9310 (OUTLIER) cc_final: 0.8737 (t-90) outliers start: 34 outliers final: 23 residues processed: 71 average time/residue: 0.0890 time to fit residues: 9.4808 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 : 0.367 ------------------------------------------------------------------------------- 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 75 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 132 LEU 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 38 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.042908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.029638 restraints weight = 73486.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.030689 restraints weight = 38218.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.031359 restraints weight = 26035.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.031742 restraints weight = 20651.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.032017 restraints weight = 18100.902| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2372 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= 0.149 Angle : 0.609 14.803 14806 Z= 0.327 Chirality : 0.042 0.267 1641 Planarity : 0.004 0.054 1559 Dihedral : 23.295 154.148 2279 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.47 % Allowed : 22.17 % 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: 1.01 (0.28), residues: 991 helix: 1.36 (0.25), residues: 450 sheet: -0.33 (0.41), residues: 149 loop : 0.45 (0.36), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1194 TYR 0.015 0.001 TYR A1012 PHE 0.027 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 0.00307 / 0.15 (10640) covalent geometry : angle 0.60903 / 0.33 (14806) hydrogen bonds : bond 0.03430 / 2.24 ( 474) hydrogen bonds : angle 4.22429 / 3.02 ( 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 71 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 40 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 307 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7860 (tmmt) REVERT: A 593 MET cc_start: 0.9530 (ppp) cc_final: 0.9205 (ppp) REVERT: A 782 ASN cc_start: 0.9265 (m-40) cc_final: 0.8701 (t0) REVERT: A 908 ASP cc_start: 0.8416 (t0) cc_final: 0.8102 (t0) REVERT: A 938 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8599 (t80) REVERT: A 1116 HIS cc_start: 0.9339 (OUTLIER) cc_final: 0.8633 (t-90) REVERT: A 1133 MET cc_start: 0.9202 (pmm) cc_final: 0.8921 (pmm) REVERT: A 1280 HIS cc_start: 0.9276 (OUTLIER) cc_final: 0.8645 (t-90) outliers start: 31 outliers final: 24 residues processed: 68 average time/residue: 0.0817 time to fit residues: 8.4873 Evaluate side-chains 66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 38 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 75 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 132 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3186 r_free = 0.3186 target = 0.042308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.029118 restraints weight = 74944.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.030150 restraints weight = 39119.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.030804 restraints weight = 26757.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.031166 restraints weight = 21298.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.031436 restraints weight = 18781.510| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10640 Z= 0.201 Angle : 0.628 13.918 14806 Z= 0.339 Chirality : 0.042 0.277 1641 Planarity : 0.004 0.054 1559 Dihedral : 23.362 154.832 2279 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.02 % Allowed : 22.51 % Favored : 74.47 % 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: 1.33 (0.25), residues: 449 sheet: -0.41 (0.41), residues: 149 loop : 0.47 (0.36), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 912 TYR 0.015 0.001 TYR A1012 PHE 0.024 0.001 PHE A 557 TRP 0.011 0.001 TRP A1085 HIS 0.007 0.001 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 (10640) covalent geometry : angle 0.62766 / 0.34 (14806) hydrogen bonds : bond 0.03872 / 2.54 ( 474) hydrogen bonds : angle 4.30896 / 3.10 ( 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: 27 poor density : 37 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 307 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7931 (tmmt) REVERT: A 593 MET cc_start: 0.9519 (ppp) cc_final: 0.9201 (ppp) REVERT: A 782 ASN cc_start: 0.9268 (m-40) cc_final: 0.8752 (t0) REVERT: A 908 ASP cc_start: 0.8462 (t0) cc_final: 0.8141 (t0) REVERT: A 938 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8599 (t80) REVERT: A 1133 MET cc_start: 0.9200 (pmm) cc_final: 0.8940 (pmm) REVERT: A 1280 HIS cc_start: 0.9266 (OUTLIER) cc_final: 0.8652 (t-90) outliers start: 27 outliers final: 22 residues processed: 62 average time/residue: 0.0818 time to fit residues: 7.7368 Evaluate side-chains 63 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 38 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 75 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 132 LEU 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 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 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 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: 9.9990 chunk 92 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN ** 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** A1122 ASN ** 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 = 0.3166 r_free = 0.3166 target = 0.041631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.028584 restraints weight = 77635.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.029614 restraints weight = 40263.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.030237 restraints weight = 27512.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.030619 restraints weight = 22040.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.030840 restraints weight = 19399.399| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10640 Z= 0.232 Angle : 0.657 13.451 14806 Z= 0.354 Chirality : 0.043 0.293 1641 Planarity : 0.004 0.053 1559 Dihedral : 23.560 156.152 2279 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.25 % Allowed : 22.62 % 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: 0.83 (0.28), residues: 991 helix: 1.19 (0.25), residues: 447 sheet: -0.56 (0.40), residues: 150 loop : 0.48 (0.36), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 912 TYR 0.018 0.002 TYR A 61 PHE 0.021 0.002 PHE A 557 TRP 0.013 0.002 TRP A1085 HIS 0.008 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.23 (10640) covalent geometry : angle 0.65674 / 0.35 (14806) hydrogen bonds : bond 0.04257 / 2.80 ( 474) hydrogen bonds : angle 4.44900 / 3.21 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1525.04 seconds wall clock time: 27 minutes 13.38 seconds (1633.38 seconds total)