Starting phenix.real_space_refine on Sat Aug 23 06:04:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfj_40443/08_2025/8sfj_40443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfj_40443/08_2025/8sfj_40443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sfj_40443/08_2025/8sfj_40443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfj_40443/08_2025/8sfj_40443.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfj_40443/08_2025/8sfj_40443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfj_40443/08_2025/8sfj_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10207 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 8202 Classifications: {'peptide': 1001} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 959} Chain breaks: 4 Chain: "B" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 611 Classifications: {'RNA': 29} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 11, 'rna3p_pyr': 12} Link IDs: {'rna2p': 6, 'rna3p': 22} Chain: "C" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 696 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "D" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 698 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Time building chain proxies: 2.59, per 1000 atoms: 0.25 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: 0.98 Conformation dependent library (CDL) restraints added in 297.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.578A pdb=" N PHE A 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 35 through 67 removed outlier: 3.727A pdb=" N GLU A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 88 through 111 Processing helix chain 'A' and resid 118 through 132 Processing helix chain 'A' and resid 133 through 138 removed outlier: 7.052A pdb=" N GLU A 136 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 137 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 146 removed outlier: 3.914A pdb=" N LYS A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 181 Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 215 removed outlier: 4.311A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 230 removed outlier: 4.243A pdb=" N GLU A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.635A pdb=" N LEU A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 289 through 297 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.776A pdb=" N TYR A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.751A pdb=" N ALA A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 687 Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.599A pdb=" N TYR A 704 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 removed outlier: 3.615A pdb=" N TYR A 710 " --> pdb=" O ASP A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.696A pdb=" N PHE A 769 " --> pdb=" O TRP A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 940 through 949 removed outlier: 4.044A pdb=" N ASN A 946 " --> pdb=" O LYS A 942 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 949 " --> pdb=" O ASP A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 987 removed outlier: 4.055A pdb=" N HIS A 977 " --> pdb=" O SER A 973 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 998 Processing helix chain 'A' and resid 1008 through 1025 removed outlier: 3.809A pdb=" N TYR A1012 " --> pdb=" O GLU A1008 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1100 Processing helix chain 'A' and resid 1177 through 1187 Processing helix chain 'A' and resid 1198 through 1206 removed outlier: 4.360A pdb=" N LYS A1202 " --> pdb=" O ASN A1198 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN A1206 " --> pdb=" O LYS A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1224 Processing helix chain 'A' and resid 1252 through 1254 No H-bonds generated for 'chain 'A' and resid 1252 through 1254' Processing helix chain 'A' and resid 1261 through 1284 Processing helix chain 'A' and resid 1294 through 1307 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.660A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 11.319A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.660A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AA4, first strand: chain 'A' and resid 926 through 931 removed outlier: 6.435A pdb=" N VAL A 919 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN A 929 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 917 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N SER A 931 " --> pdb=" O ILE A 915 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE A 915 " --> pdb=" O SER A 931 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 905 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N GLU A 993 " --> pdb=" O ILE A 905 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N ILE A 907 " --> pdb=" O GLU A 993 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A 990 " --> pdb=" O PHE A1063 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL A1065 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A 992 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1103 through 1106 removed outlier: 4.037A pdb=" N PHE A1103 " --> pdb=" O HIS A1116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1145 through 1147 Processing sheet with id=AA7, first strand: chain 'A' and resid 1159 through 1161 Processing sheet with id=AA8, first strand: chain 'A' and resid 1164 through 1165 Processing sheet with id=AA9, first strand: chain 'A' and resid 1226 through 1229 removed outlier: 4.241A pdb=" N PHE A1249 " --> pdb=" O SER A1239 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 65 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 1.28 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=" CB ASN A1291 " pdb=" CG ASN A1291 " ideal model delta sigma weight residual 1.516 1.576 -0.060 2.50e-02 1.60e+03 5.71e+00 bond pdb=" CA ASN A1291 " pdb=" CB ASN A1291 " ideal model delta sigma weight residual 1.530 1.563 -0.034 1.50e-02 4.44e+03 4.99e+00 bond pdb=" CB ARG A1194 " pdb=" CG ARG A1194 " ideal model delta sigma weight residual 1.520 1.584 -0.064 3.00e-02 1.11e+03 4.55e+00 bond pdb=" C1' DT D 16 " pdb=" N1 DT D 16 " ideal model delta sigma weight residual 1.490 1.552 -0.062 3.00e-02 1.11e+03 4.28e+00 bond pdb=" CA GLN A 987 " pdb=" CB GLN A 987 " ideal model delta sigma weight residual 1.530 1.560 -0.030 1.50e-02 4.44e+03 4.08e+00 ... (remaining 10635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 14565 3.82 - 7.64: 167 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 - 0.120: 1551 0.120 - 0.240: 74 0.240 - 0.360: 2 0.360 - 0.480: 13 0.480 - 0.600: 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 2.35 -2.95 -0.60 2.00e-01 2.50e+01 9.01e+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 2.35 -2.81 -0.46 2.00e-01 2.50e+01 5.35e+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 2.35 -2.81 -0.46 2.00e-01 2.50e+01 5.31e+00 ... (remaining 1638 not shown) Planarity restraints: 1559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1255 " 0.115 5.00e-02 4.00e+02 1.67e-01 4.48e+01 pdb=" N PRO A1256 " -0.289 5.00e-02 4.00e+02 pdb=" CA PRO A1256 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO A1256 " 0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A1065 " -0.097 5.00e-02 4.00e+02 1.44e-01 3.33e+01 pdb=" N PRO A1066 " 0.250 5.00e-02 4.00e+02 pdb=" CA PRO A1066 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO A1066 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1085 " 0.028 2.00e-02 2.50e+03 2.76e-02 1.91e+01 pdb=" CG TRP A1085 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP A1085 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A1085 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1085 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A1085 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1085 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1085 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1085 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A1085 " 0.004 2.00e-02 2.50e+03 ... (remaining 1556 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 608 2.73 - 3.27: 9840 3.27 - 3.81: 18235 3.81 - 4.36: 21820 4.36 - 4.90: 34103 Nonbonded interactions: 84606 Sorted by model distance: nonbonded pdb=" OG SER A 931 " pdb=" OD1 ASN A 933 " model vdw 2.182 3.040 nonbonded pdb=" OG1 THR A 610 " pdb=" OE1 GLN A 611 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR A 8 " pdb=" O PRO A1042 " model vdw 2.292 3.040 nonbonded pdb=" O THR A 167 " pdb=" OG SER A 170 " model vdw 2.292 3.040 nonbonded pdb=" NZ LYS A 59 " pdb=" OD1 ASP A 312 " model vdw 2.295 3.120 ... (remaining 84601 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.780 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 : 0.005 0.067 10640 Z= 0.235 Angle : 1.186 19.101 14806 Z= 0.587 Chirality : 0.068 0.600 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 aren 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 covalent geometry : bond 0.00531 (10640) covalent geometry : angle 1.18640 (14806) hydrogen bonds : bond 0.12190 ( 474) hydrogen bonds : angle 6.28194 ( 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 : 0.242 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: 0.0855 time to fit residues: 7.5732 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 : 0.344 ------------------------------------------------------------------------------- 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: 10.0000 chunk 106 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.042865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.029689 restraints weight = 76131.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.030718 restraints weight = 40293.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.031359 restraints weight = 27490.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.031736 restraints weight = 21869.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031997 restraints weight = 19144.682| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 10640 Z= 0.306 Angle : 0.709 10.089 14806 Z= 0.384 Chirality : 0.042 0.146 1641 Planarity : 0.006 0.084 1559 Dihedral : 23.207 154.983 2280 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.70 % Allowed : 19.93 % 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 aren not related in a simple way. whole: 0.43 (0.27), residues: 991 helix: 0.65 (0.24), residues: 448 sheet: -0.34 (0.42), residues: 144 loop : 0.34 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 160 TYR 0.021 0.002 TYR A 764 PHE 0.017 0.002 PHE A1052 TRP 0.018 0.002 TRP A1085 HIS 0.015 0.002 HIS A1096 Details of bonding type rmsd covalent geometry : bond 0.00643 (10640) covalent geometry : angle 0.70928 (14806) hydrogen bonds : bond 0.04800 ( 474) hydrogen bonds : angle 4.85706 ( 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 73 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 40 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 782 ASN cc_start: 0.9270 (m-40) cc_final: 0.8743 (t0) REVERT: A 786 GLU cc_start: 0.8061 (mp0) cc_final: 0.7792 (mp0) REVERT: A 1018 MET cc_start: 0.8973 (mtm) cc_final: 0.8755 (mtm) REVERT: A 1133 MET cc_start: 0.9226 (pmm) cc_final: 0.8825 (pmm) REVERT: A 1280 HIS cc_start: 0.9223 (OUTLIER) cc_final: 0.8615 (t-90) outliers start: 33 outliers final: 19 residues processed: 68 average time/residue: 0.0663 time to fit residues: 7.0723 Evaluate side-chains 61 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 215 VAL Chi-restraints excluded: chain A residue 218 LEU 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 755 HIS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1073 ILE 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 1225 MET 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: 1.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 47 optimal weight: 0.0870 chunk 80 optimal weight: 4.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN ** 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** A1091 HIS ** 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 = 0.3227 r_free = 0.3227 target = 0.043904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.030523 restraints weight = 73908.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.031609 restraints weight = 38086.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.032316 restraints weight = 25784.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.032760 restraints weight = 20391.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.032957 restraints weight = 17658.464| |-----------------------------------------------------------------------------| r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1832 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= 0.124 Angle : 0.606 10.468 14806 Z= 0.321 Chirality : 0.040 0.241 1641 Planarity : 0.004 0.067 1559 Dihedral : 23.055 153.888 2280 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.58 % Allowed : 20.38 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.28), residues: 991 helix: 1.06 (0.25), residues: 450 sheet: -0.15 (0.42), residues: 149 loop : 0.32 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1121 TYR 0.020 0.001 TYR A 764 PHE 0.010 0.001 PHE A 999 TRP 0.016 0.001 TRP A1085 HIS 0.010 0.001 HIS A1096 Details of bonding type rmsd covalent geometry : bond 0.00271 (10640) covalent geometry : angle 0.60559 (14806) hydrogen bonds : bond 0.03193 ( 474) hydrogen bonds : angle 4.37663 ( 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 66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 782 ASN cc_start: 0.9242 (m-40) cc_final: 0.8183 (m110) REVERT: A 786 GLU cc_start: 0.8042 (mp0) cc_final: 0.7758 (mp0) REVERT: A 997 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: A 1116 HIS cc_start: 0.9373 (OUTLIER) cc_final: 0.8715 (t-90) REVERT: A 1133 MET cc_start: 0.9267 (pmm) cc_final: 0.8921 (pmm) REVERT: A 1280 HIS cc_start: 0.9332 (OUTLIER) cc_final: 0.8735 (t-90) outliers start: 23 outliers final: 11 residues processed: 65 average time/residue: 0.0868 time to fit residues: 8.6287 Evaluate side-chains 53 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 536 GLN Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 997 PHE 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 1280 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 72 optimal weight: 0.0060 chunk 27 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 overall best weight: 3.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 HIS ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.3182 r_free = 0.3182 target = 0.041994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.028865 restraints weight = 76377.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.029914 restraints weight = 39455.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.030571 restraints weight = 26759.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.030951 restraints weight = 21225.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.031211 restraints weight = 18582.270| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2345 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= 0.238 Angle : 0.620 9.295 14806 Z= 0.338 Chirality : 0.040 0.182 1641 Planarity : 0.004 0.061 1559 Dihedral : 23.147 155.218 2279 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.26 % Allowed : 19.04 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.28), residues: 991 helix: 1.23 (0.25), residues: 451 sheet: -0.23 (0.42), residues: 147 loop : 0.47 (0.35), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 912 TYR 0.017 0.002 TYR A 764 PHE 0.013 0.001 PHE A1249 TRP 0.011 0.001 TRP A1085 HIS 0.009 0.001 HIS A1096 Details of bonding type rmsd covalent geometry : bond 0.00502 (10640) covalent geometry : angle 0.62043 (14806) hydrogen bonds : bond 0.04022 ( 474) hydrogen bonds : angle 4.36911 ( 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 78 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 40 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 782 ASN cc_start: 0.9272 (m-40) cc_final: 0.8697 (t0) REVERT: A 786 GLU cc_start: 0.8040 (mp0) cc_final: 0.7751 (mp0) REVERT: A 908 ASP cc_start: 0.8424 (t0) cc_final: 0.8203 (t0) REVERT: A 938 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8639 (t80) REVERT: A 1018 MET cc_start: 0.9081 (mtm) cc_final: 0.8876 (mtm) REVERT: A 1133 MET cc_start: 0.9193 (pmm) cc_final: 0.8879 (pmm) REVERT: A 1280 HIS cc_start: 0.9279 (OUTLIER) cc_final: 0.8719 (t-90) outliers start: 38 outliers final: 25 residues processed: 75 average time/residue: 0.0715 time to fit residues: 8.2662 Evaluate side-chains 66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 39 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 536 GLN 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 707 LEU 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 1065 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1090 ASN Chi-restraints excluded: chain A residue 1110 THR 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: 9.9990 chunk 100 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 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** A1122 ASN ** 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 = 0.3169 r_free = 0.3169 target = 0.041488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.028434 restraints weight = 75842.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.029453 restraints weight = 39261.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.030089 restraints weight = 26888.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.030461 restraints weight = 21365.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.030720 restraints weight = 18796.408| |-----------------------------------------------------------------------------| r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2759 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= 0.237 Angle : 0.618 9.206 14806 Z= 0.335 Chirality : 0.040 0.166 1641 Planarity : 0.004 0.056 1559 Dihedral : 23.313 156.803 2279 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.03 % Allowed : 20.49 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.28), residues: 991 helix: 1.24 (0.25), residues: 449 sheet: -0.40 (0.42), residues: 150 loop : 0.56 (0.36), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1121 TYR 0.016 0.002 TYR A 61 PHE 0.013 0.001 PHE A 557 TRP 0.013 0.001 TRP A1085 HIS 0.008 0.001 HIS A1096 Details of bonding type rmsd covalent geometry : bond 0.00505 (10640) covalent geometry : angle 0.61754 (14806) hydrogen bonds : bond 0.03965 ( 474) hydrogen bonds : angle 4.36481 ( 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 75 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 39 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 593 MET cc_start: 0.9515 (ppp) cc_final: 0.9224 (ppp) REVERT: A 782 ASN cc_start: 0.9255 (m-40) cc_final: 0.8683 (t0) REVERT: A 786 GLU cc_start: 0.8052 (mp0) cc_final: 0.7755 (mp0) REVERT: A 908 ASP cc_start: 0.8494 (t0) cc_final: 0.8257 (t0) REVERT: A 938 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8603 (t80) REVERT: A 1133 MET cc_start: 0.9152 (pmm) cc_final: 0.8931 (pmm) REVERT: A 1280 HIS cc_start: 0.9247 (OUTLIER) cc_final: 0.8620 (t-90) outliers start: 36 outliers final: 27 residues processed: 72 average time/residue: 0.0640 time to fit residues: 7.1761 Evaluate side-chains 67 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 38 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 536 GLN 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 688 THR Chi-restraints excluded: chain A residue 707 LEU 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 1065 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1090 ASN Chi-restraints excluded: chain A residue 1160 ILE Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1280 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 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** A1122 ASN ** 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 = 0.3177 r_free = 0.3177 target = 0.041834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.028717 restraints weight = 76648.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.029772 restraints weight = 39472.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.030424 restraints weight = 26758.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.030801 restraints weight = 21231.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031079 restraints weight = 18625.060| |-----------------------------------------------------------------------------| r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10640 Z= 0.185 Angle : 0.590 8.779 14806 Z= 0.318 Chirality : 0.039 0.176 1641 Planarity : 0.004 0.053 1559 Dihedral : 23.303 156.190 2279 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.26 % Allowed : 20.83 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.28), residues: 991 helix: 1.38 (0.25), residues: 449 sheet: -0.33 (0.42), residues: 149 loop : 0.55 (0.36), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 912 TYR 0.014 0.001 TYR A 764 PHE 0.020 0.001 PHE A 557 TRP 0.013 0.001 TRP A1085 HIS 0.006 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00400 (10640) covalent geometry : angle 0.58973 (14806) hydrogen bonds : bond 0.03555 ( 474) hydrogen bonds : angle 4.24088 ( 1284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 39 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 307 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7955 (tmmt) REVERT: A 593 MET cc_start: 0.9536 (ppp) cc_final: 0.9315 (ppp) REVERT: A 782 ASN cc_start: 0.9241 (m-40) cc_final: 0.8678 (t0) REVERT: A 786 GLU cc_start: 0.8067 (mp0) cc_final: 0.7749 (mp0) REVERT: A 938 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8597 (t80) REVERT: A 1018 MET cc_start: 0.9225 (mtm) cc_final: 0.8933 (mtm) REVERT: A 1133 MET cc_start: 0.9140 (pmm) cc_final: 0.8925 (pmm) REVERT: A 1199 ILE cc_start: 0.9601 (OUTLIER) cc_final: 0.9395 (mm) REVERT: A 1280 HIS cc_start: 0.9256 (OUTLIER) cc_final: 0.8607 (t-90) outliers start: 38 outliers final: 25 residues processed: 74 average time/residue: 0.0701 time to fit residues: 8.1330 Evaluate side-chains 65 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 36 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 118 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 240 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 536 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 707 LEU 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 989 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1090 ASN Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1160 ILE Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1280 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 3 optimal weight: 0.1980 chunk 69 optimal weight: 0.0270 overall best weight: 2.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 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** A1122 ASN ** 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 = 0.3179 r_free = 0.3179 target = 0.041924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.028844 restraints weight = 75414.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.029888 restraints weight = 38879.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.030535 restraints weight = 26416.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.030931 restraints weight = 20998.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.031187 restraints weight = 18360.429| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10640 Z= 0.174 Angle : 0.594 8.619 14806 Z= 0.320 Chirality : 0.040 0.257 1641 Planarity : 0.004 0.052 1559 Dihedral : 23.351 155.720 2279 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.14 % Allowed : 21.16 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.28), residues: 991 helix: 1.33 (0.25), residues: 449 sheet: -0.48 (0.40), residues: 159 loop : 0.65 (0.36), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 912 TYR 0.015 0.001 TYR A1012 PHE 0.036 0.001 PHE A 999 TRP 0.012 0.001 TRP A1085 HIS 0.006 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00378 (10640) covalent geometry : angle 0.59436 (14806) hydrogen bonds : bond 0.03510 ( 474) hydrogen bonds : angle 4.21125 ( 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 75 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 38 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9516 (tp) cc_final: 0.9271 (tp) REVERT: A 307 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7976 (tmmt) REVERT: A 593 MET cc_start: 0.9540 (ppp) cc_final: 0.9237 (ppp) REVERT: A 786 GLU cc_start: 0.8070 (mp0) cc_final: 0.7754 (mp0) REVERT: A 938 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8621 (t80) REVERT: A 1018 MET cc_start: 0.9154 (mtm) cc_final: 0.8823 (mtm) REVERT: A 1199 ILE cc_start: 0.9599 (OUTLIER) cc_final: 0.9387 (mm) REVERT: A 1280 HIS cc_start: 0.9265 (OUTLIER) cc_final: 0.8640 (t-90) outliers start: 37 outliers final: 27 residues processed: 72 average time/residue: 0.0698 time to fit residues: 7.7850 Evaluate side-chains 66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 35 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 536 GLN 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 707 LEU 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 1065 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1090 ASN Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1160 ILE Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1280 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 60 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 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 = 0.3179 r_free = 0.3179 target = 0.042699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.029553 restraints weight = 74566.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.030576 restraints weight = 39441.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.031214 restraints weight = 27077.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.031620 restraints weight = 21634.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.031838 restraints weight = 18926.018| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10640 Z= 0.194 Angle : 0.604 8.657 14806 Z= 0.324 Chirality : 0.040 0.234 1641 Planarity : 0.004 0.051 1559 Dihedral : 23.372 155.769 2279 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.92 % Allowed : 22.06 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.28), residues: 991 helix: 1.33 (0.25), residues: 449 sheet: -0.44 (0.40), residues: 158 loop : 0.62 (0.36), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 909 TYR 0.014 0.002 TYR A 61 PHE 0.033 0.001 PHE A 999 TRP 0.012 0.001 TRP A1085 HIS 0.007 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00418 (10640) covalent geometry : angle 0.60440 (14806) hydrogen bonds : bond 0.03648 ( 474) hydrogen bonds : angle 4.23213 ( 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 74 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 39 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9544 (tp) cc_final: 0.9292 (tp) REVERT: A 174 GLU cc_start: 0.9119 (pp20) cc_final: 0.8752 (pp20) REVERT: A 307 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7974 (tmmt) REVERT: A 593 MET cc_start: 0.9529 (ppp) cc_final: 0.9197 (ppp) REVERT: A 764 TYR cc_start: 0.9393 (m-80) cc_final: 0.9170 (m-80) REVERT: A 786 GLU cc_start: 0.8072 (mp0) cc_final: 0.7755 (mp0) REVERT: A 938 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8594 (t80) REVERT: A 1018 MET cc_start: 0.9161 (mtm) cc_final: 0.8950 (mtm) REVERT: A 1199 ILE cc_start: 0.9590 (OUTLIER) cc_final: 0.9372 (mm) REVERT: A 1280 HIS cc_start: 0.9258 (OUTLIER) cc_final: 0.8629 (t-90) outliers start: 35 outliers final: 26 residues processed: 71 average time/residue: 0.0688 time to fit residues: 7.6419 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 : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 536 GLN 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 707 LEU 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 989 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1090 ASN Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1160 ILE Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1280 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 92 optimal weight: 0.0020 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 GLN ** 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 = 0.3218 r_free = 0.3218 target = 0.043474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.030334 restraints weight = 73315.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.031410 restraints weight = 37952.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.032091 restraints weight = 25629.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.032495 restraints weight = 20280.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.032774 restraints weight = 17722.834| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10640 Z= 0.118 Angle : 0.600 9.213 14806 Z= 0.312 Chirality : 0.039 0.248 1641 Planarity : 0.004 0.049 1559 Dihedral : 23.144 153.502 2279 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.46 % Allowed : 23.74 % Favored : 73.80 % 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 aren not related in a simple way. whole: 1.09 (0.28), residues: 991 helix: 1.43 (0.25), residues: 449 sheet: -0.43 (0.40), residues: 158 loop : 0.59 (0.36), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 909 TYR 0.013 0.001 TYR A 764 PHE 0.029 0.001 PHE A 999 TRP 0.011 0.001 TRP A1136 HIS 0.005 0.001 HIS A1096 Details of bonding type rmsd covalent geometry : bond 0.00261 (10640) covalent geometry : angle 0.60027 (14806) hydrogen bonds : bond 0.02948 ( 474) hydrogen bonds : angle 4.03301 ( 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 64 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 42 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 174 GLU cc_start: 0.9118 (pp20) cc_final: 0.8749 (pp20) REVERT: A 307 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7928 (tmmt) REVERT: A 593 MET cc_start: 0.9568 (ppp) cc_final: 0.9256 (ppp) REVERT: A 764 TYR cc_start: 0.9325 (m-80) cc_final: 0.9094 (m-80) REVERT: A 786 GLU cc_start: 0.8052 (mp0) cc_final: 0.7738 (mp0) REVERT: A 938 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8634 (t80) REVERT: A 1018 MET cc_start: 0.9155 (mtm) cc_final: 0.8933 (mtm) REVERT: A 1199 ILE cc_start: 0.9572 (OUTLIER) cc_final: 0.9358 (mm) REVERT: A 1280 HIS cc_start: 0.9306 (OUTLIER) cc_final: 0.8683 (t-90) outliers start: 22 outliers final: 16 residues processed: 63 average time/residue: 0.0991 time to fit residues: 9.4041 Evaluate side-chains 61 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 536 GLN 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 707 LEU 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 989 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1280 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN ** 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** A1279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.040964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.027879 restraints weight = 77440.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.028863 restraints weight = 41309.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.029496 restraints weight = 28642.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.029852 restraints weight = 22874.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.030095 restraints weight = 20212.830| |-----------------------------------------------------------------------------| r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 10640 Z= 0.348 Angle : 0.704 8.551 14806 Z= 0.380 Chirality : 0.043 0.199 1641 Planarity : 0.005 0.052 1559 Dihedral : 23.536 156.497 2279 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.91 % Allowed : 23.63 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.28), residues: 991 helix: 1.13 (0.24), residues: 449 sheet: -0.63 (0.39), residues: 159 loop : 0.59 (0.36), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 912 TYR 0.026 0.002 TYR A1064 PHE 0.031 0.002 PHE A 999 TRP 0.012 0.002 TRP A1085 HIS 0.008 0.002 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00729 (10640) covalent geometry : angle 0.70428 (14806) hydrogen bonds : bond 0.04858 ( 474) hydrogen bonds : angle 4.47564 ( 1284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 38 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9520 (tp) cc_final: 0.9301 (tp) REVERT: A 593 MET cc_start: 0.9498 (ppp) cc_final: 0.9161 (ppp) REVERT: A 786 GLU cc_start: 0.8062 (mp0) cc_final: 0.7713 (mp0) REVERT: A 938 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8649 (t80) REVERT: A 1018 MET cc_start: 0.9182 (mtm) cc_final: 0.8939 (mtm) REVERT: A 1199 ILE cc_start: 0.9584 (OUTLIER) cc_final: 0.9356 (mm) REVERT: A 1280 HIS cc_start: 0.9282 (OUTLIER) cc_final: 0.8709 (t-90) outliers start: 26 outliers final: 18 residues processed: 61 average time/residue: 0.0806 time to fit residues: 7.5572 Evaluate side-chains 57 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 36 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 707 LEU 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 989 VAL Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1280 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 77 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.042094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.028989 restraints weight = 74837.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.030035 restraints weight = 39044.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.030688 restraints weight = 26569.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.031116 restraints weight = 21126.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.031342 restraints weight = 18343.187| |-----------------------------------------------------------------------------| r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10640 Z= 0.146 Angle : 0.614 9.029 14806 Z= 0.322 Chirality : 0.040 0.260 1641 Planarity : 0.004 0.047 1559 Dihedral : 23.371 155.056 2279 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.69 % Allowed : 23.85 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.28), residues: 991 helix: 1.39 (0.25), residues: 449 sheet: -0.54 (0.39), residues: 158 loop : 0.62 (0.36), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 670 TYR 0.014 0.001 TYR A1064 PHE 0.029 0.001 PHE A 999 TRP 0.011 0.001 TRP A1085 HIS 0.006 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00323 (10640) covalent geometry : angle 0.61438 (14806) hydrogen bonds : bond 0.03321 ( 474) hydrogen bonds : angle 4.12709 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1487.63 seconds wall clock time: 26 minutes 48.23 seconds (1608.23 seconds total)