Starting phenix.real_space_refine on Thu May 1 02:51:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfj_40443/05_2025/8sfj_40443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfj_40443/05_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_40443/05_2025/8sfj_40443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfj_40443/05_2025/8sfj_40443.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfj_40443/05_2025/8sfj_40443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfj_40443/05_2025/8sfj_40443.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 7.60, per 1000 atoms: 0.74 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: 3.11 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 3.98 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: 7.66 Time building geometry restraints manager: 3.38 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: 84.740 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 36.900 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.080 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: 0.020 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.870 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.071 0.004 TRP A1085 HIS 0.034 0.002 HIS A1096 PHE 0.047 0.003 PHE A 619 TYR 0.050 0.003 TYR A1236 ARG 0.007 0.001 ARG A1003 Details of bonding type rmsd hydrogen bonds : bond 0.12190 ( 474) hydrogen bonds : angle 6.28194 ( 1284) covalent geometry : bond 0.00531 (10640) covalent geometry : angle 1.18640 (14806) *********************** 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 : 2.050 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: 0.2828 time to fit residues: 25.3751 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 : 1.094 ------------------------------------------------------------------------------- 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 91 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 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 ** 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 = 0.3165 r_free = 0.3165 target = 0.042185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.029078 restraints weight = 76803.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.030064 restraints weight = 40790.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.030699 restraints weight = 28167.471| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 10640 Z= 0.366 Angle : 0.753 10.062 14806 Z= 0.409 Chirality : 0.044 0.141 1641 Planarity : 0.006 0.081 1559 Dihedral : 23.297 156.028 2280 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.81 % Allowed : 20.60 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.27), residues: 991 helix: 0.54 (0.24), residues: 448 sheet: -0.41 (0.41), residues: 144 loop : 0.33 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1085 HIS 0.015 0.002 HIS A1096 PHE 0.022 0.002 PHE A1052 TYR 0.020 0.002 TYR A1173 ARG 0.005 0.001 ARG A 160 Details of bonding type rmsd hydrogen bonds : bond 0.05413 ( 474) hydrogen bonds : angle 4.99539 ( 1284) covalent geometry : bond 0.00764 (10640) covalent geometry : angle 0.75333 (14806) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 40 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 782 ASN cc_start: 0.9309 (m-40) cc_final: 0.8803 (t0) REVERT: A 786 GLU cc_start: 0.8084 (mp0) cc_final: 0.7797 (mp0) REVERT: A 1018 MET cc_start: 0.8980 (mtm) cc_final: 0.8760 (mtm) REVERT: A 1133 MET cc_start: 0.9228 (pmm) cc_final: 0.8826 (pmm) REVERT: A 1280 HIS cc_start: 0.9252 (OUTLIER) cc_final: 0.8642 (t-90) outliers start: 34 outliers final: 20 residues processed: 69 average time/residue: 0.2222 time to fit residues: 23.5927 Evaluate side-chains 60 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 39 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 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 1073 ILE Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1090 ASN Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 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 60 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** 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 = 0.3189 r_free = 0.3189 target = 0.042403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.029179 restraints weight = 75464.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.030231 restraints weight = 39092.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.030894 restraints weight = 26520.877| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10640 Z= 0.166 Angle : 0.617 10.076 14806 Z= 0.332 Chirality : 0.040 0.188 1641 Planarity : 0.004 0.064 1559 Dihedral : 23.238 156.119 2280 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.81 % Allowed : 20.27 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.28), residues: 991 helix: 0.98 (0.25), residues: 450 sheet: -0.32 (0.42), residues: 149 loop : 0.38 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1085 HIS 0.010 0.001 HIS A1096 PHE 0.012 0.001 PHE A 999 TYR 0.019 0.001 TYR A 764 ARG 0.003 0.000 ARG A1121 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 474) hydrogen bonds : angle 4.52414 ( 1284) covalent geometry : bond 0.00361 (10640) covalent geometry : angle 0.61680 (14806) *********************** 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 73 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 39 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: A 782 ASN cc_start: 0.9274 (m-40) cc_final: 0.8725 (t0) REVERT: A 786 GLU cc_start: 0.8076 (mp0) cc_final: 0.7700 (mp0) REVERT: A 938 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8709 (t80) REVERT: A 997 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: A 1018 MET cc_start: 0.8921 (mtm) cc_final: 0.8719 (mtm) REVERT: A 1133 MET cc_start: 0.9245 (pmm) cc_final: 0.8915 (pmm) REVERT: A 1280 HIS cc_start: 0.9299 (OUTLIER) cc_final: 0.8710 (t-90) outliers start: 34 outliers final: 21 residues processed: 70 average time/residue: 0.2475 time to fit residues: 27.3886 Evaluate side-chains 61 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 37 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 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 539 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 938 PHE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1278 LEU 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 23 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 0.0570 chunk 96 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 overall best weight: 3.3904 ------------------------------------------------------------------------------- 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 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 ** 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 = 0.3170 r_free = 0.3170 target = 0.041704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.028667 restraints weight = 75758.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.029688 restraints weight = 39613.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.030336 restraints weight = 26945.620| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10640 Z= 0.234 Angle : 0.622 9.186 14806 Z= 0.339 Chirality : 0.040 0.175 1641 Planarity : 0.004 0.059 1559 Dihedral : 23.283 156.668 2280 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.26 % Allowed : 20.72 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.28), residues: 991 helix: 1.08 (0.25), residues: 451 sheet: -0.42 (0.41), residues: 149 loop : 0.47 (0.36), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1085 HIS 0.009 0.001 HIS A1096 PHE 0.013 0.001 PHE A1249 TYR 0.016 0.002 TYR A 61 ARG 0.003 0.000 ARG A 912 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 474) hydrogen bonds : angle 4.41661 ( 1284) covalent geometry : bond 0.00499 (10640) covalent geometry : angle 0.62170 (14806) *********************** 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 77 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 39 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 782 ASN cc_start: 0.9299 (m-40) cc_final: 0.8691 (t0) REVERT: A 786 GLU cc_start: 0.8078 (mp0) cc_final: 0.7722 (mp0) REVERT: A 908 ASP cc_start: 0.8471 (t0) cc_final: 0.8181 (t0) REVERT: A 938 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8644 (t80) REVERT: A 1133 MET cc_start: 0.9197 (pmm) cc_final: 0.8914 (pmm) REVERT: A 1280 HIS cc_start: 0.9303 (OUTLIER) cc_final: 0.8690 (t-90) outliers start: 38 outliers final: 28 residues processed: 73 average time/residue: 0.2626 time to fit residues: 29.2133 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 : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 536 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 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 1080 VAL 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 51 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN ** 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 = 0.3151 r_free = 0.3151 target = 0.041303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.028162 restraints weight = 76082.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.029168 restraints weight = 40415.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.029764 restraints weight = 27777.839| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3077 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= 0.273 Angle : 0.645 8.742 14806 Z= 0.352 Chirality : 0.041 0.179 1641 Planarity : 0.004 0.055 1559 Dihedral : 23.526 158.093 2280 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.38 % Allowed : 21.05 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.28), residues: 991 helix: 1.01 (0.24), residues: 449 sheet: -0.53 (0.41), residues: 150 loop : 0.47 (0.36), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1085 HIS 0.008 0.001 HIS A 618 PHE 0.013 0.002 PHE A1249 TYR 0.018 0.002 TYR A1012 ARG 0.004 0.000 ARG A 912 Details of bonding type rmsd hydrogen bonds : bond 0.04400 ( 474) hydrogen bonds : angle 4.50815 ( 1284) covalent geometry : bond 0.00575 (10640) covalent geometry : angle 0.64506 (14806) *********************** 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 87 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 39 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8054 (tmmt) REVERT: A 593 MET cc_start: 0.9510 (ppp) cc_final: 0.9306 (ppp) REVERT: A 786 GLU cc_start: 0.8133 (mp0) cc_final: 0.7716 (mp0) REVERT: A 938 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8682 (t80) REVERT: A 1000 LYS cc_start: 0.8572 (mmtt) cc_final: 0.8307 (mmtt) REVERT: A 1018 MET cc_start: 0.9250 (mtm) cc_final: 0.8909 (mtm) REVERT: A 1199 ILE cc_start: 0.9580 (OUTLIER) cc_final: 0.9358 (mm) REVERT: A 1280 HIS cc_start: 0.9239 (OUTLIER) cc_final: 0.8616 (t-90) outliers start: 48 outliers final: 26 residues processed: 84 average time/residue: 0.2266 time to fit residues: 29.1773 Evaluate side-chains 68 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 38 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 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 989 VAL Chi-restraints excluded: chain A residue 1080 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 5.9990 chunk 14 optimal weight: 0.0370 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 3 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 107 optimal weight: 30.0000 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 overall best weight: 1.0662 ------------------------------------------------------------------------------- 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 611 GLN A 647 ASN ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1091 HIS A1122 ASN ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.042550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.029433 restraints weight = 74453.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.030504 restraints weight = 38508.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.031163 restraints weight = 26093.478| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10640 Z= 0.129 Angle : 0.598 8.889 14806 Z= 0.318 Chirality : 0.040 0.225 1641 Planarity : 0.004 0.057 1559 Dihedral : 23.289 155.717 2280 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.58 % Allowed : 23.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.28), residues: 991 helix: 1.32 (0.25), residues: 449 sheet: -0.39 (0.41), residues: 149 loop : 0.52 (0.35), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1085 HIS 0.005 0.001 HIS A1096 PHE 0.021 0.001 PHE A 557 TYR 0.013 0.002 TYR A 595 ARG 0.002 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 474) hydrogen bonds : angle 4.16347 ( 1284) covalent geometry : bond 0.00286 (10640) covalent geometry : angle 0.59833 (14806) *********************** 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 66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 764 TYR cc_start: 0.9392 (m-80) cc_final: 0.9160 (m-80) REVERT: A 786 GLU cc_start: 0.8115 (mp0) cc_final: 0.7690 (mp0) REVERT: A 908 ASP cc_start: 0.8495 (t0) cc_final: 0.8007 (t0) REVERT: A 1018 MET cc_start: 0.9113 (mtm) cc_final: 0.8892 (mtm) REVERT: A 1055 MET cc_start: 0.8952 (ppp) cc_final: 0.7933 (ppp) REVERT: A 1199 ILE cc_start: 0.9617 (OUTLIER) cc_final: 0.9412 (mm) REVERT: A 1280 HIS cc_start: 0.9299 (OUTLIER) cc_final: 0.8671 (t-90) outliers start: 23 outliers final: 17 residues processed: 65 average time/residue: 0.2994 time to fit residues: 29.0228 Evaluate side-chains 55 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 36 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 132 LEU 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 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 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1110 THR 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 1280 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 0.0170 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- 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 611 GLN ** 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 = 0.3168 r_free = 0.3168 target = 0.041957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.028833 restraints weight = 76046.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.029859 restraints weight = 39860.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.030501 restraints weight = 27184.094| |-----------------------------------------------------------------------------| r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10640 Z= 0.207 Angle : 0.611 8.296 14806 Z= 0.330 Chirality : 0.040 0.192 1641 Planarity : 0.004 0.058 1559 Dihedral : 23.409 156.043 2279 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.25 % Allowed : 23.96 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.28), residues: 991 helix: 1.26 (0.25), residues: 449 sheet: -0.38 (0.41), residues: 148 loop : 0.52 (0.35), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1085 HIS 0.006 0.001 HIS A 618 PHE 0.034 0.001 PHE A 999 TYR 0.017 0.002 TYR A1064 ARG 0.002 0.000 ARG A 912 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 474) hydrogen bonds : angle 4.22260 ( 1284) covalent geometry : bond 0.00445 (10640) covalent geometry : angle 0.61115 (14806) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 38 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: A 174 GLU cc_start: 0.9124 (pp20) cc_final: 0.8777 (pp20) REVERT: A 307 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7975 (tmmt) REVERT: A 764 TYR cc_start: 0.9374 (m-80) cc_final: 0.9090 (m-80) REVERT: A 786 GLU cc_start: 0.8127 (mp0) cc_final: 0.7819 (mp0) REVERT: A 908 ASP cc_start: 0.8556 (t0) cc_final: 0.8256 (t0) REVERT: A 938 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8684 (t80) REVERT: A 1018 MET cc_start: 0.9136 (mtm) cc_final: 0.8857 (mtm) REVERT: A 1133 MET cc_start: 0.9216 (pmm) cc_final: 0.8911 (pmm) REVERT: A 1199 ILE cc_start: 0.9593 (OUTLIER) cc_final: 0.9380 (mm) REVERT: A 1280 HIS cc_start: 0.9239 (OUTLIER) cc_final: 0.8621 (t-90) outliers start: 29 outliers final: 19 residues processed: 66 average time/residue: 0.2061 time to fit residues: 20.9030 Evaluate side-chains 59 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 36 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL 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 186 SER Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 307 LYS 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 1110 THR 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 25 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 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 = 0.3139 r_free = 0.3139 target = 0.040890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.027848 restraints weight = 78226.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.028851 restraints weight = 40974.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.029414 restraints weight = 28151.347| |-----------------------------------------------------------------------------| r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10640 Z= 0.306 Angle : 0.675 8.641 14806 Z= 0.366 Chirality : 0.042 0.175 1641 Planarity : 0.004 0.057 1559 Dihedral : 23.679 157.754 2279 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.47 % Allowed : 24.64 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.28), residues: 991 helix: 0.97 (0.24), residues: 449 sheet: -0.54 (0.40), residues: 141 loop : 0.44 (0.35), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1085 HIS 0.008 0.001 HIS A 618 PHE 0.034 0.002 PHE A 999 TYR 0.027 0.002 TYR A1064 ARG 0.004 0.001 ARG A 912 Details of bonding type rmsd hydrogen bonds : bond 0.04753 ( 474) hydrogen bonds : angle 4.51713 ( 1284) covalent geometry : bond 0.00644 (10640) covalent geometry : angle 0.67515 (14806) *********************** 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 68 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 37 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 307 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7955 (tmmt) REVERT: A 786 GLU cc_start: 0.8154 (mp0) cc_final: 0.7750 (mp0) REVERT: A 938 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8601 (t80) REVERT: A 1199 ILE cc_start: 0.9610 (OUTLIER) cc_final: 0.9389 (mm) REVERT: A 1280 HIS cc_start: 0.9285 (OUTLIER) cc_final: 0.8656 (t-90) outliers start: 31 outliers final: 24 residues processed: 65 average time/residue: 0.2077 time to fit residues: 20.9595 Evaluate side-chains 63 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 35 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 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 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 938 PHE Chi-restraints excluded: chain A residue 1110 THR 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 1277 LEU 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 74 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 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 = 0.3183 r_free = 0.3183 target = 0.042151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.029052 restraints weight = 74859.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.030103 restraints weight = 38816.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.030761 restraints weight = 26307.722| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10640 Z= 0.132 Angle : 0.609 8.979 14806 Z= 0.321 Chirality : 0.040 0.213 1641 Planarity : 0.004 0.056 1559 Dihedral : 23.423 155.610 2279 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.80 % Allowed : 25.53 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.28), residues: 991 helix: 1.30 (0.25), residues: 449 sheet: -0.59 (0.40), residues: 158 loop : 0.59 (0.36), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1085 HIS 0.005 0.001 HIS A 618 PHE 0.030 0.001 PHE A 999 TYR 0.014 0.002 TYR A1012 ARG 0.003 0.000 ARG A 670 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 474) hydrogen bonds : angle 4.15472 ( 1284) covalent geometry : bond 0.00293 (10640) covalent geometry : angle 0.60899 (14806) *********************** 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: 25 poor density : 39 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9296 (tp) REVERT: A 174 GLU cc_start: 0.9128 (pp20) cc_final: 0.8755 (pp20) REVERT: A 764 TYR cc_start: 0.9376 (m-80) cc_final: 0.9088 (m-80) REVERT: A 786 GLU cc_start: 0.8110 (mp0) cc_final: 0.7786 (mp0) REVERT: A 908 ASP cc_start: 0.8521 (t0) cc_final: 0.8035 (t0) REVERT: A 938 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8691 (t80) REVERT: A 1199 ILE cc_start: 0.9611 (OUTLIER) cc_final: 0.9403 (mm) REVERT: A 1280 HIS cc_start: 0.9319 (OUTLIER) cc_final: 0.8660 (t-90) outliers start: 25 outliers final: 15 residues processed: 62 average time/residue: 0.2021 time to fit residues: 19.2078 Evaluate side-chains 57 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 132 LEU 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 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 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: 4.9990 chunk 52 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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 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 = 0.3161 r_free = 0.3161 target = 0.041629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.028458 restraints weight = 76826.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.029473 restraints weight = 40396.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.030064 restraints weight = 27823.427| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10640 Z= 0.233 Angle : 0.629 8.944 14806 Z= 0.338 Chirality : 0.040 0.182 1641 Planarity : 0.004 0.058 1559 Dihedral : 23.553 156.211 2279 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.35 % Allowed : 25.76 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.28), residues: 991 helix: 1.26 (0.25), residues: 449 sheet: -0.60 (0.39), residues: 158 loop : 0.58 (0.36), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1085 HIS 0.007 0.001 HIS A 618 PHE 0.031 0.002 PHE A 999 TYR 0.017 0.002 TYR A1064 ARG 0.003 0.000 ARG A 912 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 474) hydrogen bonds : angle 4.27268 ( 1284) covalent geometry : bond 0.00497 (10640) covalent geometry : angle 0.62926 (14806) ********************** 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 59 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 38 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 174 GLU cc_start: 0.9128 (pp20) cc_final: 0.8757 (pp20) REVERT: A 786 GLU cc_start: 0.8089 (mp0) cc_final: 0.7733 (mp0) REVERT: A 908 ASP cc_start: 0.8564 (t0) cc_final: 0.8291 (t0) REVERT: A 938 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8683 (t80) REVERT: A 1133 MET cc_start: 0.9399 (pmm) cc_final: 0.8653 (pmm) REVERT: A 1199 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9361 (mm) REVERT: A 1280 HIS cc_start: 0.9269 (OUTLIER) cc_final: 0.8649 (t-90) outliers start: 21 outliers final: 17 residues processed: 59 average time/residue: 0.2076 time to fit residues: 19.0148 Evaluate side-chains 57 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 37 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 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 1110 THR 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 1277 LEU 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 38 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 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 = 0.3172 r_free = 0.3172 target = 0.042032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.028979 restraints weight = 75710.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.030003 restraints weight = 39783.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.030642 restraints weight = 27212.378| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10640 Z= 0.176 Angle : 0.612 8.970 14806 Z= 0.325 Chirality : 0.040 0.194 1641 Planarity : 0.004 0.057 1559 Dihedral : 23.495 155.516 2279 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.24 % Allowed : 25.98 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.28), residues: 991 helix: 1.33 (0.25), residues: 449 sheet: -0.59 (0.39), residues: 158 loop : 0.59 (0.36), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1085 HIS 0.006 0.001 HIS A 618 PHE 0.029 0.001 PHE A 999 TYR 0.020 0.002 TYR A 764 ARG 0.002 0.000 ARG A 670 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 474) hydrogen bonds : angle 4.18282 ( 1284) covalent geometry : bond 0.00384 (10640) covalent geometry : angle 0.61164 (14806) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3345.41 seconds wall clock time: 61 minutes 37.39 seconds (3697.39 seconds total)