Starting phenix.real_space_refine on Wed Sep 25 10:43:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfj_40443/09_2024/8sfj_40443.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfj_40443/09_2024/8sfj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfj_40443/09_2024/8sfj_40443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfj_40443/09_2024/8sfj_40443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfj_40443/09_2024/8sfj_40443.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfj_40443/09_2024/8sfj_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-5461/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: 6.55, per 1000 atoms: 0.64 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: 2.57 Conformation dependent library (CDL) restraints added in 1.2 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: 3.85 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: 4.62 Time building geometry restraints manager: 3.02 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: 11.990 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 29.580 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.470 ------------------------------------------------------------------------------- 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= 0.324 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 *********************** 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 fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 1.206 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: 0.2401 time to fit residues: 21.4430 Evaluate side-chains 45 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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= 0.468 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 *********************** 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 fitting. rotamer outliers: 34 poor density : 40 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8529 (mm) REVERT: A 1133 MET cc_start: 0.8651 (pmm) cc_final: 0.8180 (pmm) outliers start: 34 outliers final: 20 residues processed: 69 average time/residue: 0.1957 time to fit residues: 20.7398 Evaluate side-chains 59 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 38 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 128 ILE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 782 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10640 Z= 0.197 Angle : 0.615 10.202 14806 Z= 0.330 Chirality : 0.040 0.212 1641 Planarity : 0.004 0.064 1559 Dihedral : 23.250 155.744 2280 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.36 % Allowed : 20.27 % 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 (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: 0.99 (0.25), residues: 450 sheet: -0.26 (0.42), residues: 149 loop : 0.36 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1085 HIS 0.010 0.001 HIS A1096 PHE 0.011 0.001 PHE A 999 TYR 0.020 0.001 TYR A 764 ARG 0.002 0.000 ARG A1121 *********************** 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 71 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 41 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 997 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7819 (m-80) REVERT: A 1133 MET cc_start: 0.8557 (pmm) cc_final: 0.8297 (pmm) outliers start: 30 outliers final: 18 residues processed: 68 average time/residue: 0.1889 time to fit residues: 20.0356 Evaluate side-chains 56 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 37 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 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** A1122 ASN ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 10640 Z= 0.473 Angle : 0.722 9.011 14806 Z= 0.395 Chirality : 0.043 0.159 1641 Planarity : 0.005 0.057 1559 Dihedral : 23.591 158.727 2280 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.82 % Allowed : 20.49 % 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 (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: 0.45 (0.27), residues: 991 helix: 0.72 (0.24), residues: 448 sheet: -0.40 (0.43), residues: 131 loop : 0.27 (0.34), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1085 HIS 0.009 0.002 HIS A1096 PHE 0.018 0.002 PHE A1052 TYR 0.020 0.002 TYR A 61 ARG 0.005 0.001 ARG A 912 *********************** 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 80 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 37 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 28 residues processed: 76 average time/residue: 0.2064 time to fit residues: 23.8501 Evaluate side-chains 65 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 37 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 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 763 LEU Chi-restraints excluded: chain A residue 873 VAL 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 1210 HIS Chi-restraints excluded: chain A residue 1225 MET Chi-restraints excluded: chain A residue 1247 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 20.0000 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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** A1122 ASN ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10640 Z= 0.178 Angle : 0.611 9.995 14806 Z= 0.326 Chirality : 0.040 0.234 1641 Planarity : 0.004 0.056 1559 Dihedral : 23.341 156.431 2280 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.91 % Allowed : 22.84 % Favored : 74.24 % 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: 0.83 (0.28), residues: 991 helix: 1.13 (0.25), residues: 451 sheet: -0.42 (0.41), residues: 149 loop : 0.48 (0.36), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1085 HIS 0.006 0.001 HIS A 618 PHE 0.013 0.001 PHE A 557 TYR 0.018 0.002 TYR A 764 ARG 0.002 0.000 ARG A 124 *********************** 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 67 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 41 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1019 LEU cc_start: 0.8690 (tt) cc_final: 0.8475 (tp) REVERT: A 1199 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8387 (mm) REVERT: A 1281 LEU cc_start: 0.8715 (tp) cc_final: 0.8420 (tt) outliers start: 26 outliers final: 14 residues processed: 66 average time/residue: 0.1979 time to fit residues: 19.7578 Evaluate side-chains 52 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 37 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 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 1122 ASN Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1247 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 54 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 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 611 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 10640 Z= 0.457 Angle : 0.714 8.655 14806 Z= 0.389 Chirality : 0.043 0.180 1641 Planarity : 0.005 0.056 1559 Dihedral : 23.700 158.588 2279 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.26 % Allowed : 23.40 % Favored : 72.34 % 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: 0.50 (0.27), residues: 991 helix: 0.81 (0.24), residues: 449 sheet: -0.55 (0.42), residues: 133 loop : 0.31 (0.34), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1258 HIS 0.008 0.002 HIS A 618 PHE 0.035 0.002 PHE A 999 TYR 0.020 0.002 TYR A 61 ARG 0.005 0.001 ARG A 912 *********************** 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 75 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 37 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 997 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8006 (m-80) REVERT: A 1199 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8468 (mm) outliers start: 38 outliers final: 27 residues processed: 71 average time/residue: 0.2206 time to fit residues: 23.5864 Evaluate side-chains 62 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 33 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 707 LEU 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 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 1225 MET Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1277 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10640 Z= 0.177 Angle : 0.615 9.487 14806 Z= 0.327 Chirality : 0.040 0.233 1641 Planarity : 0.004 0.056 1559 Dihedral : 23.407 156.051 2279 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.35 % Allowed : 24.75 % Favored : 72.90 % 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: 0.84 (0.28), residues: 991 helix: 1.15 (0.25), residues: 448 sheet: -0.39 (0.41), residues: 148 loop : 0.45 (0.35), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1085 HIS 0.006 0.001 HIS A 618 PHE 0.029 0.001 PHE A 999 TYR 0.015 0.002 TYR A 764 ARG 0.002 0.000 ARG A1121 *********************** 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 58 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 37 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 1019 LEU cc_start: 0.8663 (tt) cc_final: 0.8445 (tp) REVERT: A 1199 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8398 (mm) outliers start: 21 outliers final: 17 residues processed: 58 average time/residue: 0.2176 time to fit residues: 18.9623 Evaluate side-chains 51 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 33 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 964 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 0.0060 chunk 20 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 overall best weight: 1.8402 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10640 Z= 0.206 Angle : 0.601 8.964 14806 Z= 0.322 Chirality : 0.039 0.212 1641 Planarity : 0.004 0.058 1559 Dihedral : 23.378 155.398 2279 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.46 % Allowed : 24.97 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.90 (0.28), residues: 991 helix: 1.22 (0.25), residues: 449 sheet: -0.39 (0.41), residues: 148 loop : 0.47 (0.35), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1085 HIS 0.005 0.001 HIS A 618 PHE 0.029 0.001 PHE A 999 TYR 0.019 0.001 TYR A 764 ARG 0.002 0.000 ARG A1121 *********************** 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 56 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 34 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 1055 MET cc_start: 0.7832 (ppp) cc_final: 0.6743 (ppp) REVERT: A 1133 MET cc_start: 0.8808 (pmm) cc_final: 0.8539 (pmm) REVERT: A 1199 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8399 (mm) outliers start: 22 outliers final: 17 residues processed: 55 average time/residue: 0.1971 time to fit residues: 16.9223 Evaluate side-chains 52 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 34 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 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 1247 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10640 Z= 0.167 Angle : 0.599 9.322 14806 Z= 0.316 Chirality : 0.039 0.212 1641 Planarity : 0.004 0.058 1559 Dihedral : 23.224 153.929 2279 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.46 % Allowed : 24.86 % Favored : 72.68 % 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: 0.93 (0.28), residues: 991 helix: 1.29 (0.25), residues: 449 sheet: -0.48 (0.39), residues: 158 loop : 0.51 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1085 HIS 0.004 0.001 HIS A1096 PHE 0.027 0.001 PHE A 999 TYR 0.020 0.001 TYR A 764 ARG 0.002 0.000 ARG A 909 *********************** 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 61 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 39 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: A 174 GLU cc_start: 0.6945 (pp20) cc_final: 0.6731 (pp20) REVERT: A 1055 MET cc_start: 0.7825 (ppp) cc_final: 0.6694 (ppp) REVERT: A 1133 MET cc_start: 0.8769 (pmm) cc_final: 0.8006 (pmm) REVERT: A 1199 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8361 (mm) REVERT: A 1281 LEU cc_start: 0.8692 (tp) cc_final: 0.8449 (tt) outliers start: 22 outliers final: 18 residues processed: 60 average time/residue: 0.1877 time to fit residues: 17.4532 Evaluate side-chains 56 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 37 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 873 VAL Chi-restraints excluded: chain A residue 997 PHE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 30.0000 chunk 99 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3516 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= 0.416 Angle : 0.693 8.977 14806 Z= 0.374 Chirality : 0.042 0.178 1641 Planarity : 0.004 0.059 1559 Dihedral : 23.612 156.734 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 : 2.46 % Allowed : 25.42 % Favored : 72.12 % 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: 1.08 (0.25), residues: 448 sheet: -0.64 (0.38), residues: 159 loop : 0.48 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1258 HIS 0.008 0.001 HIS A 618 PHE 0.029 0.002 PHE A 999 TYR 0.020 0.002 TYR A 764 ARG 0.004 0.001 ARG A 912 ********************** 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 57 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 35 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 174 GLU cc_start: 0.7197 (pp20) cc_final: 0.6960 (pp20) REVERT: A 1199 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8453 (mm) outliers start: 22 outliers final: 19 residues processed: 57 average time/residue: 0.1939 time to fit residues: 17.2406 Evaluate side-chains 55 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 35 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 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 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 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 0.0970 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.042673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.029536 restraints weight = 73509.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.030592 restraints weight = 38392.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031251 restraints weight = 26290.208| |-----------------------------------------------------------------------------| r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10640 Z= 0.165 Angle : 0.620 9.975 14806 Z= 0.324 Chirality : 0.040 0.221 1641 Planarity : 0.004 0.055 1559 Dihedral : 23.346 154.489 2279 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.02 % Allowed : 26.32 % 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: 0.92 (0.28), residues: 991 helix: 1.32 (0.25), residues: 448 sheet: -0.57 (0.39), residues: 159 loop : 0.50 (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 0.027 0.001 PHE A 999 TYR 0.027 0.002 TYR A 764 ARG 0.002 0.000 ARG A 670 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1663.76 seconds wall clock time: 31 minutes 29.63 seconds (1889.63 seconds total)