Starting phenix.real_space_refine on Sat Nov 16 22:03:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfr_40449/11_2024/8sfr_40449.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfr_40449/11_2024/8sfr_40449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfr_40449/11_2024/8sfr_40449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfr_40449/11_2024/8sfr_40449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfr_40449/11_2024/8sfr_40449.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfr_40449/11_2024/8sfr_40449.cif" } resolution = 3.5 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= 0.031 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 91 5.49 5 S 23 5.16 5 C 7395 2.51 5 N 2050 2.21 5 O 2486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12045 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1240, 10138 Classifications: {'peptide': 1240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 46, 'TRANS': 1193} Chain breaks: 2 Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 826 Classifications: {'RNA': 39} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 17, 'rna3p_pyr': 15} Link IDs: {'rna2p': 7, 'rna3p': 31} 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: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 385 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Time building chain proxies: 7.95, per 1000 atoms: 0.66 Number of scatterers: 12045 At special positions: 0 Unit cell: (90.797, 106.624, 140.777, 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 23 16.00 P 91 15.00 O 2486 8.00 N 2050 7.00 C 7395 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: 3.32 Conformation dependent library (CDL) restraints added in 1.6 seconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 9 sheets defined 53.6% alpha, 10.8% beta 40 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 5.06 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 26 through 35 removed outlier: 3.875A pdb=" N GLN A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 67 Proline residue: A 52 - end of helix removed outlier: 3.787A pdb=" N ARG A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 86 removed outlier: 3.549A pdb=" N GLU A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 112 removed outlier: 3.862A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 140 through 147 removed outlier: 3.579A pdb=" N LYS A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 196 through 215 removed outlier: 3.944A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.774A pdb=" N HIS A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 removed outlier: 5.913A pdb=" N PHE A 243 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Proline residue: A 244 - end of helix Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.507A pdb=" N ILE A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 289 through 297 Processing helix chain 'A' and resid 325 through 343 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.534A pdb=" N THR A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 382 through 396 removed outlier: 4.410A pdb=" N ARG A 386 " --> pdb=" O TRP A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 415 removed outlier: 3.801A pdb=" N HIS A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 428 through 452 removed outlier: 3.507A pdb=" N SER A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.510A pdb=" N LYS A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 509 through 522 Processing helix chain 'A' and resid 570 through 574 removed outlier: 4.157A pdb=" N GLY A 573 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 610 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 639 through 647 Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.789A 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 Processing helix chain 'A' and resid 706 through 719 Proline residue: A 716 - end of helix removed outlier: 3.830A pdb=" N TYR A 719 " --> pdb=" O ASN A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.784A 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 861 through 865 removed outlier: 3.642A pdb=" N PHE A 864 " --> pdb=" O ASP A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 939 through 956 removed outlier: 4.180A pdb=" N LYS A 943 " --> pdb=" O ASP A 939 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 987 removed outlier: 3.745A pdb=" N GLN A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1025 removed outlier: 3.643A pdb=" N GLU A1016 " --> pdb=" O TYR A1012 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N MET A1018 " --> pdb=" O GLN A1014 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1100 removed outlier: 3.568A pdb=" N GLY A1100 " --> pdb=" O HIS A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1199 through 1206 removed outlier: 4.095A 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 532 removed outlier: 4.333A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 11.191A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 5.352A 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 532 Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 419 removed outlier: 4.266A pdb=" N PHE A 365 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AA5, first strand: chain 'A' and resid 926 through 931 removed outlier: 6.509A pdb=" N VAL A 919 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN A 929 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 917 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU A 993 " --> pdb=" O ILE A 907 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1103 through 1107 Processing sheet with id=AA7, first strand: chain 'A' and resid 1145 through 1147 Processing sheet with id=AA8, first strand: chain 'A' and resid 1159 through 1162 Processing sheet with id=AA9, first strand: chain 'A' and resid 1226 through 1229 removed outlier: 3.719A pdb=" N PHE A1249 " --> pdb=" O SER A1239 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 96 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 7.20 Time building geometry restraints manager: 3.81 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: 3119 1.33 - 1.45: 3194 1.45 - 1.58: 5969 1.58 - 1.70: 180 1.70 - 1.82: 38 Bond restraints: 12500 Sorted by residual: bond pdb=" C GLU A 508 " pdb=" N PRO A 509 " ideal model delta sigma weight residual 1.334 1.362 -0.028 8.40e-03 1.42e+04 1.13e+01 bond pdb=" CB ASP A1021 " pdb=" CG ASP A1021 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.06e+00 bond pdb=" CG ARG A 912 " pdb=" CD ARG A 912 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.71e+00 bond pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sigma weight residual 1.381 1.413 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" CG LEU A 475 " pdb=" CD2 LEU A 475 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.51e+00 ... (remaining 12495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.98: 17173 4.98 - 9.96: 101 9.96 - 14.94: 18 14.94 - 19.92: 3 19.92 - 24.90: 1 Bond angle restraints: 17296 Sorted by residual: angle pdb=" O3' DG D 6 " pdb=" P DA D 7 " pdb=" OP1 DA D 7 " ideal model delta sigma weight residual 108.00 132.90 -24.90 3.00e+00 1.11e-01 6.89e+01 angle pdb=" O3' DC C 7 " pdb=" P DA C 8 " pdb=" OP1 DA C 8 " ideal model delta sigma weight residual 108.00 126.22 -18.22 3.00e+00 1.11e-01 3.69e+01 angle pdb=" OP1 DA D 7 " pdb=" P DA D 7 " pdb=" OP2 DA D 7 " ideal model delta sigma weight residual 120.00 104.46 15.54 3.00e+00 1.11e-01 2.68e+01 angle pdb=" CA LYS A 48 " pdb=" CB LYS A 48 " pdb=" CG LYS A 48 " ideal model delta sigma weight residual 114.10 123.85 -9.75 2.00e+00 2.50e-01 2.38e+01 angle pdb=" OP1 DA C 8 " pdb=" P DA C 8 " pdb=" OP2 DA C 8 " ideal model delta sigma weight residual 120.00 105.73 14.27 3.00e+00 1.11e-01 2.26e+01 ... (remaining 17291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 6965 35.54 - 71.09: 443 71.09 - 106.63: 28 106.63 - 142.18: 0 142.18 - 177.72: 3 Dihedral angle restraints: 7439 sinusoidal: 3781 harmonic: 3658 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 -128.00 49.72 -177.72 1 1.70e+01 3.46e-03 6.64e+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 200.00 101.79 98.21 1 1.50e+01 4.44e-03 4.88e+01 dihedral pdb=" CA ALA A1007 " pdb=" C ALA A1007 " pdb=" N GLU A1008 " pdb=" CA GLU A1008 " ideal model delta harmonic sigma weight residual 180.00 152.46 27.54 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 7436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 1890 0.141 - 0.281: 26 0.281 - 0.422: 10 0.422 - 0.562: 2 0.562 - 0.703: 2 Chirality restraints: 1930 Sorted by residual: chirality pdb=" P DA D 7 " pdb=" OP1 DA D 7 " pdb=" OP2 DA D 7 " pdb=" O5' DA D 7 " both_signs ideal model delta sigma weight residual True 2.35 -3.05 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" P DA C 8 " pdb=" OP1 DA C 8 " pdb=" OP2 DA C 8 " pdb=" O5' DA C 8 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.61 2.00e-01 2.50e+01 9.16e+00 chirality pdb=" CG LEU A 645 " pdb=" CB LEU A 645 " pdb=" CD1 LEU A 645 " pdb=" CD2 LEU A 645 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.29e+00 ... (remaining 1927 not shown) Planarity restraints: 1895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 784 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C GLN A 784 " -0.059 2.00e-02 2.50e+03 pdb=" O GLN A 784 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA A 785 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 908 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.92e+00 pdb=" CG ASP A 908 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASP A 908 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP A 908 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT D 11 " -0.033 2.00e-02 2.50e+03 1.59e-02 6.28e+00 pdb=" N1 DT D 11 " 0.030 2.00e-02 2.50e+03 pdb=" C2 DT D 11 " 0.006 2.00e-02 2.50e+03 pdb=" O2 DT D 11 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DT D 11 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DT D 11 " -0.007 2.00e-02 2.50e+03 pdb=" O4 DT D 11 " -0.011 2.00e-02 2.50e+03 pdb=" C5 DT D 11 " -0.005 2.00e-02 2.50e+03 pdb=" C7 DT D 11 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DT D 11 " 0.005 2.00e-02 2.50e+03 ... (remaining 1892 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1674 2.75 - 3.29: 12343 3.29 - 3.82: 23069 3.82 - 4.36: 25824 4.36 - 4.90: 40318 Nonbonded interactions: 103228 Sorted by model distance: nonbonded pdb=" O ALA A1067 " pdb=" OG1 THR A1070 " model vdw 2.210 3.040 nonbonded pdb=" O LYS A 370 " pdb=" OG1 THR A 373 " model vdw 2.280 3.040 nonbonded pdb=" O ILE A 605 " pdb=" OG SER A 609 " model vdw 2.280 3.040 nonbonded pdb=" O GLY A 767 " pdb=" OG SER A 770 " model vdw 2.285 3.040 nonbonded pdb=" O LYS A1282 " pdb=" NZ LYS A1285 " model vdw 2.302 3.120 ... (remaining 103223 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 36.930 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 12500 Z= 0.395 Angle : 1.026 24.904 17296 Z= 0.490 Chirality : 0.062 0.703 1930 Planarity : 0.005 0.050 1895 Dihedral : 20.280 177.720 5071 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.18 % Allowed : 20.40 % Favored : 79.42 % 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: -0.36 (0.23), residues: 1234 helix: 0.02 (0.20), residues: 601 sheet: -0.70 (0.47), residues: 121 loop : -0.22 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 382 HIS 0.008 0.001 HIS A 363 PHE 0.031 0.002 PHE A 619 TYR 0.038 0.002 TYR A 526 ARG 0.006 0.001 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 1.261 Fit side-chains revert: symmetry clash REVERT: A 537 MET cc_start: 0.9387 (mmt) cc_final: 0.8844 (mmm) REVERT: A 604 MET cc_start: 0.9314 (mmm) cc_final: 0.9097 (mmm) outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 0.2570 time to fit residues: 20.2992 Evaluate side-chains 49 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 969 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12500 Z= 0.205 Angle : 0.614 10.342 17296 Z= 0.322 Chirality : 0.040 0.211 1930 Planarity : 0.004 0.039 1895 Dihedral : 20.195 179.371 2524 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.53 % Allowed : 18.32 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.60 (0.24), residues: 1234 helix: 1.06 (0.21), residues: 597 sheet: -0.60 (0.45), residues: 132 loop : 0.03 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.005 0.001 HIS A 363 PHE 0.013 0.001 PHE A 353 TYR 0.015 0.001 TYR A 526 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 1.401 Fit side-chains REVERT: A 1 MET cc_start: 0.8908 (tpp) cc_final: 0.8355 (tmm) REVERT: A 604 MET cc_start: 0.9310 (mmm) cc_final: 0.9051 (mmm) REVERT: A 754 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7585 (t-90) REVERT: A 786 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8285 (mp0) REVERT: A 908 ASP cc_start: 0.7354 (t0) cc_final: 0.7140 (t0) REVERT: A 912 ARG cc_start: 0.7965 (tpm170) cc_final: 0.7736 (tpm170) REVERT: A 969 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8180 (pp30) REVERT: A 1092 GLU cc_start: 0.9685 (OUTLIER) cc_final: 0.9340 (mp0) outliers start: 17 outliers final: 3 residues processed: 64 average time/residue: 0.2423 time to fit residues: 23.6984 Evaluate side-chains 54 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 ASN ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12500 Z= 0.187 Angle : 0.580 10.275 17296 Z= 0.302 Chirality : 0.039 0.221 1930 Planarity : 0.003 0.033 1895 Dihedral : 19.903 179.171 2524 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.71 % Allowed : 18.59 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.02 (0.25), residues: 1234 helix: 1.53 (0.22), residues: 606 sheet: -0.62 (0.44), residues: 132 loop : 0.12 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.002 0.001 HIS A 191 PHE 0.015 0.001 PHE A1113 TYR 0.019 0.001 TYR A1012 ARG 0.005 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 55 time to evaluate : 1.267 Fit side-chains REVERT: A 1 MET cc_start: 0.8933 (tpp) cc_final: 0.8340 (tmm) REVERT: A 20 GLU cc_start: 0.8474 (tm-30) cc_final: 0.7981 (tm-30) REVERT: A 145 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.8922 (mt0) REVERT: A 165 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8815 (t80) REVERT: A 271 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8358 (p) REVERT: A 507 MET cc_start: 0.9322 (ppp) cc_final: 0.9025 (ppp) REVERT: A 537 MET cc_start: 0.9261 (mmt) cc_final: 0.8586 (mmm) REVERT: A 604 MET cc_start: 0.9341 (mmm) cc_final: 0.9068 (mmm) REVERT: A 754 HIS cc_start: 0.8102 (OUTLIER) cc_final: 0.7642 (t-90) REVERT: A 786 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8232 (mp0) REVERT: A 912 ARG cc_start: 0.7992 (tpm170) cc_final: 0.7769 (tpm170) REVERT: A 969 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8229 (pp30) REVERT: A 1092 GLU cc_start: 0.9696 (OUTLIER) cc_final: 0.9317 (mp0) outliers start: 30 outliers final: 12 residues processed: 79 average time/residue: 0.2582 time to fit residues: 31.0060 Evaluate side-chains 67 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLN 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 271 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 61 optimal weight: 0.0040 chunk 13 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 113 optimal weight: 20.0000 chunk 34 optimal weight: 0.0980 overall best weight: 3.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12500 Z= 0.280 Angle : 0.613 10.886 17296 Z= 0.322 Chirality : 0.040 0.151 1930 Planarity : 0.003 0.033 1895 Dihedral : 19.872 178.686 2524 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.80 % Allowed : 19.49 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.11 (0.25), residues: 1234 helix: 1.63 (0.22), residues: 606 sheet: -0.70 (0.44), residues: 132 loop : 0.15 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 382 HIS 0.004 0.001 HIS A 191 PHE 0.014 0.001 PHE A1113 TYR 0.020 0.001 TYR A 526 ARG 0.005 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 50 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8985 (tpp) cc_final: 0.8247 (tmm) REVERT: A 20 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8115 (tm-30) REVERT: A 271 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8294 (p) REVERT: A 507 MET cc_start: 0.9240 (ppp) cc_final: 0.8920 (ppp) REVERT: A 604 MET cc_start: 0.9372 (mmm) cc_final: 0.9066 (mmm) REVERT: A 610 THR cc_start: 0.9690 (OUTLIER) cc_final: 0.9360 (p) REVERT: A 754 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7681 (t-90) REVERT: A 786 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8284 (mp0) REVERT: A 908 ASP cc_start: 0.7358 (t0) cc_final: 0.7131 (t0) REVERT: A 912 ARG cc_start: 0.7982 (tpm170) cc_final: 0.7755 (tpm170) REVERT: A 1092 GLU cc_start: 0.9713 (OUTLIER) cc_final: 0.9327 (mp0) outliers start: 31 outliers final: 15 residues processed: 75 average time/residue: 0.2732 time to fit residues: 30.5612 Evaluate side-chains 69 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 chunk 87 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 0.0170 chunk 113 optimal weight: 0.1980 chunk 31 optimal weight: 10.0000 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12500 Z= 0.153 Angle : 0.579 13.027 17296 Z= 0.294 Chirality : 0.039 0.277 1930 Planarity : 0.003 0.033 1895 Dihedral : 19.671 177.739 2521 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.44 % Allowed : 19.68 % Favored : 77.89 % 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: 1.30 (0.25), residues: 1234 helix: 1.89 (0.22), residues: 597 sheet: -0.65 (0.44), residues: 132 loop : 0.14 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 382 HIS 0.002 0.000 HIS A1167 PHE 0.011 0.001 PHE A1140 TYR 0.014 0.001 TYR A 595 ARG 0.006 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 53 time to evaluate : 2.559 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8947 (tpp) cc_final: 0.8249 (tmm) REVERT: A 20 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8011 (tm-30) REVERT: A 145 GLN cc_start: 0.9327 (OUTLIER) cc_final: 0.9039 (mp10) REVERT: A 271 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8289 (p) REVERT: A 363 HIS cc_start: 0.9483 (OUTLIER) cc_final: 0.9069 (t70) REVERT: A 507 MET cc_start: 0.9251 (ppp) cc_final: 0.9016 (ppp) REVERT: A 537 MET cc_start: 0.9270 (mmt) cc_final: 0.8574 (mmm) REVERT: A 604 MET cc_start: 0.9321 (mmm) cc_final: 0.9040 (mmm) REVERT: A 754 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7514 (t-90) REVERT: A 786 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8174 (mp0) REVERT: A 912 ARG cc_start: 0.7976 (tpm170) cc_final: 0.7745 (tpm170) outliers start: 27 outliers final: 11 residues processed: 75 average time/residue: 0.2621 time to fit residues: 31.0985 Evaluate side-chains 64 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1235 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 105 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12500 Z= 0.303 Angle : 0.630 12.422 17296 Z= 0.329 Chirality : 0.040 0.157 1930 Planarity : 0.003 0.032 1895 Dihedral : 19.765 179.594 2521 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.62 % Allowed : 19.77 % Favored : 77.62 % 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: 1.15 (0.25), residues: 1234 helix: 1.72 (0.22), residues: 612 sheet: -0.81 (0.46), residues: 121 loop : 0.09 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 382 HIS 0.004 0.001 HIS A 191 PHE 0.014 0.001 PHE A 198 TYR 0.022 0.001 TYR A 526 ARG 0.005 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 52 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9020 (tpp) cc_final: 0.8195 (tmm) REVERT: A 20 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8094 (tm-30) REVERT: A 48 LYS cc_start: 0.9418 (pttm) cc_final: 0.9199 (ptpp) REVERT: A 145 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.9032 (mp10) REVERT: A 165 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8649 (t80) REVERT: A 271 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8283 (p) REVERT: A 507 MET cc_start: 0.9194 (ppp) cc_final: 0.8941 (ppp) REVERT: A 604 MET cc_start: 0.9295 (mmm) cc_final: 0.8995 (mmm) REVERT: A 754 HIS cc_start: 0.8078 (OUTLIER) cc_final: 0.7635 (t-90) REVERT: A 786 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8263 (mp0) REVERT: A 912 ARG cc_start: 0.7998 (tpm170) cc_final: 0.7756 (tpm170) REVERT: A 1092 GLU cc_start: 0.9712 (OUTLIER) cc_final: 0.9333 (mp0) outliers start: 29 outliers final: 15 residues processed: 75 average time/residue: 0.2586 time to fit residues: 29.0723 Evaluate side-chains 72 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 145 GLN 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 271 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12500 Z= 0.274 Angle : 0.619 12.388 17296 Z= 0.321 Chirality : 0.040 0.161 1930 Planarity : 0.003 0.032 1895 Dihedral : 19.808 179.688 2521 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.53 % Allowed : 20.13 % Favored : 77.35 % 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: 1.12 (0.25), residues: 1234 helix: 1.69 (0.21), residues: 613 sheet: -0.73 (0.46), residues: 119 loop : 0.03 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 382 HIS 0.003 0.001 HIS A1280 PHE 0.013 0.001 PHE A1113 TYR 0.016 0.001 TYR A 61 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 55 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9029 (tpp) cc_final: 0.8092 (tmm) REVERT: A 20 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8163 (tm-30) REVERT: A 145 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.9004 (mp10) REVERT: A 165 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8554 (t80) REVERT: A 271 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8218 (p) REVERT: A 363 HIS cc_start: 0.9462 (OUTLIER) cc_final: 0.9077 (t70) REVERT: A 507 MET cc_start: 0.9163 (ppp) cc_final: 0.8882 (ppp) REVERT: A 604 MET cc_start: 0.9239 (mmm) cc_final: 0.8956 (mmm) REVERT: A 754 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7454 (t-90) REVERT: A 786 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: A 912 ARG cc_start: 0.7975 (tpm170) cc_final: 0.7744 (tpm170) REVERT: A 1074 ASP cc_start: 0.9573 (OUTLIER) cc_final: 0.8736 (p0) REVERT: A 1092 GLU cc_start: 0.9726 (OUTLIER) cc_final: 0.9358 (mp0) outliers start: 28 outliers final: 16 residues processed: 78 average time/residue: 0.2708 time to fit residues: 31.6409 Evaluate side-chains 74 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 50 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 145 GLN 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 271 THR Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1074 ASP Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12500 Z= 0.218 Angle : 0.610 14.625 17296 Z= 0.311 Chirality : 0.039 0.181 1930 Planarity : 0.003 0.032 1895 Dihedral : 19.751 179.608 2521 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.71 % Allowed : 20.58 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.23 (0.25), residues: 1234 helix: 1.78 (0.22), residues: 613 sheet: -0.70 (0.44), residues: 130 loop : 0.13 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 382 HIS 0.003 0.001 HIS A 191 PHE 0.010 0.001 PHE A1113 TYR 0.023 0.001 TYR A 526 ARG 0.003 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 55 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9061 (tpp) cc_final: 0.8116 (tmm) REVERT: A 20 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8141 (tm-30) REVERT: A 145 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.9004 (mp10) REVERT: A 165 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8511 (t80) REVERT: A 271 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8232 (p) REVERT: A 363 HIS cc_start: 0.9461 (OUTLIER) cc_final: 0.9061 (t70) REVERT: A 507 MET cc_start: 0.9164 (ppp) cc_final: 0.8875 (ppp) REVERT: A 604 MET cc_start: 0.9190 (mmm) cc_final: 0.8914 (mmm) REVERT: A 709 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.9075 (tm-30) REVERT: A 754 HIS cc_start: 0.8027 (OUTLIER) cc_final: 0.7480 (t-90) REVERT: A 786 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8207 (mp0) REVERT: A 912 ARG cc_start: 0.7996 (tpm170) cc_final: 0.7764 (tpm170) REVERT: A 1074 ASP cc_start: 0.9584 (OUTLIER) cc_final: 0.8640 (p0) REVERT: A 1092 GLU cc_start: 0.9727 (OUTLIER) cc_final: 0.9358 (mp0) outliers start: 30 outliers final: 17 residues processed: 80 average time/residue: 0.2597 time to fit residues: 30.6206 Evaluate side-chains 77 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 145 GLN 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 271 THR Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1074 ASP Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1235 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12500 Z= 0.245 Angle : 0.637 14.654 17296 Z= 0.325 Chirality : 0.040 0.335 1930 Planarity : 0.003 0.032 1895 Dihedral : 19.742 179.532 2521 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.53 % Allowed : 21.03 % Favored : 76.44 % 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: 1.16 (0.25), residues: 1234 helix: 1.70 (0.21), residues: 613 sheet: -0.76 (0.44), residues: 130 loop : 0.13 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 382 HIS 0.003 0.001 HIS A 191 PHE 0.014 0.001 PHE A1113 TYR 0.017 0.001 TYR A 61 ARG 0.001 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 52 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9088 (tpp) cc_final: 0.8134 (tmm) REVERT: A 20 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8185 (tm-30) REVERT: A 145 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8998 (mp10) REVERT: A 165 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8531 (t80) REVERT: A 271 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8250 (p) REVERT: A 363 HIS cc_start: 0.9460 (OUTLIER) cc_final: 0.9068 (t70) REVERT: A 507 MET cc_start: 0.9159 (ppp) cc_final: 0.8871 (ppp) REVERT: A 604 MET cc_start: 0.9203 (mmm) cc_final: 0.8933 (mmm) REVERT: A 709 GLU cc_start: 0.9260 (OUTLIER) cc_final: 0.9058 (tm-30) REVERT: A 754 HIS cc_start: 0.8036 (OUTLIER) cc_final: 0.7490 (t-90) REVERT: A 786 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8209 (mp0) REVERT: A 912 ARG cc_start: 0.7972 (tpm170) cc_final: 0.7724 (tpm170) REVERT: A 1074 ASP cc_start: 0.9579 (OUTLIER) cc_final: 0.8624 (p0) REVERT: A 1092 GLU cc_start: 0.9725 (OUTLIER) cc_final: 0.9351 (mp0) outliers start: 28 outliers final: 17 residues processed: 77 average time/residue: 0.2873 time to fit residues: 33.1930 Evaluate side-chains 77 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 145 GLN 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 271 THR Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1074 ASP Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12500 Z= 0.214 Angle : 0.629 14.814 17296 Z= 0.317 Chirality : 0.040 0.347 1930 Planarity : 0.003 0.032 1895 Dihedral : 19.705 179.501 2521 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.53 % Allowed : 20.85 % Favored : 76.62 % 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: 1.19 (0.25), residues: 1234 helix: 1.72 (0.21), residues: 614 sheet: -0.70 (0.44), residues: 130 loop : 0.15 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 382 HIS 0.003 0.001 HIS A 191 PHE 0.011 0.001 PHE A1113 TYR 0.025 0.001 TYR A 526 ARG 0.001 0.000 ARG A 499 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 52 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9091 (tpp) cc_final: 0.8060 (tmm) REVERT: A 20 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8148 (tm-30) REVERT: A 145 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.8999 (mp10) REVERT: A 165 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8518 (t80) REVERT: A 271 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8231 (p) REVERT: A 363 HIS cc_start: 0.9473 (OUTLIER) cc_final: 0.9080 (t70) REVERT: A 507 MET cc_start: 0.9160 (ppp) cc_final: 0.8869 (ppp) REVERT: A 604 MET cc_start: 0.9165 (mmm) cc_final: 0.8897 (mmm) REVERT: A 709 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.9050 (tm-30) REVERT: A 754 HIS cc_start: 0.8034 (OUTLIER) cc_final: 0.7520 (t-90) REVERT: A 786 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8192 (mp0) REVERT: A 912 ARG cc_start: 0.7982 (tpm170) cc_final: 0.7745 (tpm170) REVERT: A 1074 ASP cc_start: 0.9572 (OUTLIER) cc_final: 0.8604 (p0) REVERT: A 1092 GLU cc_start: 0.9725 (OUTLIER) cc_final: 0.9348 (mp0) outliers start: 28 outliers final: 17 residues processed: 77 average time/residue: 0.2555 time to fit residues: 29.2583 Evaluate side-chains 78 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 52 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 145 GLN 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 271 THR Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1074 ASP Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1235 ASP Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 HIS A 969 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.041910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.030375 restraints weight = 81825.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.031612 restraints weight = 40582.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.032434 restraints weight = 26642.550| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12500 Z= 0.164 Angle : 0.620 15.198 17296 Z= 0.307 Chirality : 0.039 0.288 1930 Planarity : 0.003 0.032 1895 Dihedral : 19.543 179.809 2521 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.44 % Allowed : 20.85 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.30 (0.25), residues: 1234 helix: 1.82 (0.22), residues: 608 sheet: -0.58 (0.44), residues: 135 loop : 0.19 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 382 HIS 0.002 0.000 HIS A 977 PHE 0.012 0.001 PHE A1113 TYR 0.016 0.001 TYR A 595 ARG 0.002 0.000 ARG A1194 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2009.98 seconds wall clock time: 38 minutes 13.34 seconds (2293.34 seconds total)