Starting phenix.real_space_refine on Sat Nov 16 16:02:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfi_40442/11_2024/8sfi_40442.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfi_40442/11_2024/8sfi_40442.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/8sfi_40442/11_2024/8sfi_40442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfi_40442/11_2024/8sfi_40442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfi_40442/11_2024/8sfi_40442.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfi_40442/11_2024/8sfi_40442.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= 0.000 sd= 0.030 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 69 5.49 5 S 23 5.16 5 C 7114 2.51 5 N 1952 2.21 5 O 2319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 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: 11477 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1227, 10030 Classifications: {'peptide': 1227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 46, 'TRANS': 1180} Chain breaks: 3 Chain: "B" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 588 Classifications: {'RNA': 28} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 12} Link IDs: {'rna2p': 6, 'rna3p': 21} Chain: "C" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 453 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Time building chain proxies: 7.77, per 1000 atoms: 0.68 Number of scatterers: 11477 At special positions: 0 Unit cell: (98.294, 100.793, 147.441, 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 69 15.00 O 2319 8.00 N 1952 7.00 C 7114 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: 2.97 Conformation dependent library (CDL) restraints added in 1.3 seconds 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2342 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 10 sheets defined 54.4% alpha, 10.4% beta 27 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 35 through 67 removed outlier: 3.692A 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 removed outlier: 3.694A pdb=" N SER A 77 " --> pdb=" O TRP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 111 removed outlier: 3.857A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 133 removed outlier: 4.408A pdb=" N PHE A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.545A pdb=" N LEU A 137 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 147 removed outlier: 3.745A pdb=" N LYS A 144 " --> pdb=" O GLY A 140 " (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 181 removed outlier: 3.904A pdb=" N VAL A 179 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 215 removed outlier: 3.932A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 230 Processing helix chain 'A' and resid 236 through 241 removed outlier: 3.685A pdb=" N PHE A 241 " --> pdb=" O ILE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.570A pdb=" N SER A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 344 Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 379 removed outlier: 3.840A pdb=" N SER A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 402 through 415 removed outlier: 4.161A pdb=" N HIS A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 Processing helix chain 'A' and resid 430 through 450 removed outlier: 3.688A pdb=" N LYS A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.509A pdb=" N LYS A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A 474 " --> pdb=" O GLN A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 removed outlier: 3.899A pdb=" N MET A 507 " --> pdb=" O ILE A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 600 through 605 removed outlier: 3.506A pdb=" N MET A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 621 removed outlier: 3.583A pdb=" N GLN A 620 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.555A pdb=" N TYR A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.660A pdb=" N ALA A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 685 removed outlier: 3.855A pdb=" N SER A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 704 Processing helix chain 'A' and resid 707 through 715 Processing helix chain 'A' and resid 727 through 738 removed outlier: 3.617A pdb=" N ILE A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 751 removed outlier: 3.861A pdb=" N ALA A 751 " --> pdb=" O LYS A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.580A 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: 3.584A pdb=" N THR A 865 " --> pdb=" O ARG A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 940 through 954 removed outlier: 3.502A pdb=" N VAL A 952 " --> pdb=" O GLU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 987 removed outlier: 3.936A pdb=" N GLY A 962 " --> pdb=" O TRP A 958 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A 963 " --> pdb=" O SER A 959 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N HIS A 977 " --> pdb=" O SER A 973 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1025 removed outlier: 4.009A 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 1189 Processing helix chain 'A' and resid 1200 through 1205 removed outlier: 3.964A pdb=" N GLU A1205 " --> pdb=" O PRO A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1224 Processing helix chain 'A' and resid 1250 through 1254 Processing helix chain 'A' and resid 1261 through 1284 removed outlier: 3.603A pdb=" N SER A1284 " --> pdb=" O HIS A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1306 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.492A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET A 593 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.492A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA4, first strand: chain 'A' and resid 596 through 597 Processing sheet with id=AA5, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AA6, first strand: chain 'A' and resid 926 through 931 removed outlier: 4.333A pdb=" N GLU A 993 " --> pdb=" O ILE A 907 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ARG A 909 " --> pdb=" O GLU A 993 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A1065 " --> pdb=" O LEU A 992 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1103 through 1107 removed outlier: 3.980A pdb=" N PHE A1103 " --> pdb=" O HIS A1116 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1145 through 1147 Processing sheet with id=AA9, first strand: chain 'A' and resid 1159 through 1165 removed outlier: 6.612A pdb=" N ARG A1159 " --> pdb=" O ARG A1174 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG A1174 " --> pdb=" O ARG A1159 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL A1161 " --> pdb=" O ARG A1172 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ARG A1172 " --> pdb=" O VAL A1161 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL A1163 " --> pdb=" O THR A1170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1226 through 1228 506 hydrogen bonds defined for protein. 1419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 5.87 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2956 1.34 - 1.46: 2772 1.46 - 1.58: 5970 1.58 - 1.70: 138 1.70 - 1.82: 38 Bond restraints: 11874 Sorted by residual: bond pdb=" CB PRO A 648 " pdb=" CG PRO A 648 " ideal model delta sigma weight residual 1.492 1.654 -0.162 5.00e-02 4.00e+02 1.05e+01 bond pdb=" CB LYS A 468 " pdb=" CG LYS A 468 " ideal model delta sigma weight residual 1.520 1.601 -0.081 3.00e-02 1.11e+03 7.24e+00 bond pdb=" CB LYS A 965 " pdb=" CG LYS A 965 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.54e+00 bond pdb=" CB LYS A1109 " pdb=" CG LYS A1109 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.41e+00 bond pdb=" CB ARG A 411 " pdb=" CG ARG A 411 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.24e+00 ... (remaining 11869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 15964 2.71 - 5.42: 251 5.42 - 8.13: 64 8.13 - 10.84: 55 10.84 - 13.55: 13 Bond angle restraints: 16347 Sorted by residual: angle pdb=" CA PRO A 648 " pdb=" N PRO A 648 " pdb=" CD PRO A 648 " ideal model delta sigma weight residual 112.00 98.45 13.55 1.40e+00 5.10e-01 9.37e+01 angle pdb=" N ASP A 939 " pdb=" CA ASP A 939 " pdb=" C ASP A 939 " ideal model delta sigma weight residual 110.24 118.36 -8.12 1.30e+00 5.92e-01 3.90e+01 angle pdb=" CB LYS A 468 " pdb=" CG LYS A 468 " pdb=" CD LYS A 468 " ideal model delta sigma weight residual 111.30 123.87 -12.57 2.30e+00 1.89e-01 2.99e+01 angle pdb=" C PHE A 938 " pdb=" CA PHE A 938 " pdb=" CB PHE A 938 " ideal model delta sigma weight residual 111.74 120.37 -8.63 1.59e+00 3.96e-01 2.95e+01 angle pdb=" CA LYS A1109 " pdb=" CB LYS A1109 " pdb=" CG LYS A1109 " ideal model delta sigma weight residual 114.10 124.72 -10.62 2.00e+00 2.50e-01 2.82e+01 ... (remaining 16342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.65: 6491 30.65 - 61.29: 550 61.29 - 91.94: 38 91.94 - 122.58: 0 122.58 - 153.23: 2 Dihedral angle restraints: 7081 sinusoidal: 3463 harmonic: 3618 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 46.77 153.23 1 1.50e+01 4.44e-03 8.08e+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 53.50 146.50 1 1.50e+01 4.44e-03 7.82e+01 dihedral pdb=" CA THR A 522 " pdb=" C THR A 522 " pdb=" N LYS A 523 " pdb=" CA LYS A 523 " ideal model delta harmonic sigma weight residual -180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 7078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1695 0.104 - 0.208: 100 0.208 - 0.311: 6 0.311 - 0.415: 11 0.415 - 0.519: 4 Chirality restraints: 1816 Sorted by residual: chirality pdb=" CG LEU A 471 " pdb=" CB LEU A 471 " pdb=" CD1 LEU A 471 " pdb=" CD2 LEU A 471 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.73e+00 chirality pdb=" P DC C 26 " pdb=" OP1 DC C 26 " pdb=" OP2 DC C 26 " pdb=" O5' DC C 26 " both_signs ideal model delta sigma weight residual True 2.35 -2.77 -0.43 2.00e-01 2.50e+01 4.54e+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 -2.76 -0.42 2.00e-01 2.50e+01 4.40e+00 ... (remaining 1813 not shown) Planarity restraints: 1852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 605 " 0.089 5.00e-02 4.00e+02 1.32e-01 2.78e+01 pdb=" N PRO A 606 " -0.228 5.00e-02 4.00e+02 pdb=" CA PRO A 606 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 606 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 537 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO A 538 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 538 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 538 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 647 " -0.065 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO A 648 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 648 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 648 " -0.049 5.00e-02 4.00e+02 ... (remaining 1849 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1305 2.75 - 3.29: 11003 3.29 - 3.83: 20297 3.83 - 4.36: 23053 4.36 - 4.90: 38033 Nonbonded interactions: 93691 Sorted by model distance: nonbonded pdb=" O GLU A 441 " pdb=" OG SER A 444 " model vdw 2.218 3.040 nonbonded pdb=" O ASN A1090 " pdb=" OG SER A1093 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR A 11 " pdb=" OD1 ASN A1024 " model vdw 2.290 3.040 nonbonded pdb=" O GLN A 437 " pdb=" OG SER A 440 " model vdw 2.299 3.040 nonbonded pdb=" O LYS A 429 " pdb=" OG SER A 432 " model vdw 2.300 3.040 ... (remaining 93686 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: 2.490 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.340 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 0.162 11874 Z= 0.324 Angle : 1.079 13.549 16347 Z= 0.527 Chirality : 0.063 0.519 1816 Planarity : 0.008 0.132 1852 Dihedral : 19.823 153.226 4739 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.46 % Allowed : 24.27 % Favored : 75.27 % 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: -1.06 (0.23), residues: 1219 helix: -0.55 (0.20), residues: 589 sheet: -0.85 (0.42), residues: 148 loop : -0.59 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1085 HIS 0.006 0.001 HIS A 445 PHE 0.049 0.003 PHE A1117 TYR 0.030 0.002 TYR A 746 ARG 0.012 0.001 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 THR cc_start: 0.8148 (m) cc_final: 0.7882 (t) outliers start: 5 outliers final: 2 residues processed: 101 average time/residue: 0.2446 time to fit residues: 36.8935 Evaluate side-chains 58 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 1192 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.0070 chunk 97 optimal weight: 0.0060 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 30.0000 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 11874 Z= 0.218 Angle : 0.599 8.486 16347 Z= 0.313 Chirality : 0.041 0.247 1816 Planarity : 0.005 0.071 1852 Dihedral : 18.233 149.463 2219 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.65 % Allowed : 20.99 % 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: 0.38 (0.24), residues: 1219 helix: 1.04 (0.21), residues: 607 sheet: -0.91 (0.42), residues: 152 loop : -0.25 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1085 HIS 0.006 0.001 HIS A 447 PHE 0.020 0.001 PHE A 496 TYR 0.013 0.001 TYR A 61 ARG 0.004 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6660 (tpt) cc_final: 0.6444 (tpt) REVERT: A 619 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7728 (m-80) outliers start: 29 outliers final: 12 residues processed: 84 average time/residue: 0.2106 time to fit residues: 27.7370 Evaluate side-chains 61 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1283 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 10.0000 chunk 36 optimal weight: 30.0000 chunk 96 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11874 Z= 0.329 Angle : 0.620 8.780 16347 Z= 0.331 Chirality : 0.041 0.155 1816 Planarity : 0.004 0.055 1852 Dihedral : 18.563 150.106 2219 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.63 % Favored : 97.29 % Rotamer: Outliers : 4.01 % Allowed : 19.89 % Favored : 76.09 % 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 (0.25), residues: 1219 helix: 1.51 (0.21), residues: 621 sheet: -0.83 (0.42), residues: 154 loop : 0.02 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 544 HIS 0.006 0.001 HIS A1269 PHE 0.017 0.002 PHE A 496 TYR 0.019 0.002 TYR A 61 ARG 0.003 0.000 ARG A1094 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 42 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 23 residues processed: 81 average time/residue: 0.2544 time to fit residues: 32.0186 Evaluate side-chains 58 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 35 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1084 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 1283 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 116 optimal weight: 0.0020 chunk 123 optimal weight: 8.9990 chunk 61 optimal weight: 0.0980 chunk 110 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 overall best weight: 4.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11874 Z= 0.350 Angle : 0.629 13.803 16347 Z= 0.331 Chirality : 0.042 0.151 1816 Planarity : 0.004 0.048 1852 Dihedral : 18.656 152.313 2219 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 3.28 % Allowed : 20.16 % Favored : 76.55 % 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: 1219 helix: 1.64 (0.21), residues: 617 sheet: -0.90 (0.41), residues: 154 loop : 0.04 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 544 HIS 0.006 0.001 HIS A1269 PHE 0.017 0.002 PHE A1049 TYR 0.018 0.002 TYR A 61 ARG 0.003 0.000 ARG A 681 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 40 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 24 residues processed: 73 average time/residue: 0.2445 time to fit residues: 27.7732 Evaluate side-chains 59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 35 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1280 HIS Chi-restraints excluded: chain A residue 1283 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1227 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11874 Z= 0.244 Angle : 0.575 14.188 16347 Z= 0.298 Chirality : 0.040 0.160 1816 Planarity : 0.004 0.043 1852 Dihedral : 18.575 151.855 2219 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.71 % Favored : 97.21 % Rotamer: Outliers : 3.19 % Allowed : 20.53 % Favored : 76.28 % 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: 1.18 (0.25), residues: 1219 helix: 1.77 (0.22), residues: 624 sheet: -0.87 (0.41), residues: 154 loop : 0.09 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1085 HIS 0.005 0.001 HIS A1269 PHE 0.014 0.001 PHE A 496 TYR 0.016 0.001 TYR A 61 ARG 0.005 0.000 ARG A1306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 41 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 PHE cc_start: 0.8229 (m-80) cc_final: 0.7896 (m-80) REVERT: A 1306 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7145 (mmt-90) outliers start: 35 outliers final: 22 residues processed: 74 average time/residue: 0.2611 time to fit residues: 30.7207 Evaluate side-chains 62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 39 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1084 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 1280 HIS Chi-restraints excluded: chain A residue 1283 GLU Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1306 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11874 Z= 0.318 Angle : 0.606 10.923 16347 Z= 0.318 Chirality : 0.041 0.161 1816 Planarity : 0.004 0.043 1852 Dihedral : 18.588 152.014 2219 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 3.28 % Allowed : 20.26 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1219 helix: 1.74 (0.21), residues: 624 sheet: -0.87 (0.41), residues: 154 loop : 0.11 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 544 HIS 0.005 0.001 HIS A1269 PHE 0.012 0.001 PHE A 201 TYR 0.020 0.002 TYR A 61 ARG 0.005 0.000 ARG A1306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 42 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 PHE cc_start: 0.8279 (m-10) cc_final: 0.7964 (m-80) REVERT: A 507 MET cc_start: 0.8148 (ppp) cc_final: 0.7593 (ppp) REVERT: A 544 TRP cc_start: 0.8109 (OUTLIER) cc_final: 0.7597 (m100) outliers start: 36 outliers final: 25 residues processed: 76 average time/residue: 0.2566 time to fit residues: 29.3859 Evaluate side-chains 65 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 39 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 544 TRP Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1084 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 1280 HIS Chi-restraints excluded: chain A residue 1283 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11874 Z= 0.171 Angle : 0.574 13.769 16347 Z= 0.292 Chirality : 0.039 0.167 1816 Planarity : 0.004 0.041 1852 Dihedral : 18.436 151.112 2219 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.38 % Favored : 97.54 % Rotamer: Outliers : 2.74 % Allowed : 21.35 % Favored : 75.91 % 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: 1.46 (0.25), residues: 1219 helix: 1.99 (0.22), residues: 612 sheet: -0.68 (0.42), residues: 154 loop : 0.28 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1085 HIS 0.004 0.001 HIS A1269 PHE 0.028 0.001 PHE A 496 TYR 0.012 0.001 TYR A 61 ARG 0.013 0.000 ARG A1306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 46 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 PHE cc_start: 0.8194 (m-10) cc_final: 0.7919 (m-80) REVERT: A 507 MET cc_start: 0.8022 (ppp) cc_final: 0.7717 (ppp) REVERT: A 544 TRP cc_start: 0.7791 (OUTLIER) cc_final: 0.7464 (m100) outliers start: 30 outliers final: 23 residues processed: 74 average time/residue: 0.2218 time to fit residues: 25.4701 Evaluate side-chains 65 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 41 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 544 TRP Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 1084 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 1278 LEU Chi-restraints excluded: chain A residue 1283 GLU Chi-restraints excluded: chain A residue 1302 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 84 optimal weight: 0.0670 chunk 60 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.3120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11874 Z= 0.176 Angle : 0.566 12.751 16347 Z= 0.289 Chirality : 0.039 0.171 1816 Planarity : 0.003 0.040 1852 Dihedral : 18.337 149.409 2219 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Rotamer: Outliers : 2.28 % Allowed : 21.44 % Favored : 76.28 % 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: 1.55 (0.25), residues: 1219 helix: 2.10 (0.22), residues: 610 sheet: -0.63 (0.42), residues: 154 loop : 0.27 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1085 HIS 0.004 0.001 HIS A1269 PHE 0.010 0.001 PHE A 496 TYR 0.012 0.001 TYR A 61 ARG 0.003 0.000 ARG A1306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 44 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 PHE cc_start: 0.8133 (m-10) cc_final: 0.7922 (m-80) REVERT: A 507 MET cc_start: 0.8042 (ppp) cc_final: 0.7829 (ppp) REVERT: A 544 TRP cc_start: 0.7822 (OUTLIER) cc_final: 0.7431 (m100) outliers start: 25 outliers final: 24 residues processed: 67 average time/residue: 0.2539 time to fit residues: 26.9344 Evaluate side-chains 66 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 41 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 544 TRP Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 1084 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 1278 LEU Chi-restraints excluded: chain A residue 1280 HIS Chi-restraints excluded: chain A residue 1283 GLU Chi-restraints excluded: chain A residue 1302 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 0.0040 chunk 35 optimal weight: 0.2980 chunk 103 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 11874 Z= 0.150 Angle : 0.560 13.823 16347 Z= 0.281 Chirality : 0.039 0.165 1816 Planarity : 0.003 0.039 1852 Dihedral : 18.173 147.452 2219 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.46 % Favored : 97.46 % Rotamer: Outliers : 1.92 % Allowed : 21.72 % 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: 1.63 (0.25), residues: 1219 helix: 2.15 (0.22), residues: 604 sheet: -0.47 (0.42), residues: 152 loop : 0.31 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1085 HIS 0.003 0.000 HIS A1269 PHE 0.010 0.001 PHE A 435 TYR 0.010 0.001 TYR A 595 ARG 0.002 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 507 MET cc_start: 0.7963 (ppp) cc_final: 0.7457 (ppp) REVERT: A 544 TRP cc_start: 0.7725 (OUTLIER) cc_final: 0.7326 (m100) outliers start: 21 outliers final: 18 residues processed: 67 average time/residue: 0.2493 time to fit residues: 25.4497 Evaluate side-chains 61 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 544 TRP Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1283 GLU Chi-restraints excluded: chain A residue 1302 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 0.2980 chunk 127 optimal weight: 6.9990 chunk 117 optimal weight: 0.0070 chunk 101 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 108 optimal weight: 0.0040 overall best weight: 0.6412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11874 Z= 0.160 Angle : 0.579 13.567 16347 Z= 0.292 Chirality : 0.039 0.162 1816 Planarity : 0.003 0.041 1852 Dihedral : 18.147 146.726 2219 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.63 % Favored : 97.29 % Rotamer: Outliers : 1.92 % Allowed : 21.90 % Favored : 76.19 % 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: 1.69 (0.25), residues: 1219 helix: 2.16 (0.22), residues: 605 sheet: -0.35 (0.42), residues: 152 loop : 0.36 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1085 HIS 0.003 0.000 HIS A1269 PHE 0.031 0.001 PHE A 353 TYR 0.009 0.001 TYR A 47 ARG 0.009 0.000 ARG A 947 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 507 MET cc_start: 0.7932 (ppp) cc_final: 0.7583 (ppp) REVERT: A 544 TRP cc_start: 0.7783 (OUTLIER) cc_final: 0.7351 (m100) outliers start: 21 outliers final: 18 residues processed: 66 average time/residue: 0.2055 time to fit residues: 21.9011 Evaluate side-chains 61 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 544 TRP Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1283 GLU Chi-restraints excluded: chain A residue 1302 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 20.0000 chunk 93 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 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 = 0.3243 r_free = 0.3243 target = 0.050619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.033928 restraints weight = 69782.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.034977 restraints weight = 33417.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.035564 restraints weight = 22466.890| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 11874 Z= 0.327 Angle : 0.637 13.226 16347 Z= 0.333 Chirality : 0.041 0.179 1816 Planarity : 0.004 0.039 1852 Dihedral : 18.403 148.419 2219 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 2.01 % Allowed : 22.45 % Favored : 75.55 % 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: 1.64 (0.26), residues: 1219 helix: 2.12 (0.22), residues: 612 sheet: -0.52 (0.42), residues: 157 loop : 0.39 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 544 HIS 0.006 0.001 HIS A1269 PHE 0.013 0.002 PHE A 496 TYR 0.019 0.002 TYR A 61 ARG 0.007 0.000 ARG A 947 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2059.93 seconds wall clock time: 39 minutes 18.44 seconds (2358.44 seconds total)