Starting phenix.real_space_refine on Thu May 15 20:02:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fu3_29452/05_2025/8fu3_29452_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fu3_29452/05_2025/8fu3_29452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fu3_29452/05_2025/8fu3_29452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fu3_29452/05_2025/8fu3_29452.map" model { file = "/net/cci-nas-00/data/ceres_data/8fu3_29452/05_2025/8fu3_29452_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fu3_29452/05_2025/8fu3_29452_neut.cif" } resolution = 2.88 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= 0.006 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 S 76 5.16 5 C 8652 2.51 5 N 2308 2.21 5 O 2522 1.98 5 F 5 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13563 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1367, 11153 Classifications: {'peptide': 1367} Link IDs: {'PTRANS': 47, 'TRANS': 1319} Chain breaks: 3 Chain: "B" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 886 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "C" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 479 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "D" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 468 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "E" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 536 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'YBK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.96, per 1000 atoms: 0.59 Number of scatterers: 13563 At special positions: 0 Unit cell: (104.96, 134.48, 99.22, 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 76 16.00 F 5 9.00 O 2522 8.00 N 2308 7.00 C 8652 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: 3.47 Conformation dependent library (CDL) restraints added in 1.7 seconds 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3206 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 9 sheets defined 64.4% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 24 through 36 Processing helix chain 'A' and resid 44 through 53 removed outlier: 3.558A pdb=" N ARG A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 83 through 93 removed outlier: 3.859A pdb=" N PHE A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 132 removed outlier: 3.932A pdb=" N VAL A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 198 Processing helix chain 'A' and resid 201 through 228 Processing helix chain 'A' and resid 265 through 296 Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 327 through 334 removed outlier: 4.101A pdb=" N ILE A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 348 removed outlier: 3.558A pdb=" N PHE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 379 Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.548A pdb=" N ILE A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.523A pdb=" N LEU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.523A pdb=" N PHE A 426 " --> pdb=" O TYR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 448 removed outlier: 3.512A pdb=" N ILE A 445 " --> pdb=" O ASP A 441 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 478 Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 491 through 499 Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 545 through 553 removed outlier: 4.909A pdb=" N TRP A 550 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.888A pdb=" N LEU A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 595 through 603 Processing helix chain 'A' and resid 633 through 651 Processing helix chain 'A' and resid 652 through 659 Proline residue: A 656 - end of helix removed outlier: 3.731A pdb=" N LEU A 659 " --> pdb=" O PRO A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 708 Processing helix chain 'A' and resid 709 through 724 removed outlier: 4.874A pdb=" N ILE A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N CYS A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 740 Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 781 through 800 Processing helix chain 'A' and resid 828 through 850 Processing helix chain 'A' and resid 868 through 872 removed outlier: 3.884A pdb=" N LYS A 871 " --> pdb=" O PHE A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 900 through 918 removed outlier: 3.893A pdb=" N GLU A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 939 Processing helix chain 'A' and resid 940 through 944 removed outlier: 3.862A pdb=" N HIS A 944 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 966 Processing helix chain 'A' and resid 970 through 979 Processing helix chain 'A' and resid 980 through 981 No H-bonds generated for 'chain 'A' and resid 980 through 981' Processing helix chain 'A' and resid 982 through 986 Processing helix chain 'A' and resid 992 through 997 Processing helix chain 'A' and resid 1003 through 1021 removed outlier: 3.938A pdb=" N TYR A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 Processing helix chain 'A' and resid 1052 through 1060 Processing helix chain 'A' and resid 1072 through 1077 Processing helix chain 'A' and resid 1077 through 1086 Processing helix chain 'A' and resid 1090 through 1099 Processing helix chain 'A' and resid 1099 through 1109 Processing helix chain 'A' and resid 1118 through 1128 Processing helix chain 'A' and resid 1130 through 1142 Processing helix chain 'A' and resid 1146 through 1153 removed outlier: 4.954A pdb=" N LEU A1151 " --> pdb=" O THR A1148 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS A1153 " --> pdb=" O ILE A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1174 Processing helix chain 'A' and resid 1174 through 1180 Processing helix chain 'A' and resid 1198 through 1211 Processing helix chain 'A' and resid 1223 through 1227 Processing helix chain 'A' and resid 1277 through 1281 Processing helix chain 'A' and resid 1282 through 1299 Processing helix chain 'A' and resid 1304 through 1317 Processing helix chain 'A' and resid 1320 through 1325 Processing helix chain 'A' and resid 1335 through 1339 removed outlier: 4.121A pdb=" N HIS A1338 " --> pdb=" O ASN A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1359 removed outlier: 3.542A pdb=" N THR A1359 " --> pdb=" O TYR A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1377 Processing helix chain 'A' and resid 1384 through 1404 Processing helix chain 'A' and resid 1416 through 1419 Processing helix chain 'A' and resid 1432 through 1443 Processing helix chain 'A' and resid 1444 through 1447 Processing helix chain 'A' and resid 1452 through 1460 removed outlier: 4.042A pdb=" N GLU A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A1459 " --> pdb=" O GLN A1455 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE A1460 " --> pdb=" O TYR A1456 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 150 Processing helix chain 'B' and resid 174 through 183 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 203 through 210 Processing helix chain 'B' and resid 217 through 228 Processing helix chain 'C' and resid 131 through 157 Processing helix chain 'C' and resid 158 through 164 Processing helix chain 'C' and resid 166 through 172 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'D' and resid 129 through 157 removed outlier: 3.577A pdb=" N ALA D 157 " --> pdb=" O VAL D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 185 Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 135 through 154 Processing helix chain 'E' and resid 155 through 158 Processing helix chain 'E' and resid 173 through 197 removed outlier: 3.643A pdb=" N MET E 177 " --> pdb=" O LEU E 173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 82 removed outlier: 4.412A pdb=" N VAL A 263 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 629 through 631 removed outlier: 6.244A pdb=" N VAL A 614 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 803 through 809 removed outlier: 3.839A pdb=" N TYR A 691 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 873 through 875 removed outlier: 3.880A pdb=" N ILE A 873 " --> pdb=" O TYR A 880 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1228 through 1231 Processing sheet with id=AA8, first strand: chain 'A' and resid 1271 through 1272 Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 159 782 hydrogen bonds defined for protein. 2190 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.19 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2368 1.31 - 1.44: 3422 1.44 - 1.57: 7886 1.57 - 1.70: 1 1.70 - 1.82: 129 Bond restraints: 13806 Sorted by residual: bond pdb=" C14 YBK A2201 " pdb=" N16 YBK A2201 " ideal model delta sigma weight residual 1.349 1.462 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" N11 YBK A2201 " pdb=" N12 YBK A2201 " ideal model delta sigma weight residual 1.289 1.395 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C25 YBK A2201 " pdb=" C27 YBK A2201 " ideal model delta sigma weight residual 1.479 1.395 0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C03 YBK A2201 " pdb=" O02 YBK A2201 " ideal model delta sigma weight residual 1.331 1.412 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" N PRO A 528 " pdb=" CA PRO A 528 " ideal model delta sigma weight residual 1.466 1.427 0.039 1.17e-02 7.31e+03 1.13e+01 ... (remaining 13801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 16125 1.55 - 3.10: 2205 3.10 - 4.65: 214 4.65 - 6.20: 86 6.20 - 7.75: 36 Bond angle restraints: 18666 Sorted by residual: angle pdb=" C ALA A 749 " pdb=" N PRO A 750 " pdb=" CA PRO A 750 " ideal model delta sigma weight residual 119.66 125.42 -5.76 7.20e-01 1.93e+00 6.41e+01 angle pdb=" C TYR A 880 " pdb=" N PRO A 881 " pdb=" CA PRO A 881 " ideal model delta sigma weight residual 120.03 127.58 -7.55 9.90e-01 1.02e+00 5.82e+01 angle pdb=" C LEU A 527 " pdb=" N PRO A 528 " pdb=" CA PRO A 528 " ideal model delta sigma weight residual 119.90 127.45 -7.55 1.02e+00 9.61e-01 5.48e+01 angle pdb=" C LEU A1129 " pdb=" N PRO A1130 " pdb=" CA PRO A1130 " ideal model delta sigma weight residual 119.56 126.97 -7.41 1.02e+00 9.61e-01 5.28e+01 angle pdb=" C LEU A1447 " pdb=" N PRO A1448 " pdb=" CA PRO A1448 " ideal model delta sigma weight residual 120.21 127.00 -6.79 9.60e-01 1.09e+00 5.00e+01 ... (remaining 18661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 8126 17.51 - 35.03: 242 35.03 - 52.54: 68 52.54 - 70.06: 17 70.06 - 87.57: 4 Dihedral angle restraints: 8457 sinusoidal: 3518 harmonic: 4939 Sorted by residual: dihedral pdb=" CA GLY D 158 " pdb=" C GLY D 158 " pdb=" N PRO D 159 " pdb=" CA PRO D 159 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA LEU A 527 " pdb=" C LEU A 527 " pdb=" N PRO A 528 " pdb=" CA PRO A 528 " ideal model delta harmonic sigma weight residual 180.00 163.90 16.10 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CG ARG C 182 " pdb=" CD ARG C 182 " pdb=" NE ARG C 182 " pdb=" CZ ARG C 182 " ideal model delta sinusoidal sigma weight residual 180.00 -139.23 -40.77 2 1.50e+01 4.44e-03 9.10e+00 ... (remaining 8454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1538 0.064 - 0.128: 545 0.128 - 0.192: 66 0.192 - 0.256: 4 0.256 - 0.320: 1 Chirality restraints: 2154 Sorted by residual: chirality pdb=" CA PRO A 528 " pdb=" N PRO A 528 " pdb=" C PRO A 528 " pdb=" CB PRO A 528 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA ILE A1353 " pdb=" N ILE A1353 " pdb=" C ILE A1353 " pdb=" CB ILE A1353 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA TRP A 932 " pdb=" N TRP A 932 " pdb=" C TRP A 932 " pdb=" CB TRP A 932 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2151 not shown) Planarity restraints: 2347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 426 " -0.035 2.00e-02 2.50e+03 2.16e-02 8.14e+00 pdb=" CG PHE A 426 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 426 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 426 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE A 426 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 426 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 426 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 710 " -0.037 2.00e-02 2.50e+03 1.96e-02 7.68e+00 pdb=" CG TYR A 710 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 710 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 710 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 710 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A 710 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 710 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 710 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 586 " -0.036 2.00e-02 2.50e+03 1.88e-02 7.07e+00 pdb=" CG TYR A 586 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 586 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 586 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR A 586 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 586 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 586 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 586 " -0.025 2.00e-02 2.50e+03 ... (remaining 2344 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4821 2.84 - 3.36: 14351 3.36 - 3.87: 24282 3.87 - 4.39: 29879 4.39 - 4.90: 47368 Nonbonded interactions: 120701 Sorted by model distance: nonbonded pdb=" O HIS A 325 " pdb=" N GLU A 327 " model vdw 2.330 3.120 nonbonded pdb=" O ILE A 514 " pdb=" OG SER A 517 " model vdw 2.357 3.040 nonbonded pdb=" OG SER A 543 " pdb=" OG SER A 615 " model vdw 2.359 3.040 nonbonded pdb=" OD2 ASP A1290 " pdb=" NZ LYS A1294 " model vdw 2.370 3.120 nonbonded pdb=" OE1 GLU A 534 " pdb=" NZ LYS A1136 " model vdw 2.390 3.120 ... (remaining 120696 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 Found NCS groups: ncs_group { reference = (chain 'C' and resid 131 through 188) selection = (chain 'D' and resid 131 through 188) selection = (chain 'E' and resid 131 through 188) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 33.570 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.014 0.113 13806 Z= 0.806 Angle : 1.150 7.746 18666 Z= 0.806 Chirality : 0.060 0.320 2154 Planarity : 0.005 0.036 2347 Dihedral : 10.399 87.569 5251 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.57 % Favored : 97.89 % Rotamer: Outliers : 0.07 % Allowed : 0.59 % Favored : 99.35 % 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: 0.75 (0.19), residues: 1657 helix: 0.51 (0.15), residues: 955 sheet: 0.42 (0.58), residues: 73 loop : 0.79 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.006 TRP A 207 HIS 0.005 0.001 HIS A1011 PHE 0.035 0.004 PHE A 426 TYR 0.037 0.005 TYR A 710 ARG 0.004 0.001 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.15161 ( 782) hydrogen bonds : angle 6.11256 ( 2190) covalent geometry : bond 0.01444 (13806) covalent geometry : angle 1.14951 (18666) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 1.694 Fit side-chains REVERT: A 63 LYS cc_start: 0.7371 (mttt) cc_final: 0.6893 (pttp) REVERT: A 83 GLU cc_start: 0.7972 (tt0) cc_final: 0.7328 (tt0) REVERT: A 101 GLU cc_start: 0.5735 (tt0) cc_final: 0.5397 (tt0) REVERT: A 129 ASN cc_start: 0.7880 (t0) cc_final: 0.7626 (t0) REVERT: A 198 GLN cc_start: 0.7275 (pt0) cc_final: 0.7017 (pt0) REVERT: A 203 TRP cc_start: 0.6379 (m100) cc_final: 0.5689 (m100) REVERT: A 220 GLN cc_start: 0.7322 (tt0) cc_final: 0.6983 (mt0) REVERT: A 312 GLN cc_start: 0.6675 (mm-40) cc_final: 0.6468 (mt0) REVERT: A 340 MET cc_start: 0.6414 (tpt) cc_final: 0.5454 (mtp) REVERT: A 354 LYS cc_start: 0.7148 (tttt) cc_final: 0.6386 (mmtp) REVERT: A 370 LYS cc_start: 0.7630 (tttt) cc_final: 0.7366 (ttmt) REVERT: A 373 LYS cc_start: 0.8096 (tttt) cc_final: 0.7704 (tttm) REVERT: A 386 LYS cc_start: 0.7778 (mmtm) cc_final: 0.7572 (mtmp) REVERT: A 413 ASP cc_start: 0.7022 (t0) cc_final: 0.6770 (t0) REVERT: A 434 VAL cc_start: 0.7040 (t) cc_final: 0.6674 (p) REVERT: A 445 ILE cc_start: 0.7973 (tp) cc_final: 0.7673 (mm) REVERT: A 446 ASN cc_start: 0.6309 (m-40) cc_final: 0.6107 (m-40) REVERT: A 449 GLU cc_start: 0.6705 (tt0) cc_final: 0.6403 (tt0) REVERT: A 450 THR cc_start: 0.7171 (m) cc_final: 0.6806 (m) REVERT: A 567 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6556 (mt-10) REVERT: A 594 GLU cc_start: 0.7292 (mp0) cc_final: 0.6973 (mm-30) REVERT: A 718 ASP cc_start: 0.6672 (t70) cc_final: 0.6150 (m-30) REVERT: A 801 LYS cc_start: 0.6977 (mmtm) cc_final: 0.6441 (mppt) REVERT: A 803 SER cc_start: 0.7644 (t) cc_final: 0.7349 (p) REVERT: A 805 THR cc_start: 0.7559 (m) cc_final: 0.7289 (t) REVERT: A 848 TYR cc_start: 0.6837 (m-80) cc_final: 0.6506 (m-80) REVERT: A 859 GLU cc_start: 0.6118 (mt-10) cc_final: 0.5712 (mp0) REVERT: A 902 LYS cc_start: 0.7293 (mmtt) cc_final: 0.6766 (tttp) REVERT: A 967 ASN cc_start: 0.8076 (t0) cc_final: 0.7775 (t0) REVERT: A 1071 LYS cc_start: 0.6408 (mmtp) cc_final: 0.5975 (mmtt) REVERT: A 1091 LYS cc_start: 0.7861 (mttt) cc_final: 0.7472 (mmmt) REVERT: A 1145 LYS cc_start: 0.6600 (mtmt) cc_final: 0.6075 (ptpt) REVERT: A 1171 LYS cc_start: 0.7032 (mttt) cc_final: 0.6733 (mtpt) REVERT: A 1244 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7508 (mp0) REVERT: A 1272 THR cc_start: 0.7442 (m) cc_final: 0.7158 (p) REVERT: A 1290 ASP cc_start: 0.6910 (t70) cc_final: 0.6413 (m-30) REVERT: A 1322 GLU cc_start: 0.5971 (mp0) cc_final: 0.5700 (mp0) REVERT: A 1339 ARG cc_start: 0.7589 (mmt90) cc_final: 0.6214 (mtm180) REVERT: A 1364 ASP cc_start: 0.7565 (t0) cc_final: 0.7091 (t0) REVERT: A 1379 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7098 (mm-30) REVERT: A 1409 ARG cc_start: 0.7713 (ptp-110) cc_final: 0.7444 (ptp-170) REVERT: A 1421 LEU cc_start: 0.8567 (tp) cc_final: 0.8365 (tm) REVERT: A 1423 LYS cc_start: 0.8005 (pttt) cc_final: 0.7485 (pttm) REVERT: A 1437 LYS cc_start: 0.6898 (ttmm) cc_final: 0.6467 (ttpp) REVERT: B 187 MET cc_start: 0.3333 (mtm) cc_final: 0.2618 (ppp) REVERT: B 213 GLU cc_start: 0.6622 (tt0) cc_final: 0.6092 (mp0) REVERT: C 170 MET cc_start: 0.7545 (mtp) cc_final: 0.7157 (mtp) REVERT: D 170 MET cc_start: 0.5344 (mmm) cc_final: 0.5129 (mmm) outliers start: 1 outliers final: 0 residues processed: 369 average time/residue: 1.2578 time to fit residues: 506.7338 Evaluate side-chains 214 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 58 HIS A 247 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS A 415 ASN A 547 ASN A 563 GLN ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 HIS A 874 GLN A 991 ASN A1037 ASN A1069 GLN A1247 ASN ** A1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1360 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.172226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.145335 restraints weight = 15482.963| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.57 r_work: 0.3558 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13806 Z= 0.159 Angle : 0.570 7.251 18666 Z= 0.306 Chirality : 0.041 0.165 2154 Planarity : 0.004 0.036 2347 Dihedral : 4.279 25.071 1859 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.63 % Favored : 98.25 % Rotamer: Outliers : 3.33 % Allowed : 8.50 % Favored : 88.17 % 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: 1.70 (0.20), residues: 1657 helix: 1.54 (0.16), residues: 970 sheet: 0.40 (0.64), residues: 67 loop : 0.74 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 932 HIS 0.004 0.001 HIS A 568 PHE 0.023 0.002 PHE A 426 TYR 0.017 0.002 TYR A 746 ARG 0.007 0.001 ARG A1370 Details of bonding type rmsd hydrogen bonds : bond 0.04825 ( 782) hydrogen bonds : angle 4.52577 ( 2190) covalent geometry : bond 0.00357 (13806) covalent geometry : angle 0.57002 (18666) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 236 time to evaluate : 1.693 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.6056 (ttm) cc_final: 0.5558 (ttt) REVERT: A 194 MET cc_start: 0.8584 (tpt) cc_final: 0.8380 (tpt) REVERT: A 203 TRP cc_start: 0.6303 (m100) cc_final: 0.5768 (m100) REVERT: A 335 VAL cc_start: 0.8018 (OUTLIER) cc_final: 0.7777 (t) REVERT: A 340 MET cc_start: 0.7884 (tpt) cc_final: 0.7320 (mtp) REVERT: A 354 LYS cc_start: 0.8345 (tttt) cc_final: 0.7917 (mmtp) REVERT: A 694 LYS cc_start: 0.7972 (mttt) cc_final: 0.6960 (pttp) REVERT: A 782 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7564 (tp-100) REVERT: A 848 TYR cc_start: 0.8205 (m-80) cc_final: 0.7964 (m-80) REVERT: A 967 ASN cc_start: 0.8091 (t0) cc_final: 0.7836 (t0) REVERT: A 1339 ARG cc_start: 0.8114 (mmt90) cc_final: 0.7388 (mtm-85) REVERT: A 1371 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8441 (mp) REVERT: A 1378 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6838 (t0) REVERT: A 1437 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7532 (ttpp) REVERT: B 187 MET cc_start: 0.3130 (mtm) cc_final: 0.2855 (ptm) REVERT: C 170 MET cc_start: 0.8207 (mtp) cc_final: 0.7998 (mtp) REVERT: D 170 MET cc_start: 0.6620 (mmm) cc_final: 0.6402 (mmm) REVERT: E 195 MET cc_start: 0.5506 (mmm) cc_final: 0.5030 (mmm) outliers start: 51 outliers final: 17 residues processed: 268 average time/residue: 1.2590 time to fit residues: 369.2195 Evaluate side-chains 200 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1334 VAL Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1378 ASP Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1405 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain E residue 148 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 5 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 209 ASN A 220 GLN A 224 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN A1279 GLN A1330 GLN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.164454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.136185 restraints weight = 15506.873| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.53 r_work: 0.3445 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13806 Z= 0.223 Angle : 0.614 7.101 18666 Z= 0.322 Chirality : 0.043 0.180 2154 Planarity : 0.005 0.069 2347 Dihedral : 4.535 22.726 1859 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.11 % Favored : 97.77 % Rotamer: Outliers : 3.73 % Allowed : 10.98 % Favored : 85.29 % 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: 1.20 (0.20), residues: 1657 helix: 1.25 (0.16), residues: 982 sheet: -0.27 (0.65), residues: 67 loop : 0.35 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 932 HIS 0.008 0.001 HIS A 325 PHE 0.026 0.003 PHE A1054 TYR 0.021 0.002 TYR A 746 ARG 0.005 0.001 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.04824 ( 782) hydrogen bonds : angle 4.57941 ( 2190) covalent geometry : bond 0.00519 (13806) covalent geometry : angle 0.61355 (18666) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 191 time to evaluate : 1.738 Fit side-chains REVERT: A 16 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8152 (m-30) REVERT: A 203 TRP cc_start: 0.6566 (m100) cc_final: 0.5958 (m100) REVERT: A 243 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8088 (tp40) REVERT: A 349 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7605 (mm-30) REVERT: A 354 LYS cc_start: 0.8502 (tttt) cc_final: 0.8036 (mmtp) REVERT: A 539 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.7027 (p0) REVERT: A 694 LYS cc_start: 0.8038 (mttt) cc_final: 0.6963 (pptt) REVERT: A 782 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7713 (tp-100) REVERT: A 1339 ARG cc_start: 0.8245 (mmt90) cc_final: 0.7556 (mtm-85) REVERT: A 1378 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7077 (m-30) REVERT: A 1379 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7721 (mm-30) REVERT: C 170 MET cc_start: 0.8379 (mtp) cc_final: 0.8097 (mtp) REVERT: D 149 LEU cc_start: 0.7813 (mt) cc_final: 0.7557 (mm) REVERT: D 170 MET cc_start: 0.6529 (mmm) cc_final: 0.6121 (mmm) outliers start: 57 outliers final: 22 residues processed: 230 average time/residue: 1.1261 time to fit residues: 286.5133 Evaluate side-chains 193 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1334 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1378 ASP Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 160 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 76 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 114 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 209 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN A 727 GLN A1022 HIS ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.168407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.141958 restraints weight = 15396.100| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.42 r_work: 0.3497 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13806 Z= 0.124 Angle : 0.503 6.446 18666 Z= 0.266 Chirality : 0.039 0.174 2154 Planarity : 0.004 0.047 2347 Dihedral : 4.167 21.546 1859 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.99 % Favored : 97.95 % Rotamer: Outliers : 2.68 % Allowed : 12.75 % Favored : 84.58 % 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: 1.49 (0.21), residues: 1657 helix: 1.53 (0.16), residues: 974 sheet: -0.05 (0.66), residues: 72 loop : 0.39 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 932 HIS 0.004 0.001 HIS A 325 PHE 0.035 0.002 PHE A 314 TYR 0.017 0.001 TYR A 746 ARG 0.005 0.000 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 782) hydrogen bonds : angle 4.32923 ( 2190) covalent geometry : bond 0.00273 (13806) covalent geometry : angle 0.50348 (18666) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 1.427 Fit side-chains REVERT: A 203 TRP cc_start: 0.6541 (m100) cc_final: 0.5928 (m100) REVERT: A 243 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8210 (tp40) REVERT: A 314 PHE cc_start: 0.6669 (t80) cc_final: 0.6324 (t80) REVERT: A 349 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7446 (mm-30) REVERT: A 354 LYS cc_start: 0.8489 (tttt) cc_final: 0.8065 (mmtp) REVERT: A 694 LYS cc_start: 0.7887 (mttt) cc_final: 0.6905 (pttp) REVERT: A 1159 LEU cc_start: 0.8309 (mt) cc_final: 0.8100 (mm) REVERT: A 1290 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7154 (m-30) REVERT: A 1304 ASN cc_start: 0.7800 (t0) cc_final: 0.7572 (t0) REVERT: A 1311 GLU cc_start: 0.7865 (tp30) cc_final: 0.7560 (tp30) REVERT: A 1339 ARG cc_start: 0.8186 (mmt90) cc_final: 0.7492 (mtm180) REVERT: A 1379 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: C 170 MET cc_start: 0.8366 (mtp) cc_final: 0.8109 (mtp) REVERT: D 170 MET cc_start: 0.6584 (mmm) cc_final: 0.6230 (mmm) outliers start: 41 outliers final: 19 residues processed: 211 average time/residue: 1.1715 time to fit residues: 273.7549 Evaluate side-chains 191 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1153 LYS Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1334 VAL Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain E residue 148 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 8 optimal weight: 8.9990 chunk 90 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 66 optimal weight: 0.2980 chunk 68 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 236 ASN A 296 ASN A 812 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.167513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140650 restraints weight = 15578.513| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.36 r_work: 0.3470 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13806 Z= 0.141 Angle : 0.509 6.785 18666 Z= 0.268 Chirality : 0.040 0.176 2154 Planarity : 0.004 0.048 2347 Dihedral : 4.134 21.658 1859 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.35 % Favored : 97.59 % Rotamer: Outliers : 3.01 % Allowed : 13.27 % Favored : 83.73 % 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 (0.21), residues: 1657 helix: 1.54 (0.16), residues: 979 sheet: -0.15 (0.64), residues: 72 loop : 0.32 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 932 HIS 0.004 0.001 HIS A 829 PHE 0.023 0.002 PHE A 704 TYR 0.018 0.002 TYR A 746 ARG 0.004 0.000 ARG A 511 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 782) hydrogen bonds : angle 4.30694 ( 2190) covalent geometry : bond 0.00319 (13806) covalent geometry : angle 0.50881 (18666) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 1.628 Fit side-chains REVERT: A 203 TRP cc_start: 0.6652 (m100) cc_final: 0.6007 (m100) REVERT: A 243 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8250 (tp40) REVERT: A 279 ARG cc_start: 0.7381 (mmp80) cc_final: 0.7145 (mtp85) REVERT: A 314 PHE cc_start: 0.6620 (t80) cc_final: 0.6008 (t80) REVERT: A 349 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7482 (mm-30) REVERT: A 354 LYS cc_start: 0.8527 (tttt) cc_final: 0.8067 (mmtp) REVERT: A 539 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.7003 (p0) REVERT: A 692 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7330 (pt) REVERT: A 694 LYS cc_start: 0.7931 (mttt) cc_final: 0.6943 (pttp) REVERT: A 1290 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7180 (m-30) REVERT: A 1304 ASN cc_start: 0.7798 (t0) cc_final: 0.7562 (t0) REVERT: A 1311 GLU cc_start: 0.7924 (tp30) cc_final: 0.7641 (tp30) REVERT: A 1339 ARG cc_start: 0.8208 (mmt90) cc_final: 0.7552 (mtm-85) REVERT: A 1379 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: B 170 MET cc_start: 0.6224 (OUTLIER) cc_final: 0.5591 (ptm) REVERT: C 170 MET cc_start: 0.8380 (mtp) cc_final: 0.8134 (mtp) REVERT: D 170 MET cc_start: 0.6550 (mmm) cc_final: 0.6183 (mmm) REVERT: E 195 MET cc_start: 0.5026 (tpp) cc_final: 0.4749 (tpt) outliers start: 46 outliers final: 22 residues processed: 211 average time/residue: 1.1495 time to fit residues: 268.0461 Evaluate side-chains 193 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 1153 LYS Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1334 VAL Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1450 LYS Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain E residue 148 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 6 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 129 ASN A 739 HIS A 812 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.167891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.140305 restraints weight = 15679.602| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.51 r_work: 0.3490 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13806 Z= 0.137 Angle : 0.506 7.086 18666 Z= 0.266 Chirality : 0.039 0.184 2154 Planarity : 0.004 0.048 2347 Dihedral : 4.113 21.591 1859 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.41 % Favored : 97.53 % Rotamer: Outliers : 3.01 % Allowed : 13.59 % Favored : 83.40 % 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: 1.47 (0.21), residues: 1657 helix: 1.58 (0.16), residues: 978 sheet: -0.24 (0.64), residues: 73 loop : 0.28 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 932 HIS 0.004 0.001 HIS A 829 PHE 0.025 0.002 PHE A 704 TYR 0.018 0.002 TYR A 746 ARG 0.006 0.000 ARG A1286 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 782) hydrogen bonds : angle 4.27416 ( 2190) covalent geometry : bond 0.00314 (13806) covalent geometry : angle 0.50620 (18666) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 1.733 Fit side-chains REVERT: A 203 TRP cc_start: 0.6602 (m100) cc_final: 0.5961 (m100) REVERT: A 243 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8243 (tp40) REVERT: A 314 PHE cc_start: 0.6675 (t80) cc_final: 0.5958 (t80) REVERT: A 349 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7457 (mm-30) REVERT: A 354 LYS cc_start: 0.8516 (tttt) cc_final: 0.8028 (mmtp) REVERT: A 539 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6900 (p0) REVERT: A 692 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7362 (pt) REVERT: A 694 LYS cc_start: 0.7939 (mttt) cc_final: 0.6949 (pttp) REVERT: A 1159 LEU cc_start: 0.8308 (mt) cc_final: 0.8050 (mm) REVERT: A 1290 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7139 (m-30) REVERT: A 1304 ASN cc_start: 0.7791 (t0) cc_final: 0.7545 (t0) REVERT: A 1311 GLU cc_start: 0.7884 (tp30) cc_final: 0.7650 (tp30) REVERT: A 1339 ARG cc_start: 0.8192 (mmt90) cc_final: 0.7506 (mtm-85) REVERT: A 1379 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: B 170 MET cc_start: 0.6180 (OUTLIER) cc_final: 0.5566 (ptm) REVERT: C 170 MET cc_start: 0.8365 (mtp) cc_final: 0.8113 (mtp) REVERT: D 170 MET cc_start: 0.6566 (mmm) cc_final: 0.6173 (mmm) REVERT: E 195 MET cc_start: 0.4934 (tpp) cc_final: 0.4705 (tpt) outliers start: 46 outliers final: 24 residues processed: 210 average time/residue: 1.0872 time to fit residues: 253.3771 Evaluate side-chains 200 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1153 LYS Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1334 VAL Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 160 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 198 GLN A 812 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.166841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.140250 restraints weight = 15489.454| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.36 r_work: 0.3461 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13806 Z= 0.154 Angle : 0.530 7.407 18666 Z= 0.276 Chirality : 0.040 0.186 2154 Planarity : 0.004 0.047 2347 Dihedral : 4.157 21.181 1859 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.53 % Favored : 97.40 % Rotamer: Outliers : 2.61 % Allowed : 14.31 % Favored : 83.07 % 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: 1.41 (0.21), residues: 1657 helix: 1.53 (0.16), residues: 978 sheet: -0.26 (0.65), residues: 73 loop : 0.24 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 932 HIS 0.004 0.001 HIS A 829 PHE 0.023 0.002 PHE A 704 TYR 0.019 0.002 TYR A 746 ARG 0.005 0.000 ARG A1286 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 782) hydrogen bonds : angle 4.31843 ( 2190) covalent geometry : bond 0.00356 (13806) covalent geometry : angle 0.52969 (18666) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 1.559 Fit side-chains REVERT: A 203 TRP cc_start: 0.6633 (m100) cc_final: 0.6020 (m100) REVERT: A 243 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8259 (tp40) REVERT: A 314 PHE cc_start: 0.6575 (t80) cc_final: 0.5143 (t80) REVERT: A 349 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7502 (mm-30) REVERT: A 354 LYS cc_start: 0.8527 (tttt) cc_final: 0.8068 (mmtp) REVERT: A 539 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6959 (p0) REVERT: A 692 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7469 (pt) REVERT: A 694 LYS cc_start: 0.7978 (mttt) cc_final: 0.7001 (pttp) REVERT: A 1159 LEU cc_start: 0.8358 (mt) cc_final: 0.8088 (mm) REVERT: A 1290 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7160 (m-30) REVERT: A 1304 ASN cc_start: 0.7824 (t0) cc_final: 0.7569 (t0) REVERT: A 1339 ARG cc_start: 0.8199 (mmt90) cc_final: 0.7554 (mtm-85) REVERT: A 1378 ASP cc_start: 0.7423 (p0) cc_final: 0.7016 (m-30) REVERT: B 170 MET cc_start: 0.6202 (OUTLIER) cc_final: 0.5594 (ptm) REVERT: B 187 MET cc_start: 0.3779 (OUTLIER) cc_final: 0.3480 (mpp) REVERT: C 170 MET cc_start: 0.8390 (mtp) cc_final: 0.8133 (mtp) REVERT: D 170 MET cc_start: 0.6738 (mmm) cc_final: 0.6341 (mmm) REVERT: E 195 MET cc_start: 0.4966 (tpp) cc_final: 0.4745 (tpt) outliers start: 40 outliers final: 26 residues processed: 203 average time/residue: 1.1503 time to fit residues: 258.9755 Evaluate side-chains 200 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 480 TRP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1153 LYS Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1334 VAL Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 160 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 66 optimal weight: 0.0670 chunk 74 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 812 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.135071 restraints weight = 15515.837| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.45 r_work: 0.3405 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13806 Z= 0.159 Angle : 0.535 9.192 18666 Z= 0.278 Chirality : 0.040 0.184 2154 Planarity : 0.004 0.047 2347 Dihedral : 4.185 21.469 1859 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.66 % Favored : 97.28 % Rotamer: Outliers : 3.01 % Allowed : 14.12 % Favored : 82.88 % 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: 1.35 (0.21), residues: 1657 helix: 1.49 (0.16), residues: 978 sheet: -0.41 (0.64), residues: 75 loop : 0.24 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 932 HIS 0.003 0.001 HIS A 773 PHE 0.021 0.002 PHE A 704 TYR 0.020 0.002 TYR A 746 ARG 0.005 0.000 ARG A 511 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 782) hydrogen bonds : angle 4.34038 ( 2190) covalent geometry : bond 0.00368 (13806) covalent geometry : angle 0.53525 (18666) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 1.620 Fit side-chains REVERT: A 203 TRP cc_start: 0.6615 (m100) cc_final: 0.6023 (m100) REVERT: A 243 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8279 (tp40) REVERT: A 314 PHE cc_start: 0.6582 (t80) cc_final: 0.5129 (t80) REVERT: A 349 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7506 (mm-30) REVERT: A 354 LYS cc_start: 0.8458 (tttt) cc_final: 0.7996 (mmtp) REVERT: A 539 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.7010 (p0) REVERT: A 692 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7381 (pt) REVERT: A 694 LYS cc_start: 0.8048 (mttt) cc_final: 0.6946 (pttp) REVERT: A 1159 LEU cc_start: 0.8357 (mt) cc_final: 0.8079 (mm) REVERT: A 1290 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7187 (m-30) REVERT: A 1304 ASN cc_start: 0.7860 (t0) cc_final: 0.7583 (t0) REVERT: A 1339 ARG cc_start: 0.8211 (mmt90) cc_final: 0.7494 (mtm-85) REVERT: A 1378 ASP cc_start: 0.7368 (p0) cc_final: 0.6978 (m-30) REVERT: B 170 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.5513 (ptm) REVERT: B 187 MET cc_start: 0.3747 (OUTLIER) cc_final: 0.3468 (mpp) REVERT: C 170 MET cc_start: 0.8385 (mtp) cc_final: 0.8105 (mtp) REVERT: D 170 MET cc_start: 0.6706 (mmm) cc_final: 0.6289 (mmm) REVERT: E 195 MET cc_start: 0.4964 (tpp) cc_final: 0.4731 (tpt) outliers start: 46 outliers final: 27 residues processed: 208 average time/residue: 1.0915 time to fit residues: 252.7646 Evaluate side-chains 206 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1153 LYS Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1334 VAL Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 160 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 111 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 67 optimal weight: 0.0870 chunk 138 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 446 ASN ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.165395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.136136 restraints weight = 15341.714| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.71 r_work: 0.3440 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13806 Z= 0.128 Angle : 0.511 9.639 18666 Z= 0.266 Chirality : 0.039 0.188 2154 Planarity : 0.004 0.048 2347 Dihedral : 4.073 20.365 1859 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.60 % Favored : 97.34 % Rotamer: Outliers : 2.42 % Allowed : 14.58 % Favored : 83.01 % 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: 1.47 (0.21), residues: 1657 helix: 1.59 (0.16), residues: 974 sheet: -0.28 (0.64), residues: 73 loop : 0.26 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 932 HIS 0.003 0.001 HIS A 773 PHE 0.019 0.002 PHE A 704 TYR 0.019 0.002 TYR A 746 ARG 0.004 0.000 ARG A1286 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 782) hydrogen bonds : angle 4.27191 ( 2190) covalent geometry : bond 0.00289 (13806) covalent geometry : angle 0.51081 (18666) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 1.518 Fit side-chains REVERT: A 203 TRP cc_start: 0.6627 (m100) cc_final: 0.5976 (m100) REVERT: A 243 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8245 (tp40) REVERT: A 279 ARG cc_start: 0.7446 (mmp80) cc_final: 0.6526 (tpt90) REVERT: A 314 PHE cc_start: 0.6456 (t80) cc_final: 0.5076 (t80) REVERT: A 335 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7903 (t) REVERT: A 354 LYS cc_start: 0.8417 (tttt) cc_final: 0.7873 (mmtp) REVERT: A 359 SER cc_start: 0.8421 (t) cc_final: 0.8080 (m) REVERT: A 539 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6954 (p0) REVERT: A 694 LYS cc_start: 0.8023 (mttt) cc_final: 0.6819 (pttp) REVERT: A 1159 LEU cc_start: 0.8294 (mt) cc_final: 0.8070 (mm) REVERT: A 1290 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7120 (m-30) REVERT: A 1304 ASN cc_start: 0.7790 (t0) cc_final: 0.7489 (t0) REVERT: A 1339 ARG cc_start: 0.8165 (mmt90) cc_final: 0.7380 (mtm-85) REVERT: B 170 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.5425 (ptm) REVERT: B 187 MET cc_start: 0.3801 (OUTLIER) cc_final: 0.3465 (mpp) REVERT: C 170 MET cc_start: 0.8300 (mtp) cc_final: 0.8011 (mtp) REVERT: D 170 MET cc_start: 0.6625 (mmm) cc_final: 0.6180 (mmm) REVERT: E 195 MET cc_start: 0.4697 (tpp) cc_final: 0.4407 (tpt) outliers start: 37 outliers final: 25 residues processed: 205 average time/residue: 1.0109 time to fit residues: 230.9418 Evaluate side-chains 204 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 480 TRP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1153 LYS Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1334 VAL Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 160 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 129 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 153 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 812 ASN A1330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.163287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134414 restraints weight = 15407.626| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.51 r_work: 0.3407 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13806 Z= 0.168 Angle : 0.559 9.379 18666 Z= 0.290 Chirality : 0.041 0.187 2154 Planarity : 0.004 0.049 2347 Dihedral : 4.204 21.318 1859 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 2.75 % Allowed : 14.64 % Favored : 82.61 % 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: 1.32 (0.21), residues: 1657 helix: 1.49 (0.16), residues: 971 sheet: -0.43 (0.63), residues: 75 loop : 0.21 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 932 HIS 0.003 0.001 HIS A 773 PHE 0.019 0.002 PHE A 704 TYR 0.020 0.002 TYR A 746 ARG 0.005 0.000 ARG A 511 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 782) hydrogen bonds : angle 4.36862 ( 2190) covalent geometry : bond 0.00389 (13806) covalent geometry : angle 0.55906 (18666) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 1.766 Fit side-chains REVERT: A 203 TRP cc_start: 0.6638 (m100) cc_final: 0.6033 (m100) REVERT: A 243 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8251 (tp40) REVERT: A 314 PHE cc_start: 0.6608 (t80) cc_final: 0.5137 (t80) REVERT: A 335 VAL cc_start: 0.8250 (OUTLIER) cc_final: 0.7958 (t) REVERT: A 354 LYS cc_start: 0.8469 (tttt) cc_final: 0.7984 (mmtp) REVERT: A 539 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.6991 (p0) REVERT: A 694 LYS cc_start: 0.8102 (mttt) cc_final: 0.6944 (pptt) REVERT: A 1290 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7165 (m-30) REVERT: A 1339 ARG cc_start: 0.8222 (mmt90) cc_final: 0.7516 (mtm-85) REVERT: A 1378 ASP cc_start: 0.7363 (p0) cc_final: 0.7075 (m-30) REVERT: B 170 MET cc_start: 0.6183 (OUTLIER) cc_final: 0.5540 (ptm) REVERT: B 187 MET cc_start: 0.3735 (OUTLIER) cc_final: 0.3422 (mpp) REVERT: C 170 MET cc_start: 0.8415 (mtp) cc_final: 0.8130 (mtp) REVERT: C 175 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: E 195 MET cc_start: 0.4760 (tpp) cc_final: 0.4519 (tpt) outliers start: 42 outliers final: 27 residues processed: 201 average time/residue: 1.1036 time to fit residues: 245.8730 Evaluate side-chains 200 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 480 TRP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 1153 LYS Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1334 VAL Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 175 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 78 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 150 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 603 ASN A 812 ASN ** A1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.166534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.137882 restraints weight = 15505.032| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.67 r_work: 0.3464 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13806 Z= 0.117 Angle : 0.509 9.307 18666 Z= 0.266 Chirality : 0.039 0.180 2154 Planarity : 0.004 0.051 2347 Dihedral : 3.998 19.620 1859 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.53 % Favored : 97.40 % Rotamer: Outliers : 2.16 % Allowed : 15.62 % Favored : 82.22 % 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: 1.51 (0.21), residues: 1657 helix: 1.63 (0.16), residues: 970 sheet: -0.22 (0.64), residues: 73 loop : 0.27 (0.27), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 932 HIS 0.003 0.001 HIS A 734 PHE 0.018 0.002 PHE A 704 TYR 0.017 0.001 TYR A 746 ARG 0.005 0.000 ARG A 511 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 782) hydrogen bonds : angle 4.23955 ( 2190) covalent geometry : bond 0.00260 (13806) covalent geometry : angle 0.50946 (18666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9668.73 seconds wall clock time: 167 minutes 24.47 seconds (10044.47 seconds total)