Starting phenix.real_space_refine on Thu Jun 12 05:07:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fu3_29452/06_2025/8fu3_29452_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fu3_29452/06_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_29452/06_2025/8fu3_29452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fu3_29452/06_2025/8fu3_29452.map" model { file = "/net/cci-nas-00/data/ceres_data/8fu3_29452/06_2025/8fu3_29452_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fu3_29452/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.38, per 1000 atoms: 0.62 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: 3.64 Conformation dependent library (CDL) restraints added in 1.8 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: 1.74 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: 5.41 Time building geometry restraints manager: 4.14 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.890 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:26.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.860 ------------------------------------------------------------------------------- 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 : 1.772 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: 1.3572 time to fit residues: 547.4123 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 : 1.584 ------------------------------------------------------------------------------- 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 = 0.172223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.145355 restraints weight = 15484.737| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.57 r_work: 0.3560 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 1.699 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.6052 (ttm) cc_final: 0.5548 (ttt) REVERT: A 194 MET cc_start: 0.8571 (tpt) cc_final: 0.8358 (tpt) REVERT: A 203 TRP cc_start: 0.6324 (m100) cc_final: 0.5787 (m100) REVERT: A 335 VAL cc_start: 0.8018 (OUTLIER) cc_final: 0.7779 (t) REVERT: A 340 MET cc_start: 0.7850 (tpt) cc_final: 0.7316 (mtp) REVERT: A 354 LYS cc_start: 0.8355 (tttt) cc_final: 0.7921 (mmtp) REVERT: A 694 LYS cc_start: 0.7978 (mttt) cc_final: 0.6966 (pttp) REVERT: A 782 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7539 (tp-100) REVERT: A 848 TYR cc_start: 0.8198 (m-80) cc_final: 0.7959 (m-80) REVERT: A 967 ASN cc_start: 0.8083 (t0) cc_final: 0.7829 (t0) REVERT: A 1339 ARG cc_start: 0.8118 (mmt90) cc_final: 0.7385 (mtm-85) REVERT: A 1371 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8440 (mp) REVERT: A 1378 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6839 (t0) REVERT: A 1437 LYS cc_start: 0.7988 (ttmm) cc_final: 0.7527 (ttpp) REVERT: B 187 MET cc_start: 0.3135 (mtm) cc_final: 0.2860 (ptm) REVERT: C 170 MET cc_start: 0.8204 (mtp) cc_final: 0.7997 (mtp) REVERT: D 170 MET cc_start: 0.6608 (mmm) cc_final: 0.6388 (mmm) REVERT: E 195 MET cc_start: 0.5503 (mmm) cc_final: 0.5025 (mmm) outliers start: 51 outliers final: 17 residues processed: 268 average time/residue: 1.3173 time to fit residues: 386.0238 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 : 1.613 ------------------------------------------------------------------------------- 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: 2.9990 chunk 95 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 209 ASN A 220 GLN A 224 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1279 GLN A1330 GLN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.164849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136516 restraints weight = 15542.155| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.47 r_work: 0.3449 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13806 Z= 0.222 Angle : 0.605 6.755 18666 Z= 0.318 Chirality : 0.043 0.180 2154 Planarity : 0.004 0.069 2347 Dihedral : 4.488 22.778 1859 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.05 % Favored : 97.83 % Rotamer: Outliers : 3.66 % Allowed : 10.92 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.20), residues: 1657 helix: 1.28 (0.16), residues: 982 sheet: -0.07 (0.66), residues: 65 loop : 0.37 (0.26), residues: 610 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 0.025 0.003 PHE A1054 TYR 0.020 0.002 TYR A 746 ARG 0.004 0.001 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.04797 ( 782) hydrogen bonds : angle 4.56205 ( 2190) covalent geometry : bond 0.00517 (13806) covalent geometry : angle 0.60523 (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 247 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 191 time to evaluate : 1.564 Fit side-chains REVERT: A 16 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8149 (m-30) REVERT: A 203 TRP cc_start: 0.6527 (m100) cc_final: 0.5926 (m100) REVERT: A 243 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8068 (tp40) REVERT: A 349 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7601 (mm-30) REVERT: A 354 LYS cc_start: 0.8499 (tttt) cc_final: 0.8036 (mmtp) REVERT: A 539 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.7017 (p0) REVERT: A 694 LYS cc_start: 0.8024 (mttt) cc_final: 0.6975 (pptt) REVERT: A 782 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7700 (tp-100) REVERT: A 1339 ARG cc_start: 0.8230 (mmt90) cc_final: 0.7540 (mtm-85) REVERT: A 1379 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7646 (mm-30) REVERT: B 222 LYS cc_start: 0.7674 (tttt) cc_final: 0.7466 (tttp) REVERT: C 170 MET cc_start: 0.8375 (mtp) cc_final: 0.8105 (mtp) REVERT: D 170 MET cc_start: 0.6512 (mmm) cc_final: 0.6125 (mmm) outliers start: 56 outliers final: 23 residues processed: 227 average time/residue: 1.1632 time to fit residues: 291.7148 Evaluate side-chains 192 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 1.676 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain E residue 148 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 76 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 114 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 727 GLN A1022 HIS ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.169170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.142447 restraints weight = 15414.031| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.48 r_work: 0.3509 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13806 Z= 0.118 Angle : 0.496 6.461 18666 Z= 0.263 Chirality : 0.039 0.183 2154 Planarity : 0.004 0.046 2347 Dihedral : 4.145 21.549 1859 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.05 % Favored : 97.89 % Rotamer: Outliers : 2.35 % Allowed : 13.20 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.21), residues: 1657 helix: 1.53 (0.16), residues: 976 sheet: -0.03 (0.66), residues: 72 loop : 0.42 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 932 HIS 0.004 0.001 HIS A 325 PHE 0.027 0.002 PHE A 314 TYR 0.016 0.001 TYR A 746 ARG 0.004 0.000 ARG A 511 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 782) hydrogen bonds : angle 4.30785 ( 2190) covalent geometry : bond 0.00255 (13806) covalent geometry : angle 0.49612 (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 224 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 1.478 Fit side-chains revert: symmetry clash REVERT: A 203 TRP cc_start: 0.6531 (m100) cc_final: 0.5903 (m100) REVERT: A 243 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8214 (tp40) REVERT: A 314 PHE cc_start: 0.6629 (t80) cc_final: 0.6361 (t80) REVERT: A 349 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7447 (mm-30) REVERT: A 354 LYS cc_start: 0.8485 (tttt) cc_final: 0.8076 (mmtp) REVERT: A 694 LYS cc_start: 0.7902 (mttt) cc_final: 0.6887 (pttp) REVERT: A 1159 LEU cc_start: 0.8294 (mt) cc_final: 0.8087 (mm) REVERT: A 1290 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: A 1339 ARG cc_start: 0.8188 (mmt90) cc_final: 0.7492 (mtm180) REVERT: A 1379 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: C 170 MET cc_start: 0.8363 (mtp) cc_final: 0.8121 (mtp) REVERT: D 170 MET cc_start: 0.6539 (mmm) cc_final: 0.6210 (mmm) outliers start: 36 outliers final: 16 residues processed: 210 average time/residue: 1.1975 time to fit residues: 278.1420 Evaluate side-chains 185 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 1.499 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 8 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 66 optimal weight: 0.0370 chunk 68 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 overall best weight: 1.4064 ------------------------------------------------------------------------------- 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 ** A1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.166886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.139752 restraints weight = 15585.349| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.45 r_work: 0.3470 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13806 Z= 0.151 Angle : 0.516 6.705 18666 Z= 0.272 Chirality : 0.040 0.178 2154 Planarity : 0.004 0.047 2347 Dihedral : 4.163 21.619 1859 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.35 % Favored : 97.59 % Rotamer: Outliers : 2.75 % Allowed : 13.73 % Favored : 83.53 % 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: 1.48 (0.21), residues: 1657 helix: 1.53 (0.16), residues: 977 sheet: -0.13 (0.65), residues: 72 loop : 0.37 (0.26), residues: 608 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 0.023 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 0.04046 ( 782) hydrogen bonds : angle 4.32253 ( 2190) covalent geometry : bond 0.00346 (13806) covalent geometry : angle 0.51582 (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 218 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 1.536 Fit side-chains revert: symmetry clash REVERT: A 203 TRP cc_start: 0.6628 (m100) cc_final: 0.5996 (m100) REVERT: A 243 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8244 (tp40) REVERT: A 314 PHE cc_start: 0.6752 (t80) cc_final: 0.5296 (t80) REVERT: A 349 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7525 (mm-30) REVERT: A 354 LYS cc_start: 0.8507 (tttt) cc_final: 0.8097 (mmtp) REVERT: A 539 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.7024 (p0) REVERT: A 692 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7333 (pt) REVERT: A 694 LYS cc_start: 0.7950 (mttt) cc_final: 0.6955 (pttp) REVERT: A 1339 ARG cc_start: 0.8211 (mmt90) cc_final: 0.7537 (mtm-85) REVERT: A 1379 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: C 170 MET cc_start: 0.8371 (mtp) cc_final: 0.8124 (mtp) REVERT: D 170 MET cc_start: 0.6534 (mmm) cc_final: 0.6168 (mmm) REVERT: E 195 MET cc_start: 0.5143 (tpp) cc_final: 0.4876 (tpt) outliers start: 42 outliers final: 20 residues processed: 205 average time/residue: 1.1817 time to fit residues: 268.3380 Evaluate side-chains 189 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 6 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 98 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 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 = 0.3936 r_free = 0.3936 target = 0.167760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.140481 restraints weight = 15686.554| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.46 r_work: 0.3487 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13806 Z= 0.133 Angle : 0.501 7.073 18666 Z= 0.263 Chirality : 0.039 0.184 2154 Planarity : 0.004 0.048 2347 Dihedral : 4.110 21.345 1859 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.41 % Favored : 97.53 % Rotamer: Outliers : 2.88 % Allowed : 13.86 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.21), residues: 1657 helix: 1.58 (0.16), residues: 978 sheet: -0.26 (0.64), residues: 73 loop : 0.31 (0.26), residues: 606 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 0.024 0.002 PHE A 704 TYR 0.018 0.002 TYR A 746 ARG 0.005 0.000 ARG A1286 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 782) hydrogen bonds : angle 4.25908 ( 2190) covalent geometry : bond 0.00302 (13806) covalent geometry : angle 0.50126 (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 223 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TRP cc_start: 0.6563 (m100) cc_final: 0.5950 (m100) REVERT: A 243 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8236 (tp40) REVERT: A 349 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7467 (mm-30) REVERT: A 354 LYS cc_start: 0.8515 (tttt) cc_final: 0.8053 (mmtp) REVERT: A 539 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.7007 (p0) REVERT: A 692 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7422 (pt) REVERT: A 694 LYS cc_start: 0.7969 (mttt) cc_final: 0.6974 (pttp) REVERT: A 859 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5987 (mm-30) REVERT: A 1159 LEU cc_start: 0.8290 (mt) cc_final: 0.8046 (mm) REVERT: A 1290 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7115 (m-30) REVERT: A 1339 ARG cc_start: 0.8201 (mmt90) cc_final: 0.7523 (mtm-85) REVERT: A 1379 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: C 170 MET cc_start: 0.8389 (mtp) cc_final: 0.8136 (mtp) REVERT: D 170 MET cc_start: 0.6604 (mmm) cc_final: 0.6212 (mmm) outliers start: 44 outliers final: 21 residues processed: 208 average time/residue: 1.0951 time to fit residues: 253.7189 Evaluate side-chains 199 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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 859 GLU 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 B residue 187 MET Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 156 SER 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: 1.9990 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 159 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 739 HIS 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 = 0.3931 r_free = 0.3931 target = 0.167385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139949 restraints weight = 15531.740| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.50 r_work: 0.3484 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13806 Z= 0.142 Angle : 0.516 7.081 18666 Z= 0.269 Chirality : 0.040 0.181 2154 Planarity : 0.004 0.049 2347 Dihedral : 4.111 20.707 1859 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.53 % Favored : 97.40 % Rotamer: Outliers : 2.61 % Allowed : 14.44 % Favored : 82.94 % 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: -0.31 (0.63), 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 0.021 0.002 PHE A 704 TYR 0.018 0.002 TYR A 221 ARG 0.004 0.000 ARG A 511 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 782) hydrogen bonds : angle 4.28359 ( 2190) covalent geometry : bond 0.00325 (13806) covalent geometry : angle 0.51600 (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 215 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 1.701 Fit side-chains revert: symmetry clash REVERT: A 203 TRP cc_start: 0.6570 (m100) cc_final: 0.5953 (m100) REVERT: A 243 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8244 (tp40) REVERT: A 314 PHE cc_start: 0.6509 (t80) cc_final: 0.5446 (t80) REVERT: A 349 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7487 (mm-30) REVERT: A 354 LYS cc_start: 0.8499 (tttt) cc_final: 0.8046 (mmtp) REVERT: A 539 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6959 (p0) REVERT: A 692 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7452 (pt) REVERT: A 694 LYS cc_start: 0.7969 (mttt) cc_final: 0.6963 (pttp) REVERT: A 859 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.5944 (mm-30) REVERT: A 1159 LEU cc_start: 0.8364 (mt) cc_final: 0.8113 (mm) REVERT: A 1339 ARG cc_start: 0.8194 (mmt90) cc_final: 0.7521 (mtm-85) REVERT: A 1379 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: C 170 MET cc_start: 0.8387 (mtp) cc_final: 0.8131 (mtp) REVERT: D 170 MET cc_start: 0.6676 (mmm) cc_final: 0.6262 (mmm) outliers start: 40 outliers final: 26 residues processed: 201 average time/residue: 1.1521 time to fit residues: 258.0906 Evaluate side-chains 199 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 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 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 859 GLU 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 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 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: 2.9990 chunk 8 optimal weight: 6.9990 chunk 66 optimal weight: 0.0010 chunk 74 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- 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 446 ASN A 812 ASN ** A1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.134021 restraints weight = 15568.841| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.57 r_work: 0.3416 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13806 Z= 0.160 Angle : 0.537 8.248 18666 Z= 0.280 Chirality : 0.041 0.178 2154 Planarity : 0.004 0.048 2347 Dihedral : 4.197 21.636 1859 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.66 % Favored : 97.28 % Rotamer: Outliers : 2.94 % Allowed : 13.99 % 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: 1.37 (0.21), residues: 1657 helix: 1.51 (0.16), residues: 978 sheet: -0.44 (0.62), residues: 75 loop : 0.26 (0.26), residues: 604 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 0.021 0.002 PHE A 704 TYR 0.019 0.002 TYR A 746 ARG 0.004 0.000 ARG A 511 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 782) hydrogen bonds : angle 4.33974 ( 2190) covalent geometry : bond 0.00370 (13806) covalent geometry : angle 0.53688 (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 218 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 1.594 Fit side-chains revert: symmetry clash REVERT: A 203 TRP cc_start: 0.6542 (m100) cc_final: 0.5891 (m100) REVERT: A 243 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8246 (tp40) REVERT: A 279 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6449 (mmt-90) REVERT: A 314 PHE cc_start: 0.6448 (t80) cc_final: 0.4963 (t80) REVERT: A 354 LYS cc_start: 0.8427 (tttt) cc_final: 0.7886 (mmtp) REVERT: A 539 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6952 (p0) REVERT: A 694 LYS cc_start: 0.8048 (mttt) cc_final: 0.6865 (pttp) REVERT: A 1159 LEU cc_start: 0.8363 (mt) cc_final: 0.8078 (mm) REVERT: A 1290 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7150 (m-30) REVERT: A 1339 ARG cc_start: 0.8189 (mmt90) cc_final: 0.7403 (mtm-85) REVERT: A 1378 ASP cc_start: 0.7354 (p0) cc_final: 0.6949 (m-30) REVERT: B 187 MET cc_start: 0.3766 (OUTLIER) cc_final: 0.3465 (mpp) REVERT: C 170 MET cc_start: 0.8347 (mtp) cc_final: 0.8053 (mtp) REVERT: D 170 MET cc_start: 0.6677 (mmm) cc_final: 0.6262 (mmm) outliers start: 45 outliers final: 25 residues processed: 205 average time/residue: 1.1591 time to fit residues: 263.3901 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 : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL 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 279 ARG 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 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 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 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: 1.9990 chunk 6 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 161 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN A1304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.165861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.136886 restraints weight = 15395.087| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.59 r_work: 0.3447 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3886 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= 0.124 Angle : 0.506 9.265 18666 Z= 0.265 Chirality : 0.039 0.184 2154 Planarity : 0.004 0.050 2347 Dihedral : 4.044 19.897 1859 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.60 % Favored : 97.34 % Rotamer: Outliers : 2.42 % Allowed : 14.64 % Favored : 82.94 % 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: 1.54 (0.21), residues: 1657 helix: 1.65 (0.17), residues: 971 sheet: -0.23 (0.64), residues: 73 loop : 0.31 (0.27), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 932 HIS 0.003 0.001 HIS A 773 PHE 0.019 0.002 PHE A 704 TYR 0.017 0.001 TYR A 746 ARG 0.006 0.000 ARG A 511 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 782) hydrogen bonds : angle 4.24736 ( 2190) covalent geometry : bond 0.00277 (13806) covalent geometry : angle 0.50553 (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 216 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: A 203 TRP cc_start: 0.6506 (m100) cc_final: 0.5879 (m100) REVERT: A 243 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8259 (tp40) REVERT: A 279 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6605 (mmt-90) REVERT: A 314 PHE cc_start: 0.6435 (t80) cc_final: 0.5055 (t80) REVERT: A 335 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7945 (t) REVERT: A 354 LYS cc_start: 0.8435 (tttt) cc_final: 0.7974 (mmtp) REVERT: A 359 SER cc_start: 0.8435 (t) cc_final: 0.8135 (m) REVERT: A 694 LYS cc_start: 0.8026 (mttt) cc_final: 0.6906 (pttp) REVERT: A 1290 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7191 (m-30) REVERT: A 1339 ARG cc_start: 0.8192 (mmt90) cc_final: 0.7460 (mtm-85) REVERT: B 187 MET cc_start: 0.3766 (OUTLIER) cc_final: 0.3427 (mpp) REVERT: C 170 MET cc_start: 0.8333 (mtp) cc_final: 0.8075 (mtp) REVERT: D 170 MET cc_start: 0.6758 (mmm) cc_final: 0.6351 (mmm) outliers start: 37 outliers final: 25 residues processed: 204 average time/residue: 1.1112 time to fit residues: 252.4369 Evaluate side-chains 199 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 1.543 ------------------------------------------------------------------------------- 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 279 ARG 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 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 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 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: 3.9990 chunk 13 optimal weight: 0.9980 chunk 153 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.163800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134908 restraints weight = 15415.184| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.62 r_work: 0.3422 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3910 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= 0.160 Angle : 0.549 9.396 18666 Z= 0.286 Chirality : 0.041 0.186 2154 Planarity : 0.004 0.049 2347 Dihedral : 4.158 21.165 1859 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.66 % Favored : 97.28 % Rotamer: Outliers : 2.35 % Allowed : 15.16 % Favored : 82.48 % 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: 1.36 (0.21), residues: 1657 helix: 1.51 (0.16), residues: 973 sheet: -0.27 (0.64), residues: 73 loop : 0.20 (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 0.021 0.002 TYR A 746 ARG 0.004 0.000 ARG A 396 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 782) hydrogen bonds : angle 4.33732 ( 2190) covalent geometry : bond 0.00370 (13806) covalent geometry : angle 0.54881 (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 209 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 1.683 Fit side-chains revert: symmetry clash REVERT: A 203 TRP cc_start: 0.6578 (m100) cc_final: 0.5944 (m100) REVERT: A 243 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8242 (tp40) REVERT: A 279 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6588 (mmt-90) REVERT: A 314 PHE cc_start: 0.6510 (t80) cc_final: 0.5048 (t80) REVERT: A 335 VAL cc_start: 0.8208 (OUTLIER) cc_final: 0.7945 (t) REVERT: A 354 LYS cc_start: 0.8434 (tttt) cc_final: 0.7938 (mmtp) REVERT: A 694 LYS cc_start: 0.8042 (mttt) cc_final: 0.6915 (pttp) REVERT: A 1095 LYS cc_start: 0.7655 (ptmt) cc_final: 0.7421 (pttt) REVERT: A 1290 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7171 (m-30) REVERT: A 1339 ARG cc_start: 0.8202 (mmt90) cc_final: 0.7461 (mtm-85) REVERT: A 1378 ASP cc_start: 0.7313 (p0) cc_final: 0.6968 (m-30) REVERT: B 187 MET cc_start: 0.3727 (OUTLIER) cc_final: 0.3437 (mpp) REVERT: C 170 MET cc_start: 0.8391 (mtp) cc_final: 0.8108 (mtp) REVERT: D 170 MET cc_start: 0.6667 (mmm) cc_final: 0.6228 (mmm) outliers start: 36 outliers final: 26 residues processed: 196 average time/residue: 1.1641 time to fit residues: 253.0650 Evaluate side-chains 199 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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 279 ARG 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 517 SER Chi-restraints excluded: chain A residue 536 ILE 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 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 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 78 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 150 optimal weight: 0.2980 chunk 120 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 51 optimal weight: 0.0370 overall best weight: 1.2462 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3901 r_free = 0.3901 target = 0.164703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135710 restraints weight = 15488.183| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.59 r_work: 0.3454 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13806 Z= 0.142 Angle : 0.530 9.278 18666 Z= 0.275 Chirality : 0.040 0.181 2154 Planarity : 0.004 0.049 2347 Dihedral : 4.126 20.222 1859 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.53 % Favored : 97.40 % Rotamer: Outliers : 2.42 % Allowed : 15.29 % Favored : 82.29 % 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: 1.39 (0.21), residues: 1657 helix: 1.51 (0.16), residues: 976 sheet: -0.27 (0.64), residues: 73 loop : 0.25 (0.27), residues: 608 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 0.020 0.002 TYR A 746 ARG 0.005 0.000 ARG A 511 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 782) hydrogen bonds : angle 4.30983 ( 2190) covalent geometry : bond 0.00324 (13806) covalent geometry : angle 0.52968 (18666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10087.99 seconds wall clock time: 173 minutes 23.71 seconds (10403.71 seconds total)