Starting phenix.real_space_refine on Thu Sep 18 00:03:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9muw_48649/09_2025/9muw_48649.cif Found real_map, /net/cci-nas-00/data/ceres_data/9muw_48649/09_2025/9muw_48649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9muw_48649/09_2025/9muw_48649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9muw_48649/09_2025/9muw_48649.map" model { file = "/net/cci-nas-00/data/ceres_data/9muw_48649/09_2025/9muw_48649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9muw_48649/09_2025/9muw_48649.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 79 5.16 5 C 7625 2.51 5 N 2049 2.21 5 O 2225 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11978 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9748 Classifications: {'peptide': 1208} Link IDs: {'PTRANS': 47, 'TRANS': 1160} Chain breaks: 8 Chain: "B" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 370 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "C" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 452 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "D" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 380 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "E" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 319 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "F" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 136 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "G" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 573 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Time building chain proxies: 2.86, per 1000 atoms: 0.24 Number of scatterers: 11978 At special positions: 0 Unit cell: (94.554, 102.897, 160.371, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 79 16.00 O 2225 8.00 N 2049 7.00 C 7625 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: 1.04 Conformation dependent library (CDL) restraints added in 661.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2858 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 9 sheets defined 62.7% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 23 through 33 Processing helix chain 'A' and resid 43 through 57 Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 87 through 96 removed outlier: 4.491A pdb=" N ASN A 93 " --> pdb=" O PRO A 89 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 137 removed outlier: 3.635A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LYS A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LYS A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 156 Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 166 through 189 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 231 through 255 Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.804A pdb=" N ARG A 264 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 280 removed outlier: 4.339A pdb=" N VAL A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 removed outlier: 4.141A pdb=" N ILE A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 309 through 326 removed outlier: 4.184A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 346 Processing helix chain 'A' and resid 349 through 355 Processing helix chain 'A' and resid 356 through 364 removed outlier: 4.092A pdb=" N PHE A 360 " --> pdb=" O PHE A 357 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG A 361 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 362 " --> pdb=" O PHE A 359 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE A 363 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY A 364 " --> pdb=" O ARG A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 382 removed outlier: 3.849A pdb=" N HIS A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 411 Processing helix chain 'A' and resid 425 through 434 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.684A pdb=" N LYS A 472 " --> pdb=" O MET A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 487 removed outlier: 3.571A pdb=" N TRP A 483 " --> pdb=" O LYS A 480 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ASP A 484 " --> pdb=" O ASP A 481 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 486 " --> pdb=" O TRP A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 504 through 512 Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.801A pdb=" N TYR A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 574 Processing helix chain 'A' and resid 575 through 579 Processing helix chain 'A' and resid 725 through 730 removed outlier: 3.547A pdb=" N ASN A 729 " --> pdb=" O LYS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 747 removed outlier: 4.630A pdb=" N ILE A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N PHE A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 760 removed outlier: 3.618A pdb=" N LYS A 757 " --> pdb=" O ASN A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 822 Proline residue: A 812 - end of helix removed outlier: 3.564A pdb=" N PHE A 815 " --> pdb=" O ILE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 874 Processing helix chain 'A' and resid 904 through 910 removed outlier: 3.828A pdb=" N SER A 908 " --> pdb=" O GLN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 940 Processing helix chain 'A' and resid 943 through 965 Processing helix chain 'A' and resid 972 through 981 Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 982 through 992 Processing helix chain 'A' and resid 993 through 997 Processing helix chain 'A' and resid 1014 through 1029 Processing helix chain 'A' and resid 1033 through 1042 removed outlier: 3.910A pdb=" N LEU A1037 " --> pdb=" O THR A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1056 Processing helix chain 'A' and resid 1067 through 1083 removed outlier: 4.089A pdb=" N ASN A1083 " --> pdb=" O THR A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1110 Processing helix chain 'A' and resid 1115 through 1126 Processing helix chain 'A' and resid 1131 through 1138 removed outlier: 3.601A pdb=" N LEU A1138 " --> pdb=" O ILE A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1179 removed outlier: 5.523A pdb=" N ASP A1166 " --> pdb=" O LEU A1162 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TYR A1167 " --> pdb=" O SER A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1204 Processing helix chain 'A' and resid 1204 through 1209 Processing helix chain 'A' and resid 1238 through 1242 Processing helix chain 'A' and resid 1291 through 1308 removed outlier: 3.763A pdb=" N SER A1296 " --> pdb=" O LYS A1292 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A1297 " --> pdb=" O ALA A1293 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1323 Processing helix chain 'A' and resid 1391 through 1407 removed outlier: 3.580A pdb=" N ALA A1395 " --> pdb=" O ILE A1391 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 542 through 573 removed outlier: 3.517A pdb=" N SER B 573 " --> pdb=" O GLY B 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 541 Processing helix chain 'C' and resid 542 through 578 Processing helix chain 'D' and resid 533 through 541 Processing helix chain 'D' and resid 542 through 574 removed outlier: 3.609A pdb=" N ILE D 546 " --> pdb=" O GLU D 542 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET D 574 " --> pdb=" O HIS D 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 541 Processing helix chain 'E' and resid 542 through 573 Processing helix chain 'F' and resid 602 through 607 Processing helix chain 'G' and resid 657 through 672 Processing helix chain 'G' and resid 674 through 686 Processing helix chain 'G' and resid 690 through 706 removed outlier: 3.941A pdb=" N ILE G 694 " --> pdb=" O ASN G 690 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE G 704 " --> pdb=" O THR G 700 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE G 705 " --> pdb=" O VAL G 701 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 removed outlier: 6.722A pdb=" N ILE A 21 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 388 Processing sheet with id=AA4, first strand: chain 'A' and resid 418 through 419 Processing sheet with id=AA5, first strand: chain 'A' and resid 553 through 555 Processing sheet with id=AA6, first strand: chain 'A' and resid 824 through 827 removed outlier: 3.686A pdb=" N ARG A 824 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 883 " --> pdb=" O THR A 720 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 891 Processing sheet with id=AA8, first strand: chain 'A' and resid 1113 through 1114 Processing sheet with id=AA9, first strand: chain 'A' and resid 1225 through 1230 694 hydrogen bonds defined for protein. 1983 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: 2.44 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3913 1.35 - 1.46: 2574 1.46 - 1.58: 5577 1.58 - 1.70: 0 1.70 - 1.82: 130 Bond restraints: 12194 Sorted by residual: bond pdb=" C LEU G 639 " pdb=" N PRO G 640 " ideal model delta sigma weight residual 1.334 1.362 -0.029 8.40e-03 1.42e+04 1.17e+01 bond pdb=" CB LYS D 541 " pdb=" CG LYS D 541 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.39e+00 bond pdb=" C ILE G 638 " pdb=" N LEU G 639 " ideal model delta sigma weight residual 1.331 1.355 -0.024 2.07e-02 2.33e+03 1.39e+00 bond pdb=" N LEU G 639 " pdb=" CA LEU G 639 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.41e-02 5.03e+03 1.31e+00 bond pdb=" CG LYS D 541 " pdb=" CD LYS D 541 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.30e+00 ... (remaining 12189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 16233 2.05 - 4.10: 173 4.10 - 6.15: 36 6.15 - 8.20: 9 8.20 - 10.25: 6 Bond angle restraints: 16457 Sorted by residual: angle pdb=" CB LYS D 541 " pdb=" CG LYS D 541 " pdb=" CD LYS D 541 " ideal model delta sigma weight residual 111.30 120.43 -9.13 2.30e+00 1.89e-01 1.58e+01 angle pdb=" C ILE G 638 " pdb=" N LEU G 639 " pdb=" CA LEU G 639 " ideal model delta sigma weight residual 121.80 129.97 -8.17 2.44e+00 1.68e-01 1.12e+01 angle pdb=" N ASP A 195 " pdb=" CA ASP A 195 " pdb=" C ASP A 195 " ideal model delta sigma weight residual 108.34 112.59 -4.25 1.31e+00 5.83e-01 1.05e+01 angle pdb=" N GLY A1129 " pdb=" CA GLY A1129 " pdb=" C GLY A1129 " ideal model delta sigma weight residual 113.18 105.50 7.68 2.37e+00 1.78e-01 1.05e+01 angle pdb=" CA THR A1128 " pdb=" CB THR A1128 " pdb=" CG2 THR A1128 " ideal model delta sigma weight residual 110.50 115.99 -5.49 1.70e+00 3.46e-01 1.04e+01 ... (remaining 16452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6455 17.76 - 35.52: 726 35.52 - 53.28: 258 53.28 - 71.04: 33 71.04 - 88.80: 18 Dihedral angle restraints: 7490 sinusoidal: 3106 harmonic: 4384 Sorted by residual: dihedral pdb=" CA THR A1128 " pdb=" C THR A1128 " pdb=" N GLY A1129 " pdb=" CA GLY A1129 " ideal model delta harmonic sigma weight residual -180.00 -153.36 -26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA SER A1126 " pdb=" C SER A1126 " pdb=" N LEU A1127 " pdb=" CA LEU A1127 " ideal model delta harmonic sigma weight residual 180.00 160.07 19.93 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLY A1129 " pdb=" C GLY A1129 " pdb=" N ALA A1130 " pdb=" CA ALA A1130 " ideal model delta harmonic sigma weight residual 180.00 162.53 17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 7487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1705 0.072 - 0.144: 167 0.144 - 0.217: 4 0.217 - 0.289: 1 0.289 - 0.361: 2 Chirality restraints: 1879 Sorted by residual: chirality pdb=" CB ILE F 598 " pdb=" CA ILE F 598 " pdb=" CG1 ILE F 598 " pdb=" CG2 ILE F 598 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CB THR A1128 " pdb=" CA THR A1128 " pdb=" OG1 THR A1128 " pdb=" CG2 THR A1128 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CG LEU D 557 " pdb=" CB LEU D 557 " pdb=" CD1 LEU D 557 " pdb=" CD2 LEU D 557 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 1876 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 535 " 0.018 2.00e-02 2.50e+03 2.46e-02 9.06e+00 pdb=" CG HIS D 535 " -0.051 2.00e-02 2.50e+03 pdb=" ND1 HIS D 535 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 HIS D 535 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 HIS D 535 " 0.008 2.00e-02 2.50e+03 pdb=" NE2 HIS D 535 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 211 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO A 212 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 231 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO A 232 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " -0.019 5.00e-02 4.00e+02 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 218 2.69 - 3.24: 11742 3.24 - 3.79: 19221 3.79 - 4.35: 25671 4.35 - 4.90: 42905 Nonbonded interactions: 99757 Sorted by model distance: nonbonded pdb=" OD1 ASN B 561 " pdb=" OG1 THR C 560 " model vdw 2.136 3.040 nonbonded pdb=" OD1 ASN A 346 " pdb=" OG1 THR G 670 " model vdw 2.153 3.040 nonbonded pdb=" O LEU A1092 " pdb=" NH2 ARG A1131 " model vdw 2.211 3.120 nonbonded pdb=" OH TYR A 523 " pdb=" OD2 ASP A 532 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR A 32 " pdb=" O GLU A 490 " model vdw 2.262 3.040 ... (remaining 99752 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 'B' and resid 538 through 578) selection = (chain 'D' and resid 538 through 578) selection = chain 'E' } 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: 6.060 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 13.290 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 0.002 0.046 12194 Z= 0.120 Angle : 0.590 10.251 16457 Z= 0.299 Chirality : 0.043 0.361 1879 Planarity : 0.004 0.038 2084 Dihedral : 17.210 88.800 4632 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.94 % Favored : 96.78 % Rotamer: Outliers : 0.37 % Allowed : 28.18 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.23), residues: 1461 helix: 1.89 (0.18), residues: 852 sheet: 0.41 (0.57), residues: 84 loop : -0.12 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 824 TYR 0.015 0.001 TYR A1167 PHE 0.019 0.001 PHE A 399 TRP 0.008 0.001 TRP A 754 HIS 0.030 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00247 (12194) covalent geometry : angle 0.58958 (16457) hydrogen bonds : bond 0.13560 ( 694) hydrogen bonds : angle 5.47834 ( 1983) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 175 time to evaluate : 0.560 Fit side-chains REVERT: A 48 GLU cc_start: 0.8231 (tp30) cc_final: 0.7941 (tp30) REVERT: A 51 ARG cc_start: 0.7905 (ttm110) cc_final: 0.7335 (mtm110) REVERT: A 81 LYS cc_start: 0.8638 (mptm) cc_final: 0.8367 (mppt) REVERT: A 289 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8228 (mtp) REVERT: A 319 MET cc_start: 0.8672 (mtp) cc_final: 0.8380 (mtp) REVERT: A 336 MET cc_start: 0.6661 (ptp) cc_final: 0.6395 (ptt) REVERT: A 361 ARG cc_start: 0.8565 (mtm-85) cc_final: 0.7529 (mtp85) REVERT: A 436 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7220 (tm-30) REVERT: A 442 ASP cc_start: 0.8071 (m-30) cc_final: 0.7729 (m-30) REVERT: A 504 ARG cc_start: 0.7636 (mtm-85) cc_final: 0.7416 (mtm-85) REVERT: A 511 ASN cc_start: 0.7784 (m-40) cc_final: 0.7108 (t0) REVERT: A 743 ASP cc_start: 0.7709 (m-30) cc_final: 0.7480 (m-30) REVERT: A 783 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8047 (mttt) REVERT: A 820 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8091 (mt-10) REVERT: A 857 LYS cc_start: 0.7378 (mtmm) cc_final: 0.6884 (mmtt) REVERT: A 893 LYS cc_start: 0.7728 (tppt) cc_final: 0.7246 (mptt) REVERT: A 894 LYS cc_start: 0.8487 (mttt) cc_final: 0.8149 (mtpt) REVERT: A 929 ASN cc_start: 0.7359 (t0) cc_final: 0.7030 (m110) REVERT: A 972 THR cc_start: 0.8050 (p) cc_final: 0.7817 (p) REVERT: A 1034 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7567 (mm-30) REVERT: A 1075 ILE cc_start: 0.7463 (mp) cc_final: 0.6922 (mp) REVERT: A 1096 LYS cc_start: 0.7215 (pttp) cc_final: 0.6929 (ptpp) REVERT: A 1253 ARG cc_start: 0.7932 (ptt180) cc_final: 0.7575 (ptp90) REVERT: A 1292 LYS cc_start: 0.8155 (tttp) cc_final: 0.6567 (pttp) REVERT: C 575 MET cc_start: 0.8033 (mtm) cc_final: 0.7506 (mmm) REVERT: E 576 ILE cc_start: 0.7703 (pp) cc_final: 0.7445 (pt) outliers start: 5 outliers final: 3 residues processed: 178 average time/residue: 0.6393 time to fit residues: 122.9548 Evaluate side-chains 159 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 155 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1291 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN A 514 ASN A 534 GLN A 968 ASN A 981 ASN ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.140664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.111256 restraints weight = 14442.688| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.98 r_work: 0.3155 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12194 Z= 0.195 Angle : 0.616 10.961 16457 Z= 0.314 Chirality : 0.044 0.239 1879 Planarity : 0.004 0.040 2084 Dihedral : 5.546 119.777 1612 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.08 % Favored : 96.65 % Rotamer: Outliers : 5.65 % Allowed : 21.93 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.23), residues: 1461 helix: 1.71 (0.18), residues: 864 sheet: -0.01 (0.54), residues: 90 loop : -0.11 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 824 TYR 0.016 0.002 TYR A 529 PHE 0.022 0.002 PHE A 399 TRP 0.020 0.002 TRP A1248 HIS 0.008 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00478 (12194) covalent geometry : angle 0.61641 (16457) hydrogen bonds : bond 0.04653 ( 694) hydrogen bonds : angle 4.45928 ( 1983) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 169 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8340 (tp30) cc_final: 0.7959 (tp30) REVERT: A 51 ARG cc_start: 0.7987 (ttm110) cc_final: 0.7412 (mtm110) REVERT: A 291 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: A 319 MET cc_start: 0.8763 (mtp) cc_final: 0.8482 (mtp) REVERT: A 333 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7371 (mp) REVERT: A 336 MET cc_start: 0.6990 (ptp) cc_final: 0.6591 (ptt) REVERT: A 357 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.7742 (m-80) REVERT: A 361 ARG cc_start: 0.8600 (mtm-85) cc_final: 0.7528 (mtp85) REVERT: A 436 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7372 (tm-30) REVERT: A 507 ASP cc_start: 0.7455 (t0) cc_final: 0.7215 (t0) REVERT: A 511 ASN cc_start: 0.7811 (m-40) cc_final: 0.7128 (t0) REVERT: A 743 ASP cc_start: 0.8004 (m-30) cc_final: 0.7575 (m-30) REVERT: A 782 GLU cc_start: 0.8203 (mp0) cc_final: 0.7977 (mp0) REVERT: A 783 LYS cc_start: 0.8632 (mtpp) cc_final: 0.8157 (mttt) REVERT: A 857 LYS cc_start: 0.7584 (mtmm) cc_final: 0.6966 (mmtt) REVERT: A 893 LYS cc_start: 0.7890 (tppt) cc_final: 0.7329 (mptt) REVERT: A 894 LYS cc_start: 0.8508 (mttt) cc_final: 0.8090 (mttt) REVERT: A 929 ASN cc_start: 0.7450 (t0) cc_final: 0.7099 (m110) REVERT: A 1032 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.7986 (mtp) REVERT: A 1096 LYS cc_start: 0.7161 (pttp) cc_final: 0.6942 (ptpp) REVERT: A 1253 ARG cc_start: 0.7975 (ptt180) cc_final: 0.7565 (ptm160) REVERT: A 1392 TYR cc_start: 0.6426 (OUTLIER) cc_final: 0.6033 (m-80) REVERT: A 1415 ASP cc_start: 0.7981 (p0) cc_final: 0.7775 (p0) REVERT: C 575 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7633 (mtm) REVERT: E 554 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6774 (m-30) REVERT: E 559 LYS cc_start: 0.8242 (mtpp) cc_final: 0.8039 (mtpt) REVERT: G 641 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.6106 (mm-30) outliers start: 76 outliers final: 26 residues processed: 223 average time/residue: 0.5402 time to fit residues: 131.5921 Evaluate side-chains 196 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1392 TYR Chi-restraints excluded: chain A residue 1428 CYS Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 642 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 53 optimal weight: 0.0980 chunk 74 optimal weight: 0.0020 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 115 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 82 optimal weight: 0.1980 chunk 14 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 GLN A1174 ASN ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.143806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.114767 restraints weight = 14455.305| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.97 r_work: 0.3181 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12194 Z= 0.112 Angle : 0.542 9.327 16457 Z= 0.276 Chirality : 0.041 0.253 1879 Planarity : 0.004 0.039 2084 Dihedral : 4.083 26.944 1605 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.67 % Favored : 97.06 % Rotamer: Outliers : 4.54 % Allowed : 23.35 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.23), residues: 1461 helix: 1.92 (0.18), residues: 868 sheet: 0.24 (0.56), residues: 90 loop : -0.04 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 504 TYR 0.011 0.001 TYR A 284 PHE 0.018 0.001 PHE A 399 TRP 0.014 0.001 TRP A1248 HIS 0.005 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00244 (12194) covalent geometry : angle 0.54185 (16457) hydrogen bonds : bond 0.03732 ( 694) hydrogen bonds : angle 4.15143 ( 1983) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 172 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8354 (tp30) cc_final: 0.8001 (tp30) REVERT: A 51 ARG cc_start: 0.7907 (ttm110) cc_final: 0.7327 (mtm110) REVERT: A 291 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: A 319 MET cc_start: 0.8762 (mtp) cc_final: 0.8386 (mtp) REVERT: A 336 MET cc_start: 0.6807 (ptp) cc_final: 0.6438 (ptt) REVERT: A 357 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.7358 (m-80) REVERT: A 361 ARG cc_start: 0.8563 (mtm-85) cc_final: 0.7490 (mtp85) REVERT: A 436 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: A 507 ASP cc_start: 0.7392 (t0) cc_final: 0.7121 (t0) REVERT: A 511 ASN cc_start: 0.7841 (m-40) cc_final: 0.7139 (t0) REVERT: A 534 GLN cc_start: 0.7679 (mt0) cc_final: 0.7456 (mm-40) REVERT: A 743 ASP cc_start: 0.7939 (m-30) cc_final: 0.7663 (m-30) REVERT: A 782 GLU cc_start: 0.8182 (mp0) cc_final: 0.7845 (mp0) REVERT: A 783 LYS cc_start: 0.8605 (mtpp) cc_final: 0.8127 (mttt) REVERT: A 857 LYS cc_start: 0.7461 (mtmm) cc_final: 0.6863 (mmtt) REVERT: A 893 LYS cc_start: 0.7877 (tppt) cc_final: 0.7307 (mptt) REVERT: A 894 LYS cc_start: 0.8485 (mttt) cc_final: 0.8081 (mtpt) REVERT: A 929 ASN cc_start: 0.7433 (t0) cc_final: 0.7057 (m110) REVERT: A 1041 MET cc_start: 0.8813 (mmt) cc_final: 0.8426 (mmt) REVERT: A 1253 ARG cc_start: 0.7868 (ptt180) cc_final: 0.7522 (ptp90) REVERT: A 1392 TYR cc_start: 0.6464 (OUTLIER) cc_final: 0.6130 (m-80) REVERT: B 581 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7600 (mmtm) REVERT: C 575 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7552 (mtm) REVERT: E 554 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6783 (m-30) REVERT: G 706 ASP cc_start: 0.5957 (m-30) cc_final: 0.5747 (m-30) outliers start: 61 outliers final: 19 residues processed: 212 average time/residue: 0.5877 time to fit residues: 135.5957 Evaluate side-chains 193 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1392 TYR Chi-restraints excluded: chain A residue 1428 CYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 642 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 117 optimal weight: 0.4980 chunk 120 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111985 restraints weight = 14413.024| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.99 r_work: 0.3158 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12194 Z= 0.152 Angle : 0.568 9.929 16457 Z= 0.288 Chirality : 0.043 0.261 1879 Planarity : 0.004 0.043 2084 Dihedral : 4.107 26.225 1604 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.87 % Favored : 96.85 % Rotamer: Outliers : 4.83 % Allowed : 23.42 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.23), residues: 1461 helix: 1.85 (0.18), residues: 873 sheet: 0.25 (0.57), residues: 90 loop : -0.06 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 504 TYR 0.013 0.001 TYR A 284 PHE 0.020 0.002 PHE A 399 TRP 0.016 0.001 TRP A1248 HIS 0.004 0.001 HIS A1423 Details of bonding type rmsd covalent geometry : bond 0.00368 (12194) covalent geometry : angle 0.56836 (16457) hydrogen bonds : bond 0.03916 ( 694) hydrogen bonds : angle 4.15182 ( 1983) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 175 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8381 (tp30) cc_final: 0.7945 (tp30) REVERT: A 51 ARG cc_start: 0.7921 (ttm110) cc_final: 0.7345 (mtm110) REVERT: A 289 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.7953 (mpp) REVERT: A 291 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: A 319 MET cc_start: 0.8783 (mtp) cc_final: 0.8375 (mtp) REVERT: A 333 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7399 (mp) REVERT: A 336 MET cc_start: 0.6939 (ptp) cc_final: 0.6518 (ptt) REVERT: A 361 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.7506 (mtp85) REVERT: A 436 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: A 507 ASP cc_start: 0.7378 (t0) cc_final: 0.7117 (t0) REVERT: A 511 ASN cc_start: 0.7867 (m-40) cc_final: 0.6925 (t0) REVERT: A 534 GLN cc_start: 0.7688 (mt0) cc_final: 0.7461 (mm-40) REVERT: A 743 ASP cc_start: 0.7985 (m-30) cc_final: 0.7539 (m-30) REVERT: A 782 GLU cc_start: 0.8241 (mp0) cc_final: 0.7879 (mp0) REVERT: A 783 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8175 (mttt) REVERT: A 857 LYS cc_start: 0.7539 (mtmm) cc_final: 0.6936 (mmtt) REVERT: A 893 LYS cc_start: 0.7850 (tppt) cc_final: 0.7280 (mptt) REVERT: A 894 LYS cc_start: 0.8491 (mttt) cc_final: 0.8048 (mttt) REVERT: A 929 ASN cc_start: 0.7429 (t0) cc_final: 0.7024 (m110) REVERT: A 1102 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8083 (tt) REVERT: A 1253 ARG cc_start: 0.7897 (ptt180) cc_final: 0.7538 (ptp90) REVERT: A 1392 TYR cc_start: 0.6695 (OUTLIER) cc_final: 0.6115 (m-80) REVERT: B 581 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7683 (mmtm) REVERT: C 571 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8100 (mm) REVERT: C 575 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7614 (mtm) REVERT: E 554 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6758 (m-30) REVERT: G 641 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.6050 (mm-30) REVERT: G 706 ASP cc_start: 0.6012 (m-30) cc_final: 0.5810 (m-30) outliers start: 65 outliers final: 27 residues processed: 215 average time/residue: 0.5584 time to fit residues: 131.1975 Evaluate side-chains 205 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1392 TYR Chi-restraints excluded: chain A residue 1428 CYS Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 642 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 147 ASN A 427 HIS ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** 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 = 0.3609 r_free = 0.3609 target = 0.138457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.109232 restraints weight = 14686.863| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.01 r_work: 0.3096 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12194 Z= 0.219 Angle : 0.636 11.384 16457 Z= 0.320 Chirality : 0.045 0.275 1879 Planarity : 0.004 0.047 2084 Dihedral : 4.345 27.182 1604 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.35 % Favored : 96.37 % Rotamer: Outliers : 6.02 % Allowed : 22.68 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.22), residues: 1461 helix: 1.72 (0.18), residues: 863 sheet: 0.07 (0.55), residues: 90 loop : -0.11 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 504 TYR 0.017 0.002 TYR A 529 PHE 0.019 0.002 PHE A 399 TRP 0.018 0.002 TRP A1248 HIS 0.006 0.001 HIS A 778 Details of bonding type rmsd covalent geometry : bond 0.00541 (12194) covalent geometry : angle 0.63565 (16457) hydrogen bonds : bond 0.04333 ( 694) hydrogen bonds : angle 4.27333 ( 1983) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 178 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8379 (tp30) cc_final: 0.8003 (tp30) REVERT: A 51 ARG cc_start: 0.7951 (ttm110) cc_final: 0.7381 (mtm110) REVERT: A 202 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7136 (mtt90) REVERT: A 204 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8052 (pttm) REVERT: A 291 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: A 306 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7120 (tt) REVERT: A 333 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7463 (mp) REVERT: A 361 ARG cc_start: 0.8605 (mtm-85) cc_final: 0.7514 (mtp85) REVERT: A 436 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: A 507 ASP cc_start: 0.7487 (t0) cc_final: 0.7212 (t0) REVERT: A 511 ASN cc_start: 0.8011 (m-40) cc_final: 0.7301 (t0) REVERT: A 534 GLN cc_start: 0.7770 (mt0) cc_final: 0.7533 (mm-40) REVERT: A 735 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7626 (tpt) REVERT: A 782 GLU cc_start: 0.8324 (mp0) cc_final: 0.8075 (mp0) REVERT: A 783 LYS cc_start: 0.8635 (mtpp) cc_final: 0.8167 (mttt) REVERT: A 857 LYS cc_start: 0.7642 (mtmm) cc_final: 0.6950 (mmtt) REVERT: A 864 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7959 (pp20) REVERT: A 893 LYS cc_start: 0.7880 (tppt) cc_final: 0.7319 (mptt) REVERT: A 894 LYS cc_start: 0.8558 (mttt) cc_final: 0.8126 (mttt) REVERT: A 929 ASN cc_start: 0.7438 (t0) cc_final: 0.7078 (m110) REVERT: A 1253 ARG cc_start: 0.7926 (ptt180) cc_final: 0.7570 (ptm160) REVERT: A 1392 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.6550 (m-80) REVERT: B 581 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7707 (mmtm) REVERT: C 575 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7706 (mtm) REVERT: E 554 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.6767 (m-30) REVERT: E 559 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7912 (mtpt) REVERT: G 641 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.5951 (mm-30) REVERT: G 669 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6659 (mtt90) outliers start: 81 outliers final: 33 residues processed: 232 average time/residue: 0.5572 time to fit residues: 141.5723 Evaluate side-chains 219 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1392 TYR Chi-restraints excluded: chain A residue 1428 CYS Chi-restraints excluded: chain A residue 1438 GLN Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain G residue 638 ILE Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 642 LEU Chi-restraints excluded: chain G residue 669 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 58 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 858 GLN ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.140263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110887 restraints weight = 14399.831| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.98 r_work: 0.3136 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12194 Z= 0.151 Angle : 0.590 10.362 16457 Z= 0.297 Chirality : 0.043 0.279 1879 Planarity : 0.004 0.046 2084 Dihedral : 4.257 27.714 1604 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.22 % Favored : 96.51 % Rotamer: Outliers : 5.43 % Allowed : 24.39 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.23), residues: 1461 helix: 1.75 (0.18), residues: 875 sheet: 0.03 (0.56), residues: 90 loop : -0.19 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 504 TYR 0.014 0.001 TYR A 284 PHE 0.033 0.002 PHE A 553 TRP 0.015 0.001 TRP A1248 HIS 0.004 0.001 HIS A1029 Details of bonding type rmsd covalent geometry : bond 0.00368 (12194) covalent geometry : angle 0.59039 (16457) hydrogen bonds : bond 0.03917 ( 694) hydrogen bonds : angle 4.16120 ( 1983) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 177 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8379 (tp30) cc_final: 0.7978 (tp30) REVERT: A 51 ARG cc_start: 0.7918 (ttm110) cc_final: 0.7352 (mtm110) REVERT: A 202 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7176 (mtt90) REVERT: A 204 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7991 (pttm) REVERT: A 289 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.7831 (mpp) REVERT: A 291 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: A 361 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.7487 (mtp85) REVERT: A 436 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7187 (tm-30) REVERT: A 507 ASP cc_start: 0.7443 (t0) cc_final: 0.7148 (t0) REVERT: A 511 ASN cc_start: 0.8002 (m-40) cc_final: 0.7085 (t0) REVERT: A 534 GLN cc_start: 0.7725 (mt0) cc_final: 0.7487 (mm-40) REVERT: A 782 GLU cc_start: 0.8328 (mp0) cc_final: 0.7940 (mp0) REVERT: A 783 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8230 (mttt) REVERT: A 853 GLU cc_start: 0.8208 (tt0) cc_final: 0.7866 (tt0) REVERT: A 857 LYS cc_start: 0.7524 (mtmm) cc_final: 0.7043 (mmtt) REVERT: A 893 LYS cc_start: 0.7885 (tppt) cc_final: 0.7311 (mptt) REVERT: A 894 LYS cc_start: 0.8564 (mttt) cc_final: 0.8115 (mttt) REVERT: A 929 ASN cc_start: 0.7413 (t0) cc_final: 0.7052 (m110) REVERT: A 1109 MET cc_start: 0.7939 (tpt) cc_final: 0.7738 (mmt) REVERT: A 1253 ARG cc_start: 0.7896 (ptt180) cc_final: 0.7518 (ptm160) REVERT: B 581 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7707 (mmtm) REVERT: C 575 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7671 (mtm) REVERT: E 554 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6754 (m-30) REVERT: E 559 LYS cc_start: 0.8131 (mtpp) cc_final: 0.7925 (mtpt) REVERT: G 669 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6625 (mtt90) outliers start: 73 outliers final: 38 residues processed: 225 average time/residue: 0.5756 time to fit residues: 141.7275 Evaluate side-chains 219 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1028 ASP Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1428 CYS Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain G residue 638 ILE Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 642 LEU Chi-restraints excluded: chain G residue 669 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 118 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 143 optimal weight: 0.0050 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.141029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111680 restraints weight = 14309.740| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.98 r_work: 0.3138 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12194 Z= 0.138 Angle : 0.588 10.535 16457 Z= 0.293 Chirality : 0.043 0.285 1879 Planarity : 0.004 0.047 2084 Dihedral : 4.205 27.280 1604 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.08 % Favored : 96.65 % Rotamer: Outliers : 5.72 % Allowed : 24.61 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.23), residues: 1461 helix: 1.82 (0.18), residues: 875 sheet: 0.05 (0.56), residues: 90 loop : -0.16 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 504 TYR 0.014 0.001 TYR A 284 PHE 0.035 0.001 PHE A 553 TRP 0.014 0.001 TRP A1248 HIS 0.004 0.001 HIS A1423 Details of bonding type rmsd covalent geometry : bond 0.00332 (12194) covalent geometry : angle 0.58776 (16457) hydrogen bonds : bond 0.03807 ( 694) hydrogen bonds : angle 4.10189 ( 1983) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 177 time to evaluate : 0.512 Fit side-chains REVERT: A 48 GLU cc_start: 0.8386 (tp30) cc_final: 0.7970 (tp30) REVERT: A 51 ARG cc_start: 0.7905 (ttm110) cc_final: 0.7348 (mtm110) REVERT: A 199 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7982 (pt) REVERT: A 202 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7009 (mtt90) REVERT: A 204 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7988 (pttm) REVERT: A 289 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.7821 (mpp) REVERT: A 291 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: A 336 MET cc_start: 0.6919 (ptp) cc_final: 0.6582 (ptt) REVERT: A 357 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.7429 (m-80) REVERT: A 361 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.7480 (mtp85) REVERT: A 436 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7169 (tm-30) REVERT: A 507 ASP cc_start: 0.7454 (t0) cc_final: 0.7170 (t0) REVERT: A 511 ASN cc_start: 0.8005 (m-40) cc_final: 0.7081 (t0) REVERT: A 534 GLN cc_start: 0.7738 (mt0) cc_final: 0.7479 (mm-40) REVERT: A 782 GLU cc_start: 0.8351 (mp0) cc_final: 0.7930 (mp0) REVERT: A 783 LYS cc_start: 0.8690 (mtpp) cc_final: 0.8233 (mttt) REVERT: A 853 GLU cc_start: 0.8186 (tt0) cc_final: 0.7814 (tt0) REVERT: A 857 LYS cc_start: 0.7496 (mtmm) cc_final: 0.7023 (mmpt) REVERT: A 893 LYS cc_start: 0.7862 (tppt) cc_final: 0.7302 (mptt) REVERT: A 894 LYS cc_start: 0.8558 (mttt) cc_final: 0.8130 (mtpt) REVERT: A 929 ASN cc_start: 0.7397 (t0) cc_final: 0.7010 (m110) REVERT: A 1109 MET cc_start: 0.7947 (tpt) cc_final: 0.7729 (mmt) REVERT: A 1253 ARG cc_start: 0.7903 (ptt180) cc_final: 0.7508 (ptm160) REVERT: A 1329 ASP cc_start: 0.6161 (p0) cc_final: 0.5949 (p0) REVERT: A 1396 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.6175 (ttm) REVERT: B 581 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7706 (mmtm) REVERT: C 575 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7622 (mtm) REVERT: E 539 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6020 (pt0) REVERT: E 554 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6751 (m-30) REVERT: G 641 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.6212 (mm-30) outliers start: 77 outliers final: 37 residues processed: 226 average time/residue: 0.5770 time to fit residues: 142.7987 Evaluate side-chains 222 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 172 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1245 MET Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain A residue 1428 CYS Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain E residue 539 GLN Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain G residue 638 ILE Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 642 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 124 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 95 optimal weight: 0.0570 chunk 6 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 138 optimal weight: 0.4980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.141349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.112086 restraints weight = 14236.842| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.98 r_work: 0.3135 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12194 Z= 0.137 Angle : 0.585 12.184 16457 Z= 0.293 Chirality : 0.043 0.282 1879 Planarity : 0.004 0.049 2084 Dihedral : 4.165 27.210 1604 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.94 % Favored : 96.78 % Rotamer: Outliers : 4.91 % Allowed : 25.06 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.23), residues: 1461 helix: 1.85 (0.18), residues: 876 sheet: 0.19 (0.57), residues: 89 loop : -0.15 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 824 TYR 0.014 0.001 TYR A 284 PHE 0.037 0.002 PHE A 553 TRP 0.013 0.001 TRP A1248 HIS 0.006 0.001 HIS A 396 Details of bonding type rmsd covalent geometry : bond 0.00329 (12194) covalent geometry : angle 0.58463 (16457) hydrogen bonds : bond 0.03726 ( 694) hydrogen bonds : angle 4.05457 ( 1983) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 177 time to evaluate : 0.513 Fit side-chains REVERT: A 51 ARG cc_start: 0.7890 (ttm110) cc_final: 0.7393 (mtm110) REVERT: A 199 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7957 (pt) REVERT: A 202 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7180 (mtt90) REVERT: A 204 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7978 (pttm) REVERT: A 289 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.7794 (mpp) REVERT: A 291 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: A 336 MET cc_start: 0.6915 (ptp) cc_final: 0.6579 (ptt) REVERT: A 361 ARG cc_start: 0.8596 (mtm-85) cc_final: 0.7486 (mtp85) REVERT: A 436 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: A 507 ASP cc_start: 0.7555 (t0) cc_final: 0.7246 (t0) REVERT: A 511 ASN cc_start: 0.8015 (m-40) cc_final: 0.7086 (t0) REVERT: A 534 GLN cc_start: 0.7737 (mt0) cc_final: 0.7472 (mm-40) REVERT: A 782 GLU cc_start: 0.8355 (mp0) cc_final: 0.7936 (mp0) REVERT: A 783 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8289 (mttt) REVERT: A 853 GLU cc_start: 0.8148 (tt0) cc_final: 0.7757 (tt0) REVERT: A 857 LYS cc_start: 0.7488 (mtmm) cc_final: 0.7016 (mmpt) REVERT: A 893 LYS cc_start: 0.7830 (tppt) cc_final: 0.7290 (mptt) REVERT: A 894 LYS cc_start: 0.8550 (mttt) cc_final: 0.8141 (mtpt) REVERT: A 929 ASN cc_start: 0.7407 (t0) cc_final: 0.7014 (m110) REVERT: A 1102 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8072 (tt) REVERT: A 1253 ARG cc_start: 0.7899 (ptt180) cc_final: 0.7511 (ptm160) REVERT: A 1396 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.6152 (ttm) REVERT: A 1433 VAL cc_start: 0.6889 (OUTLIER) cc_final: 0.6398 (t) REVERT: B 581 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7721 (mmtm) REVERT: C 575 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7623 (mtm) REVERT: E 539 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6106 (pt0) REVERT: E 554 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.6749 (m-30) REVERT: E 578 ILE cc_start: 0.7160 (tt) cc_final: 0.6830 (mm) REVERT: G 641 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.6261 (mm-30) outliers start: 66 outliers final: 37 residues processed: 221 average time/residue: 0.5590 time to fit residues: 135.3604 Evaluate side-chains 223 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1245 MET Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain A residue 1428 CYS Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain E residue 539 GLN Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain G residue 638 ILE Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 642 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 9 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111917 restraints weight = 14262.683| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.98 r_work: 0.3153 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12194 Z= 0.144 Angle : 0.593 12.962 16457 Z= 0.297 Chirality : 0.043 0.290 1879 Planarity : 0.004 0.050 2084 Dihedral : 4.191 26.507 1604 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.01 % Favored : 96.71 % Rotamer: Outliers : 4.61 % Allowed : 24.98 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.23), residues: 1461 helix: 1.82 (0.18), residues: 877 sheet: 0.19 (0.57), residues: 89 loop : -0.12 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 824 TYR 0.014 0.001 TYR A 284 PHE 0.038 0.002 PHE A 553 TRP 0.015 0.001 TRP A 915 HIS 0.005 0.001 HIS A 396 Details of bonding type rmsd covalent geometry : bond 0.00347 (12194) covalent geometry : angle 0.59331 (16457) hydrogen bonds : bond 0.03774 ( 694) hydrogen bonds : angle 4.09577 ( 1983) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 175 time to evaluate : 0.580 Fit side-chains REVERT: A 51 ARG cc_start: 0.7984 (ttm110) cc_final: 0.7316 (mtm110) REVERT: A 199 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7936 (pt) REVERT: A 202 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.7188 (mtt90) REVERT: A 204 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.8000 (pttm) REVERT: A 289 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.7798 (mpp) REVERT: A 291 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: A 336 MET cc_start: 0.6921 (ptp) cc_final: 0.6584 (ptt) REVERT: A 361 ARG cc_start: 0.8603 (mtm-85) cc_final: 0.7490 (mtp85) REVERT: A 436 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: A 507 ASP cc_start: 0.7555 (t0) cc_final: 0.7249 (t0) REVERT: A 511 ASN cc_start: 0.8019 (m-40) cc_final: 0.7086 (t0) REVERT: A 534 GLN cc_start: 0.7734 (mt0) cc_final: 0.7463 (mm-40) REVERT: A 782 GLU cc_start: 0.8369 (mp0) cc_final: 0.7928 (mp0) REVERT: A 783 LYS cc_start: 0.8761 (mtpp) cc_final: 0.8320 (mttt) REVERT: A 853 GLU cc_start: 0.8147 (tt0) cc_final: 0.7765 (tt0) REVERT: A 857 LYS cc_start: 0.7480 (mtmm) cc_final: 0.7014 (mmpt) REVERT: A 893 LYS cc_start: 0.7846 (tppt) cc_final: 0.7315 (mptt) REVERT: A 894 LYS cc_start: 0.8530 (mttt) cc_final: 0.8122 (mtpt) REVERT: A 929 ASN cc_start: 0.7414 (t0) cc_final: 0.7022 (m110) REVERT: A 1253 ARG cc_start: 0.7906 (ptt180) cc_final: 0.7520 (ptm160) REVERT: A 1396 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.6155 (ttm) REVERT: A 1433 VAL cc_start: 0.6857 (OUTLIER) cc_final: 0.6362 (t) REVERT: B 581 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7731 (mmtm) REVERT: C 575 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7621 (mtm) REVERT: E 539 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6138 (pt0) REVERT: E 554 ASP cc_start: 0.7152 (OUTLIER) cc_final: 0.6750 (m-30) REVERT: E 578 ILE cc_start: 0.7142 (tt) cc_final: 0.6778 (mm) REVERT: G 641 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.6315 (mm-30) outliers start: 62 outliers final: 33 residues processed: 219 average time/residue: 0.5660 time to fit residues: 135.9175 Evaluate side-chains 216 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain A residue 1428 CYS Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain E residue 539 GLN Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain G residue 638 ILE Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 642 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 27 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 115 optimal weight: 0.0770 chunk 14 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.142299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113030 restraints weight = 14392.408| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.99 r_work: 0.3149 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12194 Z= 0.127 Angle : 0.596 12.937 16457 Z= 0.297 Chirality : 0.042 0.280 1879 Planarity : 0.004 0.051 2084 Dihedral : 4.120 26.742 1604 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.87 % Favored : 96.85 % Rotamer: Outliers : 3.35 % Allowed : 26.39 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.23), residues: 1461 helix: 1.91 (0.18), residues: 875 sheet: 0.22 (0.57), residues: 89 loop : -0.07 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 824 TYR 0.013 0.001 TYR A 284 PHE 0.038 0.002 PHE A 553 TRP 0.019 0.001 TRP A 915 HIS 0.004 0.001 HIS A1423 Details of bonding type rmsd covalent geometry : bond 0.00302 (12194) covalent geometry : angle 0.59568 (16457) hydrogen bonds : bond 0.03608 ( 694) hydrogen bonds : angle 4.03943 ( 1983) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.499 Fit side-chains REVERT: A 51 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7450 (mtm110) REVERT: A 81 LYS cc_start: 0.8805 (mppt) cc_final: 0.8302 (mmmm) REVERT: A 199 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7854 (pt) REVERT: A 202 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7192 (mtt90) REVERT: A 204 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7992 (pttm) REVERT: A 291 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: A 336 MET cc_start: 0.6921 (ptp) cc_final: 0.6585 (ptt) REVERT: A 361 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.7494 (mtp85) REVERT: A 436 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: A 507 ASP cc_start: 0.7555 (t0) cc_final: 0.7263 (t0) REVERT: A 511 ASN cc_start: 0.8010 (m-40) cc_final: 0.7103 (t0) REVERT: A 534 GLN cc_start: 0.7705 (mt0) cc_final: 0.7437 (mm-40) REVERT: A 782 GLU cc_start: 0.8368 (mp0) cc_final: 0.7939 (mp0) REVERT: A 783 LYS cc_start: 0.8758 (mtpp) cc_final: 0.8311 (mttt) REVERT: A 853 GLU cc_start: 0.8128 (tt0) cc_final: 0.7768 (tt0) REVERT: A 857 LYS cc_start: 0.7429 (mtmm) cc_final: 0.7001 (mmpt) REVERT: A 893 LYS cc_start: 0.7849 (tppt) cc_final: 0.7319 (mptt) REVERT: A 894 LYS cc_start: 0.8528 (mttt) cc_final: 0.8141 (mtpt) REVERT: A 929 ASN cc_start: 0.7402 (t0) cc_final: 0.7008 (m110) REVERT: A 1253 ARG cc_start: 0.7963 (ptt180) cc_final: 0.7557 (ptm160) REVERT: A 1396 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.6392 (ttm) REVERT: A 1433 VAL cc_start: 0.6832 (OUTLIER) cc_final: 0.6381 (t) REVERT: B 581 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7716 (mmtm) REVERT: C 575 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7600 (mtm) REVERT: E 539 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6136 (pt0) REVERT: E 554 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6729 (m-30) REVERT: E 578 ILE cc_start: 0.7106 (tt) cc_final: 0.6793 (mm) outliers start: 45 outliers final: 23 residues processed: 204 average time/residue: 0.5610 time to fit residues: 125.0453 Evaluate side-chains 204 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain A residue 1428 CYS Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain E residue 539 GLN Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain G residue 639 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 59 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 0.0980 chunk 40 optimal weight: 0.0470 chunk 26 optimal weight: 0.0370 chunk 135 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.143865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114767 restraints weight = 14254.642| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.97 r_work: 0.3194 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12194 Z= 0.113 Angle : 0.573 12.716 16457 Z= 0.286 Chirality : 0.041 0.271 1879 Planarity : 0.004 0.051 2084 Dihedral : 4.032 26.138 1604 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.94 % Favored : 96.78 % Rotamer: Outliers : 2.38 % Allowed : 27.21 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.23), residues: 1461 helix: 2.09 (0.18), residues: 864 sheet: 0.36 (0.56), residues: 93 loop : -0.05 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 824 TYR 0.012 0.001 TYR A 284 PHE 0.037 0.001 PHE A 553 TRP 0.025 0.001 TRP A 915 HIS 0.005 0.001 HIS A1423 Details of bonding type rmsd covalent geometry : bond 0.00260 (12194) covalent geometry : angle 0.57284 (16457) hydrogen bonds : bond 0.03427 ( 694) hydrogen bonds : angle 3.95072 ( 1983) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4432.32 seconds wall clock time: 76 minutes 33.04 seconds (4593.04 seconds total)