Starting phenix.real_space_refine on Wed Jun 11 16:09:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iva_60923/06_2025/9iva_60923.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iva_60923/06_2025/9iva_60923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iva_60923/06_2025/9iva_60923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iva_60923/06_2025/9iva_60923.map" model { file = "/net/cci-nas-00/data/ceres_data/9iva_60923/06_2025/9iva_60923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iva_60923/06_2025/9iva_60923.cif" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 83 5.16 5 C 8227 2.51 5 N 2222 2.21 5 O 2410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12944 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10269 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1275, 10260 Classifications: {'peptide': 1275} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 1226} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1275, 10260 Classifications: {'peptide': 1275} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 1226} Chain breaks: 4 bond proxies already assigned to first conformer: 10458 Chain: "B" Number of atoms: 1215 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 151, 1212 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 151, 1212 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 bond proxies already assigned to first conformer: 1217 Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "D" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 558 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "E" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 463 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8540 SG CYS A1191 46.188 29.703 25.478 1.00110.13 S ATOM 10095 SG CYS A1428 41.689 30.009 26.167 1.00135.27 S ATOM 10101 SG CYS A1429 45.033 30.483 27.696 1.00128.61 S ATOM 8890 SG CYS A1236 26.566 28.786 33.344 1.00101.48 S ATOM 8913 SG CYS A1239 27.255 25.349 34.924 1.00101.22 S Time building chain proxies: 13.00, per 1000 atoms: 1.00 Number of scatterers: 12944 At special positions: 0 Unit cell: (96.725, 109.5, 168.813, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 83 16.00 O 2410 8.00 N 2222 7.00 C 8227 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1191 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1428 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1429 " pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" NE2 HIS A1423 " pdb="ZN ZN A2302 " - pdb=" ND1 HIS A1421 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1239 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1236 " Number of angles added : 1 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3086 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 7 sheets defined 61.6% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.866A pdb=" N LEU A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.532A pdb=" N SER A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 104 through 137 removed outlier: 3.734A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LYS A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LYS A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 155 Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 166 through 189 removed outlier: 3.632A pdb=" N LYS A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 193 removed outlier: 3.971A pdb=" N ARG A 193 " --> pdb=" O PRO A 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 190 through 193' Processing helix chain 'A' and resid 231 through 255 Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.879A pdb=" N ARG A 264 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 280 removed outlier: 4.415A pdb=" N VAL A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 288 removed outlier: 3.981A 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 304 through 308 Processing helix chain 'A' and resid 309 through 327 removed outlier: 3.932A 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 359 removed outlier: 3.743A pdb=" N PHE A 359 " --> pdb=" O PHE A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 359' Processing helix chain 'A' and resid 369 through 382 removed outlier: 3.555A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 410 removed outlier: 3.713A pdb=" N ARG A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 479 through 487 removed outlier: 3.648A pdb=" N TRP A 483 " --> pdb=" O LYS A 480 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASP A 484 " --> pdb=" O ASP A 481 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A 486 " --> pdb=" O TRP A 483 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 487 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 511 removed outlier: 3.574A pdb=" N ASN A 511 " --> pdb=" O ASP A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.700A 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 580 removed outlier: 3.613A pdb=" N LYS A 580 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 731 through 747 removed outlier: 4.824A pdb=" N ILE A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N PHE A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 760 removed outlier: 3.774A 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 Processing helix chain 'A' and resid 847 through 873 Processing helix chain 'A' and resid 904 through 910 removed outlier: 3.886A 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: 3.854A 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: 3.707A pdb=" N ASN A1083 " --> pdb=" O THR A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1091 removed outlier: 4.587A pdb=" N GLY A1091 " --> pdb=" O PRO A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1110 Processing helix chain 'A' and resid 1115 through 1124 Processing helix chain 'A' and resid 1126 through 1137 Processing helix chain 'A' and resid 1155 through 1179 removed outlier: 5.453A pdb=" N ASP A1166 " --> pdb=" O LEU A1162 " (cutoff:3.500A) removed outlier: 5.561A 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 1220 through 1224 Processing helix chain 'A' and resid 1236 through 1242 removed outlier: 3.609A pdb=" N GLY A1242 " --> pdb=" O ILE A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1309 Processing helix chain 'A' and resid 1312 through 1324 removed outlier: 3.999A pdb=" N GLN A1324 " --> pdb=" O TYR A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1337 Processing helix chain 'A' and resid 1391 through 1407 Processing helix chain 'B' and resid 526 through 542 Processing helix chain 'B' and resid 542 through 574 removed outlier: 4.064A pdb=" N ILE B 546 " --> pdb=" O GLU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 609 removed outlier: 3.536A pdb=" N PHE B 609 " --> pdb=" O GLN B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 672 Processing helix chain 'B' and resid 674 through 688 Processing helix chain 'B' and resid 690 through 707 removed outlier: 3.730A pdb=" N ILE B 694 " --> pdb=" O ASN B 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 541 Processing helix chain 'C' and resid 542 through 574 Processing helix chain 'D' and resid 526 through 541 Processing helix chain 'D' and resid 542 through 578 Processing helix chain 'E' and resid 526 through 541 Processing helix chain 'E' and resid 542 through 573 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA2, first strand: chain 'A' and resid 385 through 388 removed outlier: 8.539A pdb=" N MET E 575 " --> pdb=" O LEU B 594 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N MET E 577 " --> pdb=" O PRO B 596 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE B 598 " --> pdb=" O MET E 577 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 419 Processing sheet with id=AA4, first strand: chain 'A' and resid 553 through 556 removed outlier: 3.698A pdb=" N PHE A 553 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL A 537 " --> pdb=" O VAL A 763 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 765 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 824 through 827 removed outlier: 3.646A pdb=" N ARG A 824 " --> pdb=" O THR A 839 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 888 through 891 Processing sheet with id=AA7, first strand: chain 'A' and resid 1225 through 1231 740 hydrogen bonds defined for protein. 2126 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: 4.69 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4220 1.34 - 1.46: 2013 1.46 - 1.58: 6802 1.58 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 13173 Sorted by residual: bond pdb=" CA ILE B 543 " pdb=" C ILE B 543 " ideal model delta sigma weight residual 1.524 1.542 -0.017 1.05e-02 9.07e+03 2.68e+00 bond pdb=" CA ILE D 543 " pdb=" C ILE D 543 " ideal model delta sigma weight residual 1.520 1.533 -0.014 8.80e-03 1.29e+04 2.38e+00 bond pdb=" C ILE B 543 " pdb=" N PRO B 544 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.25e-02 6.40e+03 2.37e+00 bond pdb=" CG1 ILE B 536 " pdb=" CD1 ILE B 536 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.89e+00 bond pdb=" CG LEU A 242 " pdb=" CD1 LEU A 242 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.81e+00 ... (remaining 13168 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 17555 2.49 - 4.98: 190 4.98 - 7.47: 31 7.47 - 9.95: 3 9.95 - 12.44: 1 Bond angle restraints: 17780 Sorted by residual: angle pdb=" C ASP A1139 " pdb=" N THR A1140 " pdb=" CA THR A1140 " ideal model delta sigma weight residual 120.38 126.92 -6.54 1.37e+00 5.33e-01 2.28e+01 angle pdb=" C ASP B 657 " pdb=" N ASP B 658 " pdb=" CA ASP B 658 " ideal model delta sigma weight residual 121.54 129.82 -8.28 1.91e+00 2.74e-01 1.88e+01 angle pdb=" N GLY A1148 " pdb=" CA GLY A1148 " pdb=" C GLY A1148 " ideal model delta sigma weight residual 113.99 119.04 -5.05 1.28e+00 6.10e-01 1.56e+01 angle pdb=" CA SER A1152 " pdb=" C SER A1152 " pdb=" N GLY A1153 " ideal model delta sigma weight residual 117.79 113.19 4.60 1.22e+00 6.72e-01 1.42e+01 angle pdb=" N ILE B 543 " pdb=" CA ILE B 543 " pdb=" C ILE B 543 " ideal model delta sigma weight residual 108.88 116.88 -8.00 2.16e+00 2.14e-01 1.37e+01 ... (remaining 17775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 7296 16.10 - 32.20: 645 32.20 - 48.30: 150 48.30 - 64.39: 18 64.39 - 80.49: 9 Dihedral angle restraints: 8118 sinusoidal: 3376 harmonic: 4742 Sorted by residual: dihedral pdb=" CA ARG B 634 " pdb=" C ARG B 634 " pdb=" N GLU B 635 " pdb=" CA GLU B 635 " ideal model delta harmonic sigma weight residual -180.00 -163.24 -16.76 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA ARG A 551 " pdb=" C ARG A 551 " pdb=" N LEU A 552 " pdb=" CA LEU A 552 " ideal model delta harmonic sigma weight residual -180.00 -163.53 -16.47 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA THR A 880 " pdb=" C THR A 880 " pdb=" N GLU A 881 " pdb=" CA GLU A 881 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 8115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1469 0.046 - 0.092: 438 0.092 - 0.138: 115 0.138 - 0.184: 7 0.184 - 0.229: 3 Chirality restraints: 2032 Sorted by residual: chirality pdb=" CB THR A1291 " pdb=" CA THR A1291 " pdb=" OG1 THR A1291 " pdb=" CG2 THR A1291 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA GLU A 291 " pdb=" N GLU A 291 " pdb=" C GLU A 291 " pdb=" CB GLU A 291 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ASP B 658 " pdb=" N ASP B 658 " pdb=" C ASP B 658 " pdb=" CB ASP B 658 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 2029 not shown) Planarity restraints: 2258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A1084 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO A1085 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A1085 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A1085 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A1155 " 0.036 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO A1156 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A1156 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A1156 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 88 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO A 89 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " -0.025 5.00e-02 4.00e+02 ... (remaining 2255 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 6284 3.00 - 3.48: 13925 3.48 - 3.95: 21714 3.95 - 4.43: 25142 4.43 - 4.90: 39746 Nonbonded interactions: 106811 Sorted by model distance: nonbonded pdb=" OE2 GLU A1223 " pdb="ZN ZN A2301 " model vdw 2.529 2.230 nonbonded pdb=" N ASN A 211 " pdb=" O ASN A 211 " model vdw 2.531 2.496 nonbonded pdb=" N ILE A 789 " pdb=" N PHE A 790 " model vdw 2.572 2.560 nonbonded pdb=" O ASN A 929 " pdb=" ND2 ASN A 929 " model vdw 2.578 3.120 nonbonded pdb=" N SER A1152 " pdb=" N GLY A1153 " model vdw 2.613 2.560 ... (remaining 106806 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'E' and resid 525 through 579) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 40.350 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.080 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:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 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 : 0.004 0.065 13180 Z= 0.167 Angle : 0.670 12.443 17781 Z= 0.358 Chirality : 0.046 0.229 2032 Planarity : 0.005 0.064 2258 Dihedral : 13.055 80.493 5032 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.20), residues: 1591 helix: 0.94 (0.17), residues: 902 sheet: -0.06 (0.58), residues: 80 loop : -0.59 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1248 HIS 0.005 0.001 HIS C 570 PHE 0.019 0.002 PHE A 399 TYR 0.012 0.002 TYR A 284 ARG 0.007 0.001 ARG A1117 Details of bonding type rmsd hydrogen bonds : bond 0.13647 ( 740) hydrogen bonds : angle 5.99664 ( 2126) metal coordination : bond 0.00416 ( 7) metal coordination : angle 2.78952 ( 1) covalent geometry : bond 0.00365 (13173) covalent geometry : angle 0.66979 (17780) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ARG cc_start: 0.8607 (ttm110) cc_final: 0.8404 (ttp80) REVERT: A 168 GLU cc_start: 0.8378 (tp30) cc_final: 0.7966 (tp30) REVERT: A 233 GLU cc_start: 0.8882 (mp0) cc_final: 0.8369 (mp0) REVERT: A 321 GLN cc_start: 0.8496 (tp-100) cc_final: 0.8284 (tp-100) REVERT: A 376 LYS cc_start: 0.8968 (ttmm) cc_final: 0.8704 (tppp) REVERT: A 469 MET cc_start: 0.8935 (ptp) cc_final: 0.8716 (ptp) REVERT: A 824 ARG cc_start: 0.8032 (mtp-110) cc_final: 0.7268 (mpt180) REVERT: A 1028 ASP cc_start: 0.8400 (t70) cc_final: 0.8155 (t0) REVERT: A 1032 MET cc_start: 0.8544 (mtm) cc_final: 0.8270 (mtp) REVERT: B 607 SER cc_start: 0.8131 (m) cc_final: 0.7823 (p) REVERT: B 665 LYS cc_start: 0.8481 (tttm) cc_final: 0.8200 (tttm) REVERT: D 559 LYS cc_start: 0.8711 (mtpp) cc_final: 0.8473 (mtpp) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 1.4616 time to fit residues: 437.7201 Evaluate side-chains 210 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 0.0470 chunk 124 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 135 ASN A 845 ASN A 876 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 GLN B 695 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.133664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.094244 restraints weight = 28452.438| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.21 r_work: 0.3169 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13180 Z= 0.191 Angle : 0.631 11.320 17781 Z= 0.323 Chirality : 0.044 0.158 2032 Planarity : 0.005 0.050 2258 Dihedral : 4.259 16.329 1741 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.06 % Allowed : 11.53 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1591 helix: 1.59 (0.17), residues: 905 sheet: -0.43 (0.53), residues: 91 loop : -0.21 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1248 HIS 0.006 0.001 HIS C 570 PHE 0.018 0.002 PHE A 399 TYR 0.020 0.002 TYR A 32 ARG 0.017 0.001 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 740) hydrogen bonds : angle 4.65254 ( 2126) metal coordination : bond 0.00798 ( 7) metal coordination : angle 1.14577 ( 1) covalent geometry : bond 0.00458 (13173) covalent geometry : angle 0.63089 (17780) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8197 (mmmt) cc_final: 0.7976 (mmmt) REVERT: A 152 ARG cc_start: 0.8532 (ttm110) cc_final: 0.8224 (ttp80) REVERT: A 168 GLU cc_start: 0.8439 (tp30) cc_final: 0.7804 (tp30) REVERT: A 233 GLU cc_start: 0.8911 (mp0) cc_final: 0.8256 (mp0) REVERT: A 289 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7760 (mtt) REVERT: A 376 LYS cc_start: 0.8792 (ttmm) cc_final: 0.8506 (tppp) REVERT: A 472 LYS cc_start: 0.8426 (mmpt) cc_final: 0.8060 (mmpt) REVERT: A 507 ASP cc_start: 0.7156 (t70) cc_final: 0.6889 (t0) REVERT: A 824 ARG cc_start: 0.7955 (mtp-110) cc_final: 0.7062 (mpt180) REVERT: A 881 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6562 (mp0) REVERT: A 1028 ASP cc_start: 0.8322 (t70) cc_final: 0.8072 (t0) REVERT: A 1237 GLN cc_start: 0.7837 (mt0) cc_final: 0.7323 (mt0) REVERT: A 1295 ARG cc_start: 0.8074 (ptp-110) cc_final: 0.7869 (ptp-110) REVERT: A 1299 ARG cc_start: 0.8920 (tpm170) cc_final: 0.8655 (tpp80) REVERT: B 595 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7115 (mtmm) REVERT: B 607 SER cc_start: 0.7041 (m) cc_final: 0.6784 (p) REVERT: B 678 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8029 (ttm170) REVERT: B 686 ASN cc_start: 0.8553 (m110) cc_final: 0.8207 (m110) REVERT: B 695 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8508 (mp10) REVERT: C 577 MET cc_start: 0.7376 (tmt) cc_final: 0.7051 (tmt) REVERT: E 581 LYS cc_start: 0.8770 (mppt) cc_final: 0.8522 (mppt) outliers start: 30 outliers final: 3 residues processed: 238 average time/residue: 1.3756 time to fit residues: 354.1683 Evaluate side-chains 226 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 219 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain C residue 537 GLU Chi-restraints excluded: chain E residue 565 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 321 GLN A 845 ASN B 651 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.134217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.094469 restraints weight = 28100.403| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.20 r_work: 0.3163 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13180 Z= 0.151 Angle : 0.602 10.831 17781 Z= 0.307 Chirality : 0.042 0.172 2032 Planarity : 0.004 0.047 2258 Dihedral : 4.128 16.609 1741 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.78 % Allowed : 14.07 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.21), residues: 1591 helix: 1.77 (0.17), residues: 905 sheet: -0.58 (0.50), residues: 96 loop : -0.12 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1248 HIS 0.004 0.001 HIS C 570 PHE 0.022 0.001 PHE A 553 TYR 0.012 0.001 TYR A 32 ARG 0.011 0.001 ARG A1180 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 740) hydrogen bonds : angle 4.50035 ( 2126) metal coordination : bond 0.00547 ( 7) metal coordination : angle 2.10902 ( 1) covalent geometry : bond 0.00360 (13173) covalent geometry : angle 0.60135 (17780) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8150 (mmmt) cc_final: 0.7792 (mmtm) REVERT: A 152 ARG cc_start: 0.8501 (ttm110) cc_final: 0.8190 (ttp80) REVERT: A 168 GLU cc_start: 0.8371 (tp30) cc_final: 0.7721 (tp30) REVERT: A 233 GLU cc_start: 0.8906 (mp0) cc_final: 0.8275 (mp0) REVERT: A 376 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8508 (tppp) REVERT: A 436 GLU cc_start: 0.7605 (mp0) cc_final: 0.7240 (mp0) REVERT: A 471 MET cc_start: 0.8012 (mmp) cc_final: 0.7517 (mmm) REVERT: A 472 LYS cc_start: 0.8544 (mmpt) cc_final: 0.8116 (mmpt) REVERT: A 507 ASP cc_start: 0.7181 (t70) cc_final: 0.6905 (OUTLIER) REVERT: A 824 ARG cc_start: 0.7865 (mtp-110) cc_final: 0.6988 (mpt180) REVERT: A 881 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.6565 (mp0) REVERT: A 1028 ASP cc_start: 0.8319 (t70) cc_final: 0.8073 (t0) REVERT: A 1299 ARG cc_start: 0.8911 (tpm170) cc_final: 0.8500 (tpp80) REVERT: A 1306 TRP cc_start: 0.8293 (m100) cc_final: 0.8079 (m100) REVERT: B 607 SER cc_start: 0.6976 (m) cc_final: 0.6704 (p) REVERT: B 645 GLU cc_start: 0.8123 (mp0) cc_final: 0.7404 (pm20) REVERT: B 695 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8639 (mp10) REVERT: C 577 MET cc_start: 0.7380 (tmt) cc_final: 0.6847 (tmt) REVERT: E 581 LYS cc_start: 0.8749 (mppt) cc_final: 0.8412 (mppt) outliers start: 26 outliers final: 7 residues processed: 238 average time/residue: 1.4163 time to fit residues: 364.7436 Evaluate side-chains 224 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 217 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain C residue 537 GLU Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain E residue 565 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 43 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 76 ASN A 149 HIS A 365 HIS A 845 ASN B 651 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.129985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.089548 restraints weight = 33701.696| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.45 r_work: 0.3087 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13180 Z= 0.264 Angle : 0.681 13.921 17781 Z= 0.345 Chirality : 0.046 0.168 2032 Planarity : 0.005 0.050 2258 Dihedral : 4.395 17.423 1741 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.33 % Allowed : 14.82 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.21), residues: 1591 helix: 1.56 (0.17), residues: 912 sheet: -0.77 (0.50), residues: 96 loop : -0.18 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1248 HIS 0.006 0.001 HIS C 570 PHE 0.020 0.002 PHE A 399 TYR 0.022 0.002 TYR A 32 ARG 0.013 0.001 ARG A1180 Details of bonding type rmsd hydrogen bonds : bond 0.04693 ( 740) hydrogen bonds : angle 4.57031 ( 2126) metal coordination : bond 0.01319 ( 7) metal coordination : angle 1.11804 ( 1) covalent geometry : bond 0.00638 (13173) covalent geometry : angle 0.68071 (17780) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8243 (mmmt) cc_final: 0.7983 (mmmt) REVERT: A 141 ARG cc_start: 0.7902 (ptm-80) cc_final: 0.7623 (ppt90) REVERT: A 152 ARG cc_start: 0.8612 (ttm110) cc_final: 0.8342 (ttp80) REVERT: A 168 GLU cc_start: 0.8516 (tp30) cc_final: 0.7854 (tp30) REVERT: A 193 ARG cc_start: 0.7320 (mmt90) cc_final: 0.7089 (mmt90) REVERT: A 233 GLU cc_start: 0.8974 (mp0) cc_final: 0.8360 (mp0) REVERT: A 376 LYS cc_start: 0.8851 (ttmm) cc_final: 0.8617 (tppp) REVERT: A 436 GLU cc_start: 0.7659 (mp0) cc_final: 0.7230 (mp0) REVERT: A 471 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7865 (mmp) REVERT: A 472 LYS cc_start: 0.8605 (mmpt) cc_final: 0.8254 (mmmt) REVERT: A 504 ARG cc_start: 0.6689 (mtm180) cc_final: 0.6388 (ttp80) REVERT: A 507 ASP cc_start: 0.7359 (t70) cc_final: 0.7134 (t0) REVERT: A 824 ARG cc_start: 0.7935 (mtp-110) cc_final: 0.7013 (mpt180) REVERT: A 885 SER cc_start: 0.9088 (OUTLIER) cc_final: 0.8664 (t) REVERT: A 909 MET cc_start: 0.8923 (mmm) cc_final: 0.8688 (mmm) REVERT: A 1028 ASP cc_start: 0.8327 (t70) cc_final: 0.8087 (t0) REVERT: A 1299 ARG cc_start: 0.8962 (tpm170) cc_final: 0.8681 (tpp80) REVERT: A 1306 TRP cc_start: 0.8393 (m100) cc_final: 0.8157 (m100) REVERT: A 1364 ASN cc_start: 0.8351 (t0) cc_final: 0.8053 (t0) REVERT: B 645 GLU cc_start: 0.8235 (mp0) cc_final: 0.7520 (pm20) REVERT: B 686 ASN cc_start: 0.8536 (m110) cc_final: 0.8146 (m110) REVERT: C 577 MET cc_start: 0.7338 (tmt) cc_final: 0.6824 (tmt) REVERT: E 556 VAL cc_start: 0.7291 (m) cc_final: 0.6935 (p) REVERT: E 559 LYS cc_start: 0.8707 (tmmt) cc_final: 0.8454 (tmmt) REVERT: E 581 LYS cc_start: 0.8735 (mppt) cc_final: 0.8419 (mppt) outliers start: 32 outliers final: 9 residues processed: 244 average time/residue: 1.4269 time to fit residues: 376.3608 Evaluate side-chains 226 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 215 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 885 SER Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain C residue 537 GLU Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain E residue 546 ILE Chi-restraints excluded: chain E residue 565 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 845 ASN A 876 ASN A 968 ASN B 651 GLN B 690 ASN B 695 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.132880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.092903 restraints weight = 30553.237| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.35 r_work: 0.3143 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13180 Z= 0.137 Angle : 0.609 11.045 17781 Z= 0.307 Chirality : 0.043 0.165 2032 Planarity : 0.004 0.051 2258 Dihedral : 4.197 17.977 1741 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.44 % Allowed : 16.54 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.21), residues: 1591 helix: 1.86 (0.18), residues: 902 sheet: -0.57 (0.51), residues: 96 loop : -0.10 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1248 HIS 0.003 0.001 HIS A 314 PHE 0.031 0.001 PHE A 553 TYR 0.012 0.001 TYR A 284 ARG 0.012 0.001 ARG A1180 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 740) hydrogen bonds : angle 4.40975 ( 2126) metal coordination : bond 0.00422 ( 7) metal coordination : angle 1.29876 ( 1) covalent geometry : bond 0.00325 (13173) covalent geometry : angle 0.60911 (17780) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7846 (ptm-80) cc_final: 0.7602 (ppt90) REVERT: A 152 ARG cc_start: 0.8555 (ttm110) cc_final: 0.8303 (ttp80) REVERT: A 168 GLU cc_start: 0.8449 (tp30) cc_final: 0.7750 (tp30) REVERT: A 233 GLU cc_start: 0.8934 (mp0) cc_final: 0.8342 (mp0) REVERT: A 321 GLN cc_start: 0.8559 (tp40) cc_final: 0.8289 (tp-100) REVERT: A 376 LYS cc_start: 0.8808 (ttmm) cc_final: 0.8586 (tppp) REVERT: A 436 GLU cc_start: 0.7654 (mp0) cc_final: 0.7247 (mp0) REVERT: A 471 MET cc_start: 0.8171 (mmp) cc_final: 0.7782 (mmp) REVERT: A 472 LYS cc_start: 0.8622 (mmpt) cc_final: 0.8307 (mmmt) REVERT: A 507 ASP cc_start: 0.7321 (t70) cc_final: 0.7102 (t0) REVERT: A 824 ARG cc_start: 0.7899 (mtp-110) cc_final: 0.6968 (mpt180) REVERT: A 1028 ASP cc_start: 0.8318 (t70) cc_final: 0.8076 (t0) REVERT: A 1074 ASN cc_start: 0.7411 (m-40) cc_final: 0.7188 (m-40) REVERT: A 1225 MET cc_start: 0.8245 (mtp) cc_final: 0.7941 (mmm) REVERT: A 1295 ARG cc_start: 0.8032 (ptp-110) cc_final: 0.7748 (ptp-110) REVERT: A 1299 ARG cc_start: 0.8959 (tpm170) cc_final: 0.8694 (tpp80) REVERT: A 1306 TRP cc_start: 0.8378 (m100) cc_final: 0.8122 (m100) REVERT: B 607 SER cc_start: 0.7190 (m) cc_final: 0.6776 (p) REVERT: B 645 GLU cc_start: 0.8167 (mp0) cc_final: 0.7418 (pm20) REVERT: B 658 ASP cc_start: 0.7963 (p0) cc_final: 0.7754 (p0) REVERT: B 686 ASN cc_start: 0.8504 (m110) cc_final: 0.8102 (m110) REVERT: C 577 MET cc_start: 0.7298 (tmt) cc_final: 0.6790 (tmt) REVERT: E 581 LYS cc_start: 0.8760 (mppt) cc_final: 0.8507 (mppt) outliers start: 19 outliers final: 7 residues processed: 233 average time/residue: 1.6420 time to fit residues: 414.2249 Evaluate side-chains 224 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 217 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain C residue 537 GLU Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 565 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 48 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 133 optimal weight: 0.0000 chunk 117 optimal weight: 2.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 845 ASN ** A1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 GLN B 690 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.133725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.093677 restraints weight = 32189.603| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.43 r_work: 0.3157 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13180 Z= 0.133 Angle : 0.613 12.419 17781 Z= 0.308 Chirality : 0.042 0.181 2032 Planarity : 0.005 0.070 2258 Dihedral : 4.083 16.747 1741 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.72 % Allowed : 16.75 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.22), residues: 1591 helix: 1.92 (0.18), residues: 909 sheet: -0.41 (0.52), residues: 96 loop : 0.01 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1248 HIS 0.003 0.001 HIS A 314 PHE 0.016 0.001 PHE A 399 TYR 0.011 0.001 TYR A 284 ARG 0.019 0.001 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 740) hydrogen bonds : angle 4.33315 ( 2126) metal coordination : bond 0.00405 ( 7) metal coordination : angle 1.19845 ( 1) covalent geometry : bond 0.00314 (13173) covalent geometry : angle 0.61268 (17780) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7813 (ptm-80) cc_final: 0.7586 (ppt90) REVERT: A 152 ARG cc_start: 0.8538 (ttm110) cc_final: 0.8298 (ttp80) REVERT: A 161 MET cc_start: 0.8797 (ttt) cc_final: 0.8592 (ttt) REVERT: A 168 GLU cc_start: 0.8430 (tp30) cc_final: 0.7735 (tp30) REVERT: A 233 GLU cc_start: 0.8951 (mp0) cc_final: 0.8350 (mp0) REVERT: A 321 GLN cc_start: 0.8567 (tp40) cc_final: 0.8289 (tp-100) REVERT: A 376 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8231 (tppp) REVERT: A 379 GLU cc_start: 0.8666 (pt0) cc_final: 0.8082 (pp20) REVERT: A 436 GLU cc_start: 0.7659 (mp0) cc_final: 0.7251 (mp0) REVERT: A 824 ARG cc_start: 0.7892 (mtp-110) cc_final: 0.6968 (mpt180) REVERT: A 909 MET cc_start: 0.8906 (mmm) cc_final: 0.8547 (mmm) REVERT: A 968 ASN cc_start: 0.7667 (t0) cc_final: 0.7431 (t0) REVERT: A 1028 ASP cc_start: 0.8351 (t70) cc_final: 0.8113 (t0) REVERT: A 1074 ASN cc_start: 0.7387 (m-40) cc_final: 0.7156 (m-40) REVERT: A 1295 ARG cc_start: 0.8075 (ptp-110) cc_final: 0.7819 (mtm-85) REVERT: A 1299 ARG cc_start: 0.8977 (tpm170) cc_final: 0.8689 (tpp80) REVERT: A 1306 TRP cc_start: 0.8396 (m100) cc_final: 0.8164 (m100) REVERT: A 1364 ASN cc_start: 0.8363 (t0) cc_final: 0.8058 (t0) REVERT: B 550 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8398 (tt) REVERT: B 607 SER cc_start: 0.7180 (m) cc_final: 0.6764 (p) REVERT: B 645 GLU cc_start: 0.8144 (mp0) cc_final: 0.7399 (pm20) REVERT: B 678 ARG cc_start: 0.8200 (ttm170) cc_final: 0.7957 (ttm-80) REVERT: B 686 ASN cc_start: 0.8495 (m110) cc_final: 0.8127 (m110) REVERT: C 577 MET cc_start: 0.7300 (tmt) cc_final: 0.6755 (tmt) REVERT: E 581 LYS cc_start: 0.8740 (mppt) cc_final: 0.8436 (mppt) outliers start: 23 outliers final: 7 residues processed: 236 average time/residue: 1.6716 time to fit residues: 429.2514 Evaluate side-chains 219 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 211 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 560 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 10 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 845 ASN A 876 ASN ** A1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.130564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.089095 restraints weight = 46116.559| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.99 r_work: 0.3074 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 13180 Z= 0.240 Angle : 0.692 12.747 17781 Z= 0.349 Chirality : 0.046 0.184 2032 Planarity : 0.005 0.062 2258 Dihedral : 4.311 17.659 1741 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.13 % Allowed : 17.16 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.21), residues: 1591 helix: 1.69 (0.17), residues: 905 sheet: -0.49 (0.51), residues: 96 loop : -0.09 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1248 HIS 0.004 0.001 HIS C 570 PHE 0.029 0.002 PHE A 553 TYR 0.017 0.002 TYR A 32 ARG 0.016 0.001 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.04484 ( 740) hydrogen bonds : angle 4.56313 ( 2126) metal coordination : bond 0.01169 ( 7) metal coordination : angle 0.45776 ( 1) covalent geometry : bond 0.00584 (13173) covalent geometry : angle 0.69229 (17780) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8167 (mmmm) cc_final: 0.7870 (mmmt) REVERT: A 141 ARG cc_start: 0.7881 (ptm-80) cc_final: 0.7634 (ppt90) REVERT: A 152 ARG cc_start: 0.8590 (ttm110) cc_final: 0.8346 (ttp80) REVERT: A 233 GLU cc_start: 0.9006 (mp0) cc_final: 0.8371 (mp0) REVERT: A 376 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8576 (tppp) REVERT: A 436 GLU cc_start: 0.7686 (mp0) cc_final: 0.7222 (mp0) REVERT: A 909 MET cc_start: 0.8940 (mmm) cc_final: 0.8696 (mmm) REVERT: A 1028 ASP cc_start: 0.8376 (t70) cc_final: 0.8139 (t0) REVERT: A 1306 TRP cc_start: 0.8484 (m100) cc_final: 0.8251 (m100) REVERT: A 1364 ASN cc_start: 0.8355 (t0) cc_final: 0.8050 (t0) REVERT: B 645 GLU cc_start: 0.8154 (mp0) cc_final: 0.7370 (pm20) REVERT: C 577 MET cc_start: 0.7320 (tmt) cc_final: 0.6745 (tmt) REVERT: E 549 LYS cc_start: 0.8210 (ptmm) cc_final: 0.7929 (ptmt) REVERT: E 581 LYS cc_start: 0.8746 (mppt) cc_final: 0.8514 (mppt) outliers start: 29 outliers final: 12 residues processed: 224 average time/residue: 1.3814 time to fit residues: 335.8202 Evaluate side-chains 220 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1292 LYS Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 546 ILE Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 565 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 26 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 135 optimal weight: 0.0770 chunk 132 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 845 ASN A 968 ASN A1074 ASN A1324 GLN B 651 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.133695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.092985 restraints weight = 36672.769| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.63 r_work: 0.3152 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13180 Z= 0.134 Angle : 0.642 14.470 17781 Z= 0.323 Chirality : 0.042 0.180 2032 Planarity : 0.005 0.062 2258 Dihedral : 4.125 17.608 1741 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.17 % Allowed : 17.98 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.22), residues: 1591 helix: 1.91 (0.18), residues: 903 sheet: -0.30 (0.52), residues: 96 loop : 0.05 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1248 HIS 0.003 0.001 HIS A 756 PHE 0.016 0.001 PHE A 399 TYR 0.010 0.001 TYR A 284 ARG 0.015 0.001 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 740) hydrogen bonds : angle 4.40212 ( 2126) metal coordination : bond 0.00288 ( 7) metal coordination : angle 1.64707 ( 1) covalent geometry : bond 0.00314 (13173) covalent geometry : angle 0.64227 (17780) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 215 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7802 (ptm-80) cc_final: 0.7566 (ppt90) REVERT: A 152 ARG cc_start: 0.8522 (ttm110) cc_final: 0.8280 (ttp80) REVERT: A 233 GLU cc_start: 0.8987 (mp0) cc_final: 0.8392 (mp0) REVERT: A 321 GLN cc_start: 0.8586 (tp40) cc_final: 0.8297 (tp-100) REVERT: A 376 LYS cc_start: 0.8770 (ttmm) cc_final: 0.8447 (tppp) REVERT: A 379 GLU cc_start: 0.8727 (pt0) cc_final: 0.8239 (pp20) REVERT: A 436 GLU cc_start: 0.7680 (mp0) cc_final: 0.7277 (mp0) REVERT: A 909 MET cc_start: 0.8899 (mmm) cc_final: 0.8670 (mmm) REVERT: A 1028 ASP cc_start: 0.8336 (t70) cc_final: 0.8101 (t0) REVERT: A 1306 TRP cc_start: 0.8468 (m100) cc_final: 0.8209 (m100) REVERT: A 1364 ASN cc_start: 0.8320 (t0) cc_final: 0.7992 (t0) REVERT: B 645 GLU cc_start: 0.8142 (mp0) cc_final: 0.7342 (pm20) REVERT: C 577 MET cc_start: 0.7377 (tmt) cc_final: 0.6779 (tmt) REVERT: E 549 LYS cc_start: 0.8259 (ptmm) cc_final: 0.7949 (ptmt) REVERT: E 559 LYS cc_start: 0.8517 (tmmt) cc_final: 0.8199 (pptt) REVERT: E 581 LYS cc_start: 0.8726 (mppt) cc_final: 0.8475 (mppt) outliers start: 15 outliers final: 6 residues processed: 221 average time/residue: 1.3960 time to fit residues: 334.4854 Evaluate side-chains 215 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 209 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 560 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 125 optimal weight: 0.0040 chunk 146 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 845 ASN A 876 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 968 ASN A1324 GLN B 651 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.134333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.093904 restraints weight = 33278.896| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.48 r_work: 0.3172 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13180 Z= 0.131 Angle : 0.636 13.424 17781 Z= 0.320 Chirality : 0.042 0.204 2032 Planarity : 0.005 0.060 2258 Dihedral : 4.028 17.102 1741 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.75 % Allowed : 18.94 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.22), residues: 1591 helix: 1.92 (0.18), residues: 910 sheet: -0.26 (0.52), residues: 96 loop : 0.12 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1248 HIS 0.002 0.001 HIS B 671 PHE 0.027 0.001 PHE A 553 TYR 0.011 0.001 TYR A 284 ARG 0.014 0.001 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 740) hydrogen bonds : angle 4.37001 ( 2126) metal coordination : bond 0.00350 ( 7) metal coordination : angle 1.18072 ( 1) covalent geometry : bond 0.00307 (13173) covalent geometry : angle 0.63557 (17780) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 216 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8154 (mmmm) cc_final: 0.7908 (mmmt) REVERT: A 141 ARG cc_start: 0.7796 (ptm-80) cc_final: 0.7580 (ppt90) REVERT: A 152 ARG cc_start: 0.8533 (ttm110) cc_final: 0.8300 (ttp80) REVERT: A 168 GLU cc_start: 0.8438 (tp30) cc_final: 0.7754 (tp30) REVERT: A 233 GLU cc_start: 0.8952 (mp0) cc_final: 0.8349 (mp0) REVERT: A 321 GLN cc_start: 0.8586 (tp40) cc_final: 0.8296 (tp-100) REVERT: A 376 LYS cc_start: 0.8832 (ttmm) cc_final: 0.8525 (tppp) REVERT: A 379 GLU cc_start: 0.8699 (pt0) cc_final: 0.8288 (pp20) REVERT: A 436 GLU cc_start: 0.7699 (mp0) cc_final: 0.7295 (mp0) REVERT: A 909 MET cc_start: 0.8903 (mmm) cc_final: 0.8700 (mmm) REVERT: A 1028 ASP cc_start: 0.8345 (t70) cc_final: 0.8113 (t0) REVERT: A 1074 ASN cc_start: 0.7383 (m-40) cc_final: 0.7180 (m-40) REVERT: A 1295 ARG cc_start: 0.7909 (ptp-110) cc_final: 0.7582 (mtm-85) REVERT: A 1306 TRP cc_start: 0.8285 (m100) cc_final: 0.8061 (m100) REVERT: A 1364 ASN cc_start: 0.8333 (t0) cc_final: 0.8011 (t0) REVERT: B 645 GLU cc_start: 0.8189 (mp0) cc_final: 0.7384 (pm20) REVERT: C 577 MET cc_start: 0.7341 (tmt) cc_final: 0.6753 (tmt) REVERT: D 547 ILE cc_start: 0.9283 (mp) cc_final: 0.9056 (pp) REVERT: E 549 LYS cc_start: 0.8260 (ptmm) cc_final: 0.7938 (ptmt) REVERT: E 559 LYS cc_start: 0.8520 (tmmt) cc_final: 0.8146 (pptt) REVERT: E 581 LYS cc_start: 0.8730 (mppt) cc_final: 0.8472 (mppt) outliers start: 9 outliers final: 6 residues processed: 220 average time/residue: 1.3731 time to fit residues: 328.6493 Evaluate side-chains 215 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 209 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 560 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 94 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 135 optimal weight: 0.3980 chunk 117 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 845 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 968 ASN A1324 GLN B 651 GLN B 690 ASN E 561 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.133750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.093132 restraints weight = 34690.636| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.55 r_work: 0.3160 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13180 Z= 0.145 Angle : 0.658 13.480 17781 Z= 0.330 Chirality : 0.043 0.176 2032 Planarity : 0.005 0.063 2258 Dihedral : 4.040 16.436 1741 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.82 % Allowed : 18.94 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.22), residues: 1591 helix: 1.90 (0.17), residues: 910 sheet: -0.24 (0.52), residues: 96 loop : 0.15 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1248 HIS 0.002 0.001 HIS A1094 PHE 0.017 0.001 PHE A 399 TYR 0.011 0.001 TYR A 284 ARG 0.014 0.001 ARG A1180 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 740) hydrogen bonds : angle 4.38760 ( 2126) metal coordination : bond 0.00439 ( 7) metal coordination : angle 1.15724 ( 1) covalent geometry : bond 0.00347 (13173) covalent geometry : angle 0.65827 (17780) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 212 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8151 (mmmm) cc_final: 0.7895 (mmmt) REVERT: A 141 ARG cc_start: 0.7793 (ptm-80) cc_final: 0.7555 (ppt90) REVERT: A 152 ARG cc_start: 0.8531 (ttm110) cc_final: 0.8297 (ttp80) REVERT: A 233 GLU cc_start: 0.8976 (mp0) cc_final: 0.8346 (mp0) REVERT: A 376 LYS cc_start: 0.8818 (ttmm) cc_final: 0.8508 (tppp) REVERT: A 379 GLU cc_start: 0.8694 (pt0) cc_final: 0.8272 (pp20) REVERT: A 436 GLU cc_start: 0.7710 (mp0) cc_final: 0.7291 (mp0) REVERT: A 909 MET cc_start: 0.8887 (mmm) cc_final: 0.8672 (mmm) REVERT: A 929 ASN cc_start: 0.8571 (t0) cc_final: 0.8338 (t0) REVERT: A 1028 ASP cc_start: 0.8344 (t70) cc_final: 0.8109 (t0) REVERT: A 1074 ASN cc_start: 0.7405 (m-40) cc_final: 0.7185 (m-40) REVERT: A 1306 TRP cc_start: 0.8290 (m100) cc_final: 0.8057 (m100) REVERT: A 1364 ASN cc_start: 0.8336 (t0) cc_final: 0.8005 (t0) REVERT: B 547 ILE cc_start: 0.8803 (mm) cc_final: 0.8395 (pp) REVERT: B 645 GLU cc_start: 0.8166 (mp0) cc_final: 0.7365 (pm20) REVERT: B 695 GLN cc_start: 0.8929 (mm-40) cc_final: 0.8694 (mp10) REVERT: C 577 MET cc_start: 0.7402 (tmt) cc_final: 0.6803 (tmt) REVERT: E 559 LYS cc_start: 0.8455 (tmmt) cc_final: 0.8148 (pptt) REVERT: E 581 LYS cc_start: 0.8717 (mppt) cc_final: 0.8494 (mppt) outliers start: 10 outliers final: 6 residues processed: 216 average time/residue: 1.3096 time to fit residues: 307.4965 Evaluate side-chains 218 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 212 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 560 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 28 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 127 optimal weight: 0.0010 chunk 154 optimal weight: 8.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 365 HIS A 845 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 968 ASN B 651 GLN B 690 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.135155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.094416 restraints weight = 36868.013| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.67 r_work: 0.3179 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13180 Z= 0.128 Angle : 0.647 15.485 17781 Z= 0.324 Chirality : 0.042 0.179 2032 Planarity : 0.005 0.062 2258 Dihedral : 3.981 16.433 1741 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.69 % Allowed : 19.42 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.22), residues: 1591 helix: 1.93 (0.18), residues: 911 sheet: -0.12 (0.52), residues: 96 loop : 0.20 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1248 HIS 0.003 0.001 HIS B 671 PHE 0.024 0.001 PHE A 553 TYR 0.010 0.001 TYR A 284 ARG 0.019 0.001 ARG B 555 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 740) hydrogen bonds : angle 4.34012 ( 2126) metal coordination : bond 0.00265 ( 7) metal coordination : angle 1.57400 ( 1) covalent geometry : bond 0.00299 (13173) covalent geometry : angle 0.64719 (17780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13841.07 seconds wall clock time: 240 minutes 59.03 seconds (14459.03 seconds total)