Starting phenix.real_space_refine on Fri Jul 3 04:42:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s4u_24833/07_2026/7s4u_24833.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s4u_24833/07_2026/7s4u_24833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7s4u_24833/07_2026/7s4u_24833.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s4u_24833/07_2026/7s4u_24833.cif" model { file = "/net/cci-nas-00/data/ceres_data/7s4u_24833/07_2026/7s4u_24833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s4u_24833/07_2026/7s4u_24833.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s4u_24833/07_2026/7s4u_24833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s4u_24833/07_2026/7s4u_24833.map" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 142 5.49 5 S 16 5.16 5 C 7078 2.51 5 N 2093 2.21 5 O 2598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11927 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8928 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 29, 'TRANS': 1062} Chain breaks: 7 Chain: "B" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2080 Classifications: {'RNA': 97} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 48, 'rna3p_pyr': 32} Link IDs: {'rna2p': 17, 'rna3p': 79} Chain: "C" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 648 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "D" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 271 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 2.45, per 1000 atoms: 0.21 Number of scatterers: 11927 At special positions: 0 Unit cell: (89.1, 130.9, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 142 15.00 O 2598 8.00 N 2093 7.00 C 7078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 488.3 milliseconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 5 sheets defined 58.2% alpha, 8.4% beta 38 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 59 through 91 removed outlier: 3.794A pdb=" N LYS A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 76 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 101 removed outlier: 3.572A pdb=" N LEU A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 135 through 144 removed outlier: 3.612A pdb=" N LYS A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.653A pdb=" N HIS A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.547A pdb=" N SER A 179 " --> pdb=" O PRO A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 196 Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.597A pdb=" N ALA A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 237 through 246 removed outlier: 4.775A pdb=" N ALA A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.697A pdb=" N ASP A 261 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.649A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 306 removed outlier: 4.112A pdb=" N ASN A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.537A pdb=" N ILE A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS A 328 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.722A pdb=" N TYR A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLU A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix removed outlier: 3.698A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.278A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 4.009A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 435' Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 474 through 478 removed outlier: 3.567A pdb=" N ASN A 477 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE A 478 " --> pdb=" O PRO A 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 474 through 478' Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.920A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N MET A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 562 through 573 removed outlier: 3.514A pdb=" N GLU A 566 " --> pdb=" O LYS A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 612 through 626 removed outlier: 4.188A pdb=" N ASP A 618 " --> pdb=" O ASP A 614 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.720A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 687 through 691 removed outlier: 3.524A pdb=" N ARG A 691 " --> pdb=" O PHE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 700 removed outlier: 3.917A pdb=" N HIS A 698 " --> pdb=" O MET A 694 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 710 removed outlier: 5.729A pdb=" N GLU A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASP A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE A 708 " --> pdb=" O PHE A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 725 through 727 No H-bonds generated for 'chain 'A' and resid 725 through 727' Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.850A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 940 removed outlier: 3.572A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 932 " --> pdb=" O THR A 928 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 971 removed outlier: 4.266A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1000 Processing helix chain 'A' and resid 1076 through 1089 removed outlier: 4.189A pdb=" N PHE A1080 " --> pdb=" O LYS A1076 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA A1081 " --> pdb=" O GLY A1077 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N THR A1082 " --> pdb=" O ARG A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1186 removed outlier: 3.532A pdb=" N GLY A1186 " --> pdb=" O LEU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 removed outlier: 3.585A pdb=" N VAL A1233 " --> pdb=" O PRO A1229 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A1238 " --> pdb=" O ASN A1234 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A1239 " --> pdb=" O PHE A1235 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS A1241 " --> pdb=" O TYR A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1260 removed outlier: 4.191A pdb=" N GLN A1254 " --> pdb=" O GLU A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.883A pdb=" N ASN A1308 " --> pdb=" O GLU A1304 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1316 No H-bonds generated for 'chain 'A' and resid 1314 through 1316' Processing helix chain 'A' and resid 1338 through 1343 removed outlier: 3.605A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.397A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP A 18 " --> pdb=" O GLY A 49 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A1095 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 3.655A pdb=" N LYS A 30 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 10.524A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1106 through 1111 removed outlier: 6.938A pdb=" N LYS A1107 " --> pdb=" O PRO A1137 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER A1109 " --> pdb=" O ASP A1135 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP A1135 " --> pdb=" O SER A1109 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A1133 " --> pdb=" O LEU A1111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.667A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1324 through 1326 385 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 97 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 2.85 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2410 1.33 - 1.45: 3417 1.45 - 1.57: 6303 1.57 - 1.69: 281 1.69 - 1.81: 31 Bond restraints: 12442 Sorted by residual: bond pdb=" C3' DG C 12 " pdb=" C2' DG C 12 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.16e+00 bond pdb=" C3' DT C 9 " pdb=" C2' DT C 9 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.59e+00 bond pdb=" C5' DG C 35 " pdb=" C4' DG C 35 " ideal model delta sigma weight residual 1.512 1.531 -0.019 7.00e-03 2.04e+04 7.75e+00 bond pdb=" C3' DC C 17 " pdb=" C2' DC C 17 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.16e+00 bond pdb=" C3' DC D 45 " pdb=" C2' DC D 45 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.54e+00 ... (remaining 12437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 16877 1.97 - 3.94: 475 3.94 - 5.91: 50 5.91 - 7.88: 10 7.88 - 9.85: 1 Bond angle restraints: 17413 Sorted by residual: angle pdb=" O4' DT C 23 " pdb=" C4' DT C 23 " pdb=" C3' DT C 23 " ideal model delta sigma weight residual 106.00 102.58 3.42 6.00e-01 2.78e+00 3.25e+01 angle pdb=" O4' DC C 26 " pdb=" C4' DC C 26 " pdb=" C3' DC C 26 " ideal model delta sigma weight residual 106.00 103.00 3.00 6.00e-01 2.78e+00 2.50e+01 angle pdb=" N3 DT C 30 " pdb=" C4 DT C 30 " pdb=" O4 DT C 30 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT C 9 " pdb=" C4 DT C 9 " pdb=" O4 DT C 9 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT C 10 " pdb=" C4 DT C 10 " pdb=" O4 DT C 10 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 ... (remaining 17408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 6929 35.30 - 70.60: 271 70.60 - 105.90: 25 105.90 - 141.20: 4 141.20 - 176.49: 4 Dihedral angle restraints: 7233 sinusoidal: 4021 harmonic: 3212 Sorted by residual: dihedral pdb=" C4' A B 1 " pdb=" C3' A B 1 " pdb=" C2' A B 1 " pdb=" C1' A B 1 " ideal model delta sinusoidal sigma weight residual -35.00 34.21 -69.21 1 8.00e+00 1.56e-02 9.68e+01 dihedral pdb=" C5' A B 1 " pdb=" C4' A B 1 " pdb=" C3' A B 1 " pdb=" O3' A B 1 " ideal model delta sinusoidal sigma weight residual 147.00 82.33 64.67 1 8.00e+00 1.56e-02 8.58e+01 dihedral pdb=" O4' C B 69 " pdb=" C1' C B 69 " pdb=" N1 C B 69 " pdb=" C2 C B 69 " ideal model delta sinusoidal sigma weight residual 200.00 50.22 149.78 1 1.50e+01 4.44e-03 7.95e+01 ... (remaining 7230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1764 0.065 - 0.129: 240 0.129 - 0.194: 15 0.194 - 0.259: 2 0.259 - 0.324: 1 Chirality restraints: 2022 Sorted by residual: chirality pdb=" C3' A B 1 " pdb=" C4' A B 1 " pdb=" O3' A B 1 " pdb=" C2' A B 1 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" C1' G B 3 " pdb=" O4' G B 3 " pdb=" C2' G B 3 " pdb=" N9 G B 3 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C2' A B 1 " pdb=" C3' A B 1 " pdb=" O2' A B 1 " pdb=" C1' A B 1 " both_signs ideal model delta sigma weight residual False -2.52 -2.73 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2019 not shown) Planarity restraints: 1694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 3 " -0.036 2.00e-02 2.50e+03 1.61e-02 7.78e+00 pdb=" N9 G B 3 " 0.040 2.00e-02 2.50e+03 pdb=" C8 G B 3 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G B 3 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G B 3 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 3 " -0.008 2.00e-02 2.50e+03 pdb=" O6 G B 3 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G B 3 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G B 3 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 3 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 3 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G B 3 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 7 " -0.028 2.00e-02 2.50e+03 1.30e-02 4.66e+00 pdb=" N9 A B 7 " 0.031 2.00e-02 2.50e+03 pdb=" C8 A B 7 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A B 7 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 7 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A B 7 " -0.006 2.00e-02 2.50e+03 pdb=" N6 A B 7 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A B 7 " -0.000 2.00e-02 2.50e+03 pdb=" C2 A B 7 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A B 7 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A B 7 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 35 " 0.028 2.00e-02 2.50e+03 1.18e-02 4.16e+00 pdb=" N9 DG C 35 " -0.027 2.00e-02 2.50e+03 pdb=" C8 DG C 35 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG C 35 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG C 35 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG C 35 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG C 35 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG C 35 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG C 35 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG C 35 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG C 35 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG C 35 " -0.003 2.00e-02 2.50e+03 ... (remaining 1691 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 251 2.65 - 3.21: 10971 3.21 - 3.78: 18440 3.78 - 4.34: 25014 4.34 - 4.90: 38258 Nonbonded interactions: 92934 Sorted by model distance: nonbonded pdb=" O2' C B 90 " pdb=" OP1 G B 91 " model vdw 2.090 3.040 nonbonded pdb=" OG SER A 541 " pdb=" OD2 ASP A 686 " model vdw 2.105 3.040 nonbonded pdb=" OD1 ASN A 14 " pdb=" OG SER A 55 " model vdw 2.127 3.040 nonbonded pdb=" OH TYR A 373 " pdb=" O LEU A 398 " model vdw 2.159 3.040 nonbonded pdb=" O2' A B 37 " pdb=" OP1 G B 38 " model vdw 2.200 3.040 ... (remaining 92929 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.92 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.630 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.010 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 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 0.036 12442 Z= 0.281 Angle : 0.763 9.851 17413 Z= 0.488 Chirality : 0.044 0.324 2022 Planarity : 0.004 0.042 1694 Dihedral : 17.352 176.495 5147 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.25), residues: 1076 helix: -0.75 (0.22), residues: 517 sheet: -0.15 (0.52), residues: 106 loop : -0.61 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 664 TYR 0.026 0.002 TYR A 362 PHE 0.025 0.002 PHE A 478 TRP 0.014 0.002 TRP A 18 HIS 0.007 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.28 (12442) covalent geometry : angle 0.76332 / 0.49 (17413) hydrogen bonds : bond 0.16339 / 10.62 ( 482) hydrogen bonds : angle 6.30250 / 4.48 ( 1301) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.361 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1282 time to fit residues: 14.2572 Evaluate side-chains 47 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.132580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.101313 restraints weight = 23069.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.104045 restraints weight = 48949.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.103843 restraints weight = 20600.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.104676 restraints weight = 17088.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.104784 restraints weight = 14477.461| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12442 Z= 0.204 Angle : 0.730 8.808 17413 Z= 0.393 Chirality : 0.045 0.251 2022 Planarity : 0.004 0.038 1694 Dihedral : 18.362 174.505 2831 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.71 % Allowed : 3.78 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.25), residues: 1076 helix: -0.64 (0.22), residues: 528 sheet: -0.26 (0.55), residues: 104 loop : -0.78 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 664 TYR 0.031 0.002 TYR A 5 PHE 0.026 0.002 PHE A 704 TRP 0.013 0.002 TRP A 18 HIS 0.007 0.002 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (12442) covalent geometry : angle 0.72957 / 0.39 (17413) hydrogen bonds : bond 0.06790 / 4.25 ( 482) hydrogen bonds : angle 5.03111 / 3.56 ( 1301) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.398 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 60 average time/residue: 0.1217 time to fit residues: 10.3331 Evaluate side-chains 47 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 950 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 38 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 37 optimal weight: 0.0040 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.133888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.103135 restraints weight = 23151.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.105855 restraints weight = 50155.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.105825 restraints weight = 21190.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.107126 restraints weight = 16779.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.107136 restraints weight = 13702.942| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12442 Z= 0.149 Angle : 0.632 8.567 17413 Z= 0.342 Chirality : 0.041 0.228 2022 Planarity : 0.004 0.036 1694 Dihedral : 18.166 173.839 2831 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.92 % Allowed : 4.90 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.25), residues: 1076 helix: -0.35 (0.22), residues: 531 sheet: -0.28 (0.53), residues: 106 loop : -0.70 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1303 TYR 0.020 0.002 TYR A 362 PHE 0.017 0.001 PHE A 704 TRP 0.015 0.002 TRP A 18 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (12442) covalent geometry : angle 0.63236 / 0.34 (17413) hydrogen bonds : bond 0.05474 / 3.41 ( 482) hydrogen bonds : angle 4.61217 / 3.28 ( 1301) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.7983 (mmt) cc_final: 0.7634 (mmm) REVERT: A 661 ARG cc_start: 0.8299 (mmm160) cc_final: 0.8097 (mmp80) outliers start: 9 outliers final: 4 residues processed: 56 average time/residue: 0.1304 time to fit residues: 10.1180 Evaluate side-chains 47 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1146 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 99 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 402 GLN A 726 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.130564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099639 restraints weight = 23246.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.102413 restraints weight = 50265.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.102181 restraints weight = 21160.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.103129 restraints weight = 17107.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.103247 restraints weight = 14118.078| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12442 Z= 0.239 Angle : 0.711 8.834 17413 Z= 0.377 Chirality : 0.044 0.235 2022 Planarity : 0.004 0.045 1694 Dihedral : 18.193 171.706 2831 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.02 % Allowed : 6.73 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.25), residues: 1076 helix: -0.48 (0.22), residues: 533 sheet: -0.67 (0.53), residues: 106 loop : -1.11 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 403 TYR 0.033 0.002 TYR A 362 PHE 0.021 0.002 PHE A1324 TRP 0.013 0.002 TRP A 18 HIS 0.009 0.002 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.24 (12442) covalent geometry : angle 0.71124 / 0.38 (17413) hydrogen bonds : bond 0.07194 / 4.55 ( 482) hydrogen bonds : angle 4.80940 / 3.41 ( 1301) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.259 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 55 average time/residue: 0.1162 time to fit residues: 9.1471 Evaluate side-chains 52 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 24 optimal weight: 0.0050 chunk 83 optimal weight: 0.0030 chunk 90 optimal weight: 2.9990 chunk 102 optimal weight: 0.0000 chunk 34 optimal weight: 0.0970 chunk 119 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 overall best weight: 0.1606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.134829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.102663 restraints weight = 23041.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.104631 restraints weight = 49933.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.105340 restraints weight = 25266.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.106209 restraints weight = 17620.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.106486 restraints weight = 16129.915| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12442 Z= 0.122 Angle : 0.591 12.508 17413 Z= 0.314 Chirality : 0.039 0.218 2022 Planarity : 0.003 0.034 1694 Dihedral : 17.954 174.160 2831 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.61 % Allowed : 7.76 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.25), residues: 1076 helix: -0.02 (0.23), residues: 525 sheet: -0.38 (0.53), residues: 106 loop : -0.79 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1298 TYR 0.020 0.001 TYR A1242 PHE 0.012 0.001 PHE A 704 TRP 0.013 0.001 TRP A 18 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.12 (12442) covalent geometry : angle 0.59149 / 0.31 (17413) hydrogen bonds : bond 0.04730 / 2.96 ( 482) hydrogen bonds : angle 4.36340 / 3.11 ( 1301) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.380 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 57 average time/residue: 0.1164 time to fit residues: 9.5754 Evaluate side-chains 47 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1146 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 110 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 87 optimal weight: 0.1980 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.133590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.102054 restraints weight = 23197.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.103611 restraints weight = 54106.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.104708 restraints weight = 24973.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.105370 restraints weight = 17952.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.105655 restraints weight = 16520.427| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12442 Z= 0.139 Angle : 0.596 9.248 17413 Z= 0.316 Chirality : 0.039 0.223 2022 Planarity : 0.004 0.050 1694 Dihedral : 17.876 174.102 2831 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.61 % Allowed : 9.59 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.25), residues: 1076 helix: 0.04 (0.23), residues: 523 sheet: -0.51 (0.52), residues: 107 loop : -0.78 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1298 TYR 0.019 0.002 TYR A 362 PHE 0.012 0.001 PHE A1324 TRP 0.011 0.001 TRP A 18 HIS 0.005 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (12442) covalent geometry : angle 0.59642 / 0.32 (17413) hydrogen bonds : bond 0.05136 / 3.22 ( 482) hydrogen bonds : angle 4.39124 / 3.12 ( 1301) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.404 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 0.1146 time to fit residues: 8.5734 Evaluate side-chains 49 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1146 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 89 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 46 optimal weight: 0.0970 chunk 34 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.133500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.102089 restraints weight = 23010.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.104017 restraints weight = 52640.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.104965 restraints weight = 23222.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.105629 restraints weight = 17074.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.105942 restraints weight = 15483.179| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12442 Z= 0.135 Angle : 0.582 9.101 17413 Z= 0.309 Chirality : 0.039 0.223 2022 Planarity : 0.003 0.034 1694 Dihedral : 17.814 174.127 2831 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.92 % Allowed : 9.69 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.26), residues: 1076 helix: 0.12 (0.23), residues: 523 sheet: -0.48 (0.52), residues: 107 loop : -0.77 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1298 TYR 0.019 0.001 TYR A 362 PHE 0.012 0.001 PHE A1324 TRP 0.011 0.001 TRP A 18 HIS 0.004 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (12442) covalent geometry : angle 0.58166 / 0.31 (17413) hydrogen bonds : bond 0.04973 / 3.11 ( 482) hydrogen bonds : angle 4.33237 / 3.08 ( 1301) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.312 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 55 average time/residue: 0.1034 time to fit residues: 8.4471 Evaluate side-chains 54 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 117 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.133184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.102256 restraints weight = 22990.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.104714 restraints weight = 50341.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.105002 restraints weight = 21078.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.105743 restraints weight = 16695.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.105978 restraints weight = 14239.598| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12442 Z= 0.147 Angle : 0.596 9.219 17413 Z= 0.315 Chirality : 0.039 0.225 2022 Planarity : 0.003 0.035 1694 Dihedral : 17.784 173.838 2831 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.92 % Allowed : 10.00 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.26), residues: 1076 helix: 0.15 (0.23), residues: 522 sheet: -0.51 (0.52), residues: 107 loop : -0.83 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1298 TYR 0.021 0.001 TYR A 362 PHE 0.013 0.001 PHE A1324 TRP 0.011 0.001 TRP A 18 HIS 0.004 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (12442) covalent geometry : angle 0.59620 / 0.32 (17413) hydrogen bonds : bond 0.05146 / 3.23 ( 482) hydrogen bonds : angle 4.34379 / 3.09 ( 1301) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 56 average time/residue: 0.1117 time to fit residues: 9.1237 Evaluate side-chains 55 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 48 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.132591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.100156 restraints weight = 23049.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.101760 restraints weight = 51480.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.102570 restraints weight = 26740.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.103294 restraints weight = 18419.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.103686 restraints weight = 16324.801| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12442 Z= 0.166 Angle : 0.618 9.346 17413 Z= 0.325 Chirality : 0.040 0.228 2022 Planarity : 0.003 0.036 1694 Dihedral : 17.763 173.019 2831 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.71 % Allowed : 9.90 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.26), residues: 1076 helix: 0.14 (0.23), residues: 518 sheet: -0.55 (0.52), residues: 106 loop : -0.89 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1298 TYR 0.023 0.002 TYR A 362 PHE 0.016 0.001 PHE A1324 TRP 0.011 0.002 TRP A 18 HIS 0.005 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (12442) covalent geometry : angle 0.61783 / 0.33 (17413) hydrogen bonds : bond 0.05518 / 3.47 ( 482) hydrogen bonds : angle 4.41062 / 3.15 ( 1301) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 57 average time/residue: 0.1154 time to fit residues: 9.5423 Evaluate side-chains 57 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 80 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.0060 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 0.0060 chunk 107 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.0018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.132632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.102194 restraints weight = 22977.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.104521 restraints weight = 51717.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.104848 restraints weight = 21214.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.106104 restraints weight = 16478.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.106188 restraints weight = 13280.520| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12442 Z= 0.159 Angle : 0.608 9.499 17413 Z= 0.321 Chirality : 0.040 0.227 2022 Planarity : 0.003 0.039 1694 Dihedral : 17.733 172.631 2831 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.61 % Allowed : 10.00 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.26), residues: 1076 helix: 0.16 (0.23), residues: 519 sheet: -0.58 (0.51), residues: 106 loop : -0.94 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1298 TYR 0.022 0.002 TYR A 362 PHE 0.014 0.001 PHE A1324 TRP 0.009 0.002 TRP A 18 HIS 0.004 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (12442) covalent geometry : angle 0.60847 / 0.32 (17413) hydrogen bonds : bond 0.05377 / 3.37 ( 482) hydrogen bonds : angle 4.38783 / 3.13 ( 1301) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7409 (tpp) cc_final: 0.6931 (tpp) outliers start: 6 outliers final: 5 residues processed: 55 average time/residue: 0.0955 time to fit residues: 7.8593 Evaluate side-chains 55 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 53 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.132291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.100726 restraints weight = 23081.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.102827 restraints weight = 51645.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.103521 restraints weight = 22729.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.104170 restraints weight = 17269.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.104496 restraints weight = 15231.491| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12442 Z= 0.169 Angle : 0.618 9.549 17413 Z= 0.326 Chirality : 0.040 0.229 2022 Planarity : 0.004 0.039 1694 Dihedral : 17.706 172.101 2831 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.51 % Allowed : 10.20 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.26), residues: 1076 helix: 0.14 (0.23), residues: 520 sheet: -0.60 (0.51), residues: 106 loop : -0.95 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1298 TYR 0.024 0.002 TYR A 362 PHE 0.016 0.001 PHE A1324 TRP 0.011 0.002 TRP A 18 HIS 0.005 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (12442) covalent geometry : angle 0.61847 / 0.33 (17413) hydrogen bonds : bond 0.05621 / 3.53 ( 482) hydrogen bonds : angle 4.41705 / 3.16 ( 1301) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1433.69 seconds wall clock time: 25 minutes 35.99 seconds (1535.99 seconds total)