Starting phenix.real_space_refine on Tue Feb 13 23:47:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wit_32535/02_2024/7wit_32535_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wit_32535/02_2024/7wit_32535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wit_32535/02_2024/7wit_32535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wit_32535/02_2024/7wit_32535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wit_32535/02_2024/7wit_32535_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wit_32535/02_2024/7wit_32535_updated.pdb" } resolution = 3.21 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= 0.007 sd= 0.105 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 3 5.49 5 S 38 5.16 5 C 5222 2.51 5 N 1396 2.21 5 O 1450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1223": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8109 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1135, 8109 Unusual residues: {'9I0': 1, 'ATP': 1} Classifications: {'peptide': 1133, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 239} Link IDs: {'PTRANS': 35, 'TRANS': 1097, None: 2} Not linked: pdbres="ARG A1579 " pdbres="ATP A2001 " Not linked: pdbres="ATP A2001 " pdbres="9I0 A2002 " Chain breaks: 8 Unresolved non-hydrogen bonds: 860 Unresolved non-hydrogen angles: 1072 Unresolved non-hydrogen dihedrals: 686 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 6, 'ASN:plan1': 6, 'ASP:plan': 26, 'PHE:plan': 13, 'GLU:plan': 20, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 468 Time building chain proxies: 4.88, per 1000 atoms: 0.60 Number of scatterers: 8109 At special positions: 0 Unit cell: (97.185, 133.76, 77.33, 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 38 16.00 P 3 15.00 O 1450 8.00 N 1396 7.00 C 5222 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.6 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 6 sheets defined 63.6% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 231 through 242 removed outlier: 4.075A pdb=" N ALA A 235 " --> pdb=" O TRP A 232 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS A 241 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 284 through 294 removed outlier: 3.592A pdb=" N TRP A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 328 removed outlier: 3.679A pdb=" N LEU A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLY A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 355 through 399 removed outlier: 3.876A pdb=" N THR A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.940A pdb=" N CYS A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 433 Processing helix chain 'A' and resid 436 through 456 removed outlier: 5.087A pdb=" N MET A 441 " --> pdb=" O LEU A 438 " (cutoff:3.500A) Proline residue: A 442 - end of helix removed outlier: 3.792A pdb=" N ILE A 445 " --> pdb=" O PRO A 442 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 446 " --> pdb=" O VAL A 443 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 447 " --> pdb=" O GLN A 444 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 456 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 504 removed outlier: 3.576A pdb=" N ILE A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Proline residue: A 472 - end of helix removed outlier: 3.874A pdb=" N HIS A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 512 Processing helix chain 'A' and resid 515 through 564 removed outlier: 3.927A pdb=" N ALA A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 543 " --> pdb=" O TYR A 539 " (cutoff:3.500A) Proline residue: A 551 - end of helix Processing helix chain 'A' and resid 573 through 613 removed outlier: 3.681A pdb=" N ILE A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR A 588 " --> pdb=" O HIS A 584 " (cutoff:3.500A) Proline residue: A 589 - end of helix removed outlier: 4.865A pdb=" N SER A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER A 595 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 726 Processing helix chain 'A' and resid 784 through 789 Processing helix chain 'A' and resid 796 through 806 Processing helix chain 'A' and resid 809 through 814 removed outlier: 3.737A pdb=" N ILE A 814 " --> pdb=" O PRO A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 827 No H-bonds generated for 'chain 'A' and resid 825 through 827' Processing helix chain 'A' and resid 832 through 845 removed outlier: 3.516A pdb=" N ARG A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 871 Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 914 through 920 Processing helix chain 'A' and resid 998 through 1006 Processing helix chain 'A' and resid 1010 through 1024 Processing helix chain 'A' and resid 1027 through 1038 removed outlier: 3.941A pdb=" N ASP A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1105 removed outlier: 4.047A pdb=" N VAL A1086 " --> pdb=" O THR A1082 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A1087 " --> pdb=" O SER A1083 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A1104 " --> pdb=" O SER A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1115 Processing helix chain 'A' and resid 1118 through 1126 removed outlier: 3.906A pdb=" N ARG A1124 " --> pdb=" O SER A1120 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A1125 " --> pdb=" O ILE A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1134 Processing helix chain 'A' and resid 1136 through 1160 removed outlier: 3.554A pdb=" N SER A1158 " --> pdb=" O LEU A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1209 removed outlier: 3.890A pdb=" N LEU A1169 " --> pdb=" O VAL A1166 " (cutoff:3.500A) Proline residue: A1170 - end of helix removed outlier: 4.366A pdb=" N VAL A1174 " --> pdb=" O LEU A1171 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS A1175 " --> pdb=" O ALA A1172 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE A1178 " --> pdb=" O CYS A1175 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A1181 " --> pdb=" O ILE A1178 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A1184 " --> pdb=" O TYR A1181 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER A1186 " --> pdb=" O ARG A1183 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A1187 " --> pdb=" O VAL A1184 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A1190 " --> pdb=" O ARG A1187 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A1193 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A1195 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A1196 " --> pdb=" O ASP A1193 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A1198 " --> pdb=" O THR A1195 " (cutoff:3.500A) Proline residue: A1199 - end of helix removed outlier: 3.553A pdb=" N SER A1202 " --> pdb=" O PRO A1199 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A1209 " --> pdb=" O GLU A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1216 Processing helix chain 'A' and resid 1220 through 1273 removed outlier: 3.536A pdb=" N LEU A1228 " --> pdb=" O GLN A1224 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A1229 " --> pdb=" O GLN A1225 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A1237 " --> pdb=" O SER A1233 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A1241 " --> pdb=" O ALA A1237 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A1242 " --> pdb=" O SER A1238 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A1243 " --> pdb=" O LEU A1239 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU A1261 " --> pdb=" O ALA A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1288 removed outlier: 3.577A pdb=" N TYR A1287 " --> pdb=" O LEU A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1320 removed outlier: 3.820A pdb=" N GLY A1310 " --> pdb=" O GLU A1306 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA A1311 " --> pdb=" O ILE A1307 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL A1312 " --> pdb=" O GLN A1308 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A1320 " --> pdb=" O HIS A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1393 removed outlier: 3.840A pdb=" N SER A1389 " --> pdb=" O LYS A1385 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A1390 " --> pdb=" O SER A1386 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A1392 " --> pdb=" O PHE A1388 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE A1393 " --> pdb=" O SER A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1421 removed outlier: 4.062A pdb=" N SER A1420 " --> pdb=" O HIS A1416 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG A1421 " --> pdb=" O THR A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1440 No H-bonds generated for 'chain 'A' and resid 1437 through 1440' Processing helix chain 'A' and resid 1448 through 1457 Processing helix chain 'A' and resid 1461 through 1466 Processing helix chain 'A' and resid 1484 through 1498 removed outlier: 3.780A pdb=" N ARG A1498 " --> pdb=" O ARG A1494 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1526 Processing helix chain 'A' and resid 1563 through 1569 removed outlier: 3.738A pdb=" N SER A1568 " --> pdb=" O GLU A1564 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 680 through 682 Processing sheet with id= B, first strand: chain 'A' and resid 709 through 713 removed outlier: 6.850A pdb=" N TRP A 899 " --> pdb=" O MET A 710 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL A 712 " --> pdb=" O TRP A 899 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE A 901 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG A 910 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A 904 " --> pdb=" O ILE A 908 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ILE A 908 " --> pdb=" O LYS A 904 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 770 through 773 removed outlier: 7.098A pdb=" N VAL A 850 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ALA A 773 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE A 852 " --> pdb=" O ALA A 773 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR A 883 " --> pdb=" O VAL A 851 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU A 853 " --> pdb=" O THR A 883 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A 885 " --> pdb=" O LEU A 853 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 1367 through 1369 removed outlier: 3.808A pdb=" N ALA A1367 " --> pdb=" O ILE A1347 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1548 through 1552 removed outlier: 6.700A pdb=" N PHE A1503 " --> pdb=" O VAL A1534 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE A1536 " --> pdb=" O PHE A1503 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N MET A1505 " --> pdb=" O ILE A1536 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 685 through 687 removed outlier: 3.515A pdb=" N SER A 734 " --> pdb=" O PHE A 685 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR A 687 " --> pdb=" O LYS A 732 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LYS A 732 " --> pdb=" O THR A 687 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.60 Time building geometry restraints manager: 3.53 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: 2156 1.33 - 1.45: 1353 1.45 - 1.57: 4689 1.57 - 1.69: 5 1.69 - 1.81: 59 Bond restraints: 8262 Sorted by residual: bond pdb=" C12 9I0 A2002 " pdb=" O1 9I0 A2002 " ideal model delta sigma weight residual 1.250 1.328 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C10 9I0 A2002 " pdb=" C12 9I0 A2002 " ideal model delta sigma weight residual 1.545 1.493 0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" C12 9I0 A2002 " pdb=" O2 9I0 A2002 " ideal model delta sigma weight residual 1.246 1.218 0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C 9I0 A2002 " pdb=" C1 9I0 A2002 " ideal model delta sigma weight residual 1.541 1.515 0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" N 9I0 A2002 " pdb=" C8 9I0 A2002 " ideal model delta sigma weight residual 1.346 1.321 0.025 2.00e-02 2.50e+03 1.52e+00 ... (remaining 8257 not shown) Histogram of bond angle deviations from ideal: 99.89 - 107.86: 286 107.86 - 115.84: 5151 115.84 - 123.82: 5683 123.82 - 131.79: 158 131.79 - 139.77: 20 Bond angle restraints: 11298 Sorted by residual: angle pdb=" N VAL A1028 " pdb=" CA VAL A1028 " pdb=" C VAL A1028 " ideal model delta sigma weight residual 111.81 108.62 3.19 8.60e-01 1.35e+00 1.38e+01 angle pdb=" N LYS A1445 " pdb=" CA LYS A1445 " pdb=" C LYS A1445 " ideal model delta sigma weight residual 114.31 110.43 3.88 1.29e+00 6.01e-01 9.04e+00 angle pdb=" O1 9I0 A2002 " pdb=" C12 9I0 A2002 " pdb=" O2 9I0 A2002 " ideal model delta sigma weight residual 126.72 119.32 7.40 3.00e+00 1.11e-01 6.08e+00 angle pdb=" C ILE A1105 " pdb=" CA ILE A1105 " pdb=" CB ILE A1105 " ideal model delta sigma weight residual 112.26 108.76 3.50 1.62e+00 3.81e-01 4.67e+00 angle pdb=" N MET A1025 " pdb=" CA MET A1025 " pdb=" C MET A1025 " ideal model delta sigma weight residual 113.28 110.68 2.60 1.22e+00 6.72e-01 4.53e+00 ... (remaining 11293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.66: 4412 12.66 - 25.31: 349 25.31 - 37.97: 94 37.97 - 50.62: 32 50.62 - 63.28: 13 Dihedral angle restraints: 4900 sinusoidal: 1602 harmonic: 3298 Sorted by residual: dihedral pdb=" CA TYR A 539 " pdb=" C TYR A 539 " pdb=" N THR A 540 " pdb=" CA THR A 540 " ideal model delta harmonic sigma weight residual 180.00 162.16 17.84 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA HIS A1024 " pdb=" C HIS A1024 " pdb=" N MET A1025 " pdb=" CA MET A1025 " ideal model delta harmonic sigma weight residual 180.00 162.57 17.43 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ARG A 370 " pdb=" C ARG A 370 " pdb=" N THR A 371 " pdb=" CA THR A 371 " ideal model delta harmonic sigma weight residual 180.00 163.62 16.38 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 791 0.030 - 0.059: 450 0.059 - 0.089: 96 0.089 - 0.119: 58 0.119 - 0.148: 6 Chirality restraints: 1401 Sorted by residual: chirality pdb=" CA GLN A 219 " pdb=" N GLN A 219 " pdb=" C GLN A 219 " pdb=" CB GLN A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ARG A1531 " pdb=" N ARG A1531 " pdb=" C ARG A1531 " pdb=" CB ARG A1531 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA THR A 588 " pdb=" N THR A 588 " pdb=" C THR A 588 " pdb=" CB THR A 588 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1398 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 9I0 A2002 " -0.001 2.00e-02 2.50e+03 5.61e-02 4.73e+01 pdb=" O 9I0 A2002 " 0.069 2.00e-02 2.50e+03 pdb=" C2 9I0 A2002 " -0.068 2.00e-02 2.50e+03 pdb=" C3 9I0 A2002 " 0.067 2.00e-02 2.50e+03 pdb=" C8 9I0 A2002 " 0.005 2.00e-02 2.50e+03 pdb=" C9 9I0 A2002 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 316 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 317 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 317 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 317 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 588 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO A 589 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " 0.017 5.00e-02 4.00e+02 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2149 2.80 - 3.32: 8284 3.32 - 3.85: 12685 3.85 - 4.37: 14972 4.37 - 4.90: 25539 Nonbonded interactions: 63629 Sorted by model distance: nonbonded pdb=" O ALA A 554 " pdb=" OG1 THR A 558 " model vdw 2.271 2.440 nonbonded pdb=" O THR A1161 " pdb=" OG1 THR A1161 " model vdw 2.285 2.440 nonbonded pdb=" O ASP A 424 " pdb=" OG SER A 606 " model vdw 2.299 2.440 nonbonded pdb=" O ASP A 861 " pdb=" OG SER A 865 " model vdw 2.328 2.440 nonbonded pdb=" OD2 ASP A1031 " pdb=" OH TYR A1287 " model vdw 2.330 2.440 ... (remaining 63624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 3.900 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 26.190 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 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 : 0.005 0.078 8262 Z= 0.314 Angle : 0.565 7.398 11298 Z= 0.299 Chirality : 0.040 0.148 1401 Planarity : 0.004 0.056 1407 Dihedral : 11.490 63.276 2754 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.11 % Allowed : 7.04 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.25), residues: 1115 helix: -0.59 (0.18), residues: 750 sheet: -0.30 (0.70), residues: 68 loop : -0.19 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 739 HIS 0.002 0.001 HIS A 293 PHE 0.010 0.001 PHE A1217 TYR 0.011 0.001 TYR A 230 ARG 0.002 0.000 ARG A1314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7085 (mpt180) REVERT: A 469 LEU cc_start: 0.8098 (tt) cc_final: 0.7621 (mp) REVERT: A 679 VAL cc_start: 0.8567 (t) cc_final: 0.8183 (p) REVERT: A 781 ASN cc_start: 0.8563 (t0) cc_final: 0.8345 (m-40) REVERT: A 903 MET cc_start: 0.7218 (mmm) cc_final: 0.6015 (mmm) REVERT: A 1018 PHE cc_start: 0.7032 (t80) cc_final: 0.6646 (t80) REVERT: A 1253 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6065 (mp0) REVERT: A 1296 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7960 (t0) outliers start: 23 outliers final: 4 residues processed: 150 average time/residue: 0.2272 time to fit residues: 45.2101 Evaluate side-chains 94 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1296 ASN Chi-restraints excluded: chain A residue 1350 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.0040 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 45 optimal weight: 0.1980 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 102 optimal weight: 0.1980 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 836 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8262 Z= 0.148 Angle : 0.506 8.861 11298 Z= 0.261 Chirality : 0.039 0.158 1401 Planarity : 0.004 0.033 1407 Dihedral : 7.169 67.307 1273 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.71 % Allowed : 11.77 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1115 helix: 0.85 (0.19), residues: 760 sheet: -0.17 (0.73), residues: 63 loop : -0.25 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1033 HIS 0.003 0.001 HIS A1098 PHE 0.029 0.001 PHE A 738 TYR 0.012 0.001 TYR A 845 ARG 0.007 0.001 ARG A1111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6998 (mpt180) REVERT: A 469 LEU cc_start: 0.7951 (tt) cc_final: 0.7739 (mp) REVERT: A 721 SER cc_start: 0.8901 (t) cc_final: 0.8419 (m) REVERT: A 836 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7774 (tm-30) REVERT: A 903 MET cc_start: 0.7372 (mmm) cc_final: 0.6559 (mmp) REVERT: A 1184 VAL cc_start: 0.8483 (t) cc_final: 0.8273 (m) outliers start: 20 outliers final: 7 residues processed: 108 average time/residue: 0.1865 time to fit residues: 28.6349 Evaluate side-chains 86 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1350 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 836 GLN A1296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8262 Z= 0.227 Angle : 0.528 6.400 11298 Z= 0.266 Chirality : 0.040 0.144 1401 Planarity : 0.003 0.034 1407 Dihedral : 6.721 68.568 1267 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.11 % Allowed : 15.02 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1115 helix: 1.11 (0.19), residues: 758 sheet: -0.06 (0.71), residues: 69 loop : -0.38 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 430 HIS 0.004 0.001 HIS A1024 PHE 0.020 0.001 PHE A 738 TYR 0.027 0.001 TYR A 378 ARG 0.008 0.001 ARG A 878 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7044 (mpt180) REVERT: A 469 LEU cc_start: 0.7951 (tt) cc_final: 0.7703 (mp) REVERT: A 592 LEU cc_start: 0.8238 (tp) cc_final: 0.7734 (mp) REVERT: A 721 SER cc_start: 0.8879 (t) cc_final: 0.8433 (m) REVERT: A 836 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: A 903 MET cc_start: 0.7300 (mmm) cc_final: 0.5947 (mmm) outliers start: 23 outliers final: 11 residues processed: 102 average time/residue: 0.1751 time to fit residues: 25.6639 Evaluate side-chains 91 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1423 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 69 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 chunk 109 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 chunk 29 optimal weight: 0.0570 chunk 90 optimal weight: 10.0000 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8262 Z= 0.162 Angle : 0.475 6.473 11298 Z= 0.238 Chirality : 0.038 0.140 1401 Planarity : 0.003 0.032 1407 Dihedral : 6.490 69.848 1266 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.11 % Allowed : 16.37 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.19 (0.26), residues: 1115 helix: 1.36 (0.19), residues: 759 sheet: -0.03 (0.70), residues: 69 loop : -0.37 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1247 HIS 0.003 0.001 HIS A1024 PHE 0.017 0.001 PHE A 738 TYR 0.010 0.001 TYR A 378 ARG 0.007 0.000 ARG A 878 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 89 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6967 (mpt180) REVERT: A 485 GLN cc_start: 0.7634 (tt0) cc_final: 0.7217 (tm-30) REVERT: A 501 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7689 (tt0) REVERT: A 592 LEU cc_start: 0.8256 (tp) cc_final: 0.7849 (mp) REVERT: A 721 SER cc_start: 0.8762 (t) cc_final: 0.8327 (m) REVERT: A 836 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: A 903 MET cc_start: 0.7394 (mmm) cc_final: 0.5986 (mmm) outliers start: 23 outliers final: 15 residues processed: 103 average time/residue: 0.1900 time to fit residues: 27.6381 Evaluate side-chains 96 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1423 SER Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 93 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 98 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8262 Z= 0.207 Angle : 0.497 7.020 11298 Z= 0.247 Chirality : 0.039 0.139 1401 Planarity : 0.003 0.033 1407 Dihedral : 6.425 71.125 1266 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.06 % Allowed : 16.37 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1115 helix: 1.45 (0.19), residues: 756 sheet: -0.05 (0.70), residues: 69 loop : -0.38 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1247 HIS 0.003 0.001 HIS A1024 PHE 0.021 0.001 PHE A 738 TYR 0.010 0.001 TYR A 378 ARG 0.006 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 82 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6920 (mpt180) REVERT: A 485 GLN cc_start: 0.7646 (tt0) cc_final: 0.7122 (tm-30) REVERT: A 501 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7777 (tt0) REVERT: A 592 LEU cc_start: 0.8277 (tp) cc_final: 0.7862 (mp) REVERT: A 721 SER cc_start: 0.8757 (t) cc_final: 0.8335 (m) REVERT: A 903 MET cc_start: 0.7328 (mmm) cc_final: 0.5877 (mmm) REVERT: A 1290 MET cc_start: 0.7911 (tpp) cc_final: 0.7591 (tpp) outliers start: 30 outliers final: 21 residues processed: 105 average time/residue: 0.1701 time to fit residues: 26.5258 Evaluate side-chains 100 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 78 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1423 SER Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 109 optimal weight: 0.0470 chunk 90 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 0.0270 chunk 57 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8262 Z= 0.156 Angle : 0.463 6.249 11298 Z= 0.231 Chirality : 0.038 0.139 1401 Planarity : 0.003 0.032 1407 Dihedral : 6.235 73.014 1266 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.84 % Allowed : 18.13 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.26), residues: 1115 helix: 1.64 (0.19), residues: 753 sheet: -0.01 (0.70), residues: 69 loop : -0.27 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 739 HIS 0.002 0.001 HIS A1024 PHE 0.015 0.001 PHE A 738 TYR 0.010 0.001 TYR A 845 ARG 0.004 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 485 GLN cc_start: 0.7629 (tt0) cc_final: 0.7116 (tm-30) REVERT: A 592 LEU cc_start: 0.8307 (tp) cc_final: 0.7889 (mp) REVERT: A 721 SER cc_start: 0.8726 (t) cc_final: 0.8319 (m) REVERT: A 903 MET cc_start: 0.7407 (mmm) cc_final: 0.5900 (mmm) REVERT: A 1290 MET cc_start: 0.8022 (tpp) cc_final: 0.7683 (tpp) outliers start: 21 outliers final: 18 residues processed: 102 average time/residue: 0.1555 time to fit residues: 23.7230 Evaluate side-chains 99 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1423 SER Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 68 optimal weight: 0.0970 chunk 66 optimal weight: 0.0970 chunk 50 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8262 Z= 0.159 Angle : 0.462 6.570 11298 Z= 0.229 Chirality : 0.038 0.139 1401 Planarity : 0.003 0.032 1407 Dihedral : 5.834 75.278 1260 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.57 % Allowed : 18.94 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.26), residues: 1115 helix: 1.71 (0.19), residues: 754 sheet: 0.02 (0.69), residues: 69 loop : -0.28 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 430 HIS 0.003 0.001 HIS A1024 PHE 0.013 0.001 PHE A 738 TYR 0.009 0.001 TYR A 378 ARG 0.005 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 485 GLN cc_start: 0.7653 (tt0) cc_final: 0.7152 (tm-30) REVERT: A 592 LEU cc_start: 0.8234 (tp) cc_final: 0.7814 (mp) REVERT: A 721 SER cc_start: 0.8761 (t) cc_final: 0.8362 (m) REVERT: A 903 MET cc_start: 0.7347 (mmm) cc_final: 0.5829 (mmm) REVERT: A 1290 MET cc_start: 0.8146 (tpp) cc_final: 0.7775 (tpp) outliers start: 19 outliers final: 17 residues processed: 100 average time/residue: 0.1731 time to fit residues: 25.4738 Evaluate side-chains 99 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 104 optimal weight: 0.0270 chunk 95 optimal weight: 10.0000 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8262 Z= 0.191 Angle : 0.476 6.941 11298 Z= 0.236 Chirality : 0.039 0.139 1401 Planarity : 0.003 0.043 1407 Dihedral : 5.885 77.165 1260 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.25 % Allowed : 19.35 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.26), residues: 1115 helix: 1.69 (0.19), residues: 753 sheet: -0.02 (0.69), residues: 69 loop : -0.29 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 430 HIS 0.003 0.001 HIS A1024 PHE 0.013 0.001 PHE A 738 TYR 0.009 0.001 TYR A 378 ARG 0.008 0.000 ARG A 878 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7162 (m-80) cc_final: 0.6456 (m-80) REVERT: A 485 GLN cc_start: 0.7645 (tt0) cc_final: 0.7201 (tm-30) REVERT: A 592 LEU cc_start: 0.8251 (tp) cc_final: 0.7827 (mp) REVERT: A 612 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7901 (tp30) REVERT: A 721 SER cc_start: 0.8793 (t) cc_final: 0.8410 (m) REVERT: A 903 MET cc_start: 0.7494 (mmm) cc_final: 0.6009 (mmm) REVERT: A 1290 MET cc_start: 0.8171 (tpp) cc_final: 0.7810 (tpp) outliers start: 24 outliers final: 21 residues processed: 103 average time/residue: 0.1651 time to fit residues: 25.4162 Evaluate side-chains 106 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1423 SER Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8262 Z= 0.161 Angle : 0.460 7.445 11298 Z= 0.228 Chirality : 0.038 0.139 1401 Planarity : 0.003 0.031 1407 Dihedral : 5.795 77.466 1260 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.11 % Allowed : 19.49 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.26), residues: 1115 helix: 1.77 (0.19), residues: 750 sheet: 0.01 (0.69), residues: 69 loop : -0.25 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 430 HIS 0.003 0.001 HIS A1098 PHE 0.014 0.001 PHE A 738 TYR 0.009 0.001 TYR A 378 ARG 0.007 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7122 (m-80) cc_final: 0.6466 (m-80) REVERT: A 297 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6888 (mpt180) REVERT: A 485 GLN cc_start: 0.7615 (tt0) cc_final: 0.7170 (tm-30) REVERT: A 592 LEU cc_start: 0.8250 (tp) cc_final: 0.7826 (mp) REVERT: A 721 SER cc_start: 0.8799 (t) cc_final: 0.8425 (m) REVERT: A 903 MET cc_start: 0.7471 (mmm) cc_final: 0.6075 (mmm) REVERT: A 1290 MET cc_start: 0.8167 (tpp) cc_final: 0.7829 (tpp) outliers start: 23 outliers final: 22 residues processed: 106 average time/residue: 0.1750 time to fit residues: 26.8474 Evaluate side-chains 108 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1423 SER Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8262 Z= 0.224 Angle : 0.501 7.244 11298 Z= 0.248 Chirality : 0.039 0.140 1401 Planarity : 0.003 0.035 1407 Dihedral : 5.893 77.805 1260 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.25 % Allowed : 19.76 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.26), residues: 1115 helix: 1.65 (0.19), residues: 751 sheet: -0.03 (0.69), residues: 69 loop : -0.14 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 430 HIS 0.004 0.001 HIS A1024 PHE 0.018 0.001 PHE A 236 TYR 0.009 0.001 TYR A 378 ARG 0.011 0.001 ARG A 835 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7154 (m-80) cc_final: 0.6387 (m-80) REVERT: A 297 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6811 (mpt180) REVERT: A 485 GLN cc_start: 0.7657 (tt0) cc_final: 0.7234 (tm-30) REVERT: A 592 LEU cc_start: 0.8265 (tp) cc_final: 0.7833 (mp) REVERT: A 721 SER cc_start: 0.8835 (t) cc_final: 0.8472 (m) REVERT: A 903 MET cc_start: 0.7394 (mmm) cc_final: 0.6004 (mmm) REVERT: A 1290 MET cc_start: 0.8238 (tpp) cc_final: 0.7901 (tpp) outliers start: 24 outliers final: 23 residues processed: 101 average time/residue: 0.1826 time to fit residues: 26.7381 Evaluate side-chains 104 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 80 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1423 SER Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.148329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.112139 restraints weight = 12161.417| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.36 r_work: 0.3452 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8262 Z= 0.188 Angle : 0.484 7.471 11298 Z= 0.239 Chirality : 0.039 0.139 1401 Planarity : 0.003 0.031 1407 Dihedral : 5.843 77.070 1260 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.52 % Allowed : 19.76 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.26), residues: 1115 helix: 1.80 (0.19), residues: 742 sheet: -0.01 (0.68), residues: 69 loop : -0.17 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1247 HIS 0.003 0.001 HIS A1024 PHE 0.013 0.001 PHE A 738 TYR 0.009 0.001 TYR A 378 ARG 0.009 0.000 ARG A 835 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1854.36 seconds wall clock time: 34 minutes 25.01 seconds (2065.01 seconds total)