Starting phenix.real_space_refine on Thu May 15 01:06:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p51_17436/05_2025/8p51_17436.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p51_17436/05_2025/8p51_17436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p51_17436/05_2025/8p51_17436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p51_17436/05_2025/8p51_17436.map" model { file = "/net/cci-nas-00/data/ceres_data/8p51_17436/05_2025/8p51_17436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p51_17436/05_2025/8p51_17436.cif" } resolution = 3.55 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= 0.003 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 7779 2.51 5 N 2197 2.21 5 O 2378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12389 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1574, 12389 Classifications: {'peptide': 1574} Link IDs: {'PTRANS': 59, 'TRANS': 1514} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 16 residue: pdb=" N ILE A 931 " occ=0.37 ... (6 atoms not shown) pdb=" CD1 ILE A 931 " occ=0.00 residue: pdb=" N ALA A 949 " occ=0.94 ... (3 atoms not shown) pdb=" CB ALA A 949 " occ=0.21 residue: pdb=" N GLY A 972 " occ=0.51 ... (2 atoms not shown) pdb=" O GLY A 972 " occ=0.33 residue: pdb=" N ALA A 983 " occ=0.68 ... (3 atoms not shown) pdb=" CB ALA A 983 " occ=0.95 residue: pdb=" N SER A 987 " occ=0.90 ... (4 atoms not shown) pdb=" OG SER A 987 " occ=0.67 residue: pdb=" N ALA A 993 " occ=0.18 ... (3 atoms not shown) pdb=" CB ALA A 993 " occ=0.18 residue: pdb=" N ALA A1040 " occ=0.80 ... (3 atoms not shown) pdb=" CB ALA A1040 " occ=0.98 residue: pdb=" N GLN A1100 " occ=0.81 ... (7 atoms not shown) pdb=" NE2 GLN A1100 " occ=0.23 residue: pdb=" N GLY A1103 " occ=0.91 ... (2 atoms not shown) pdb=" O GLY A1103 " occ=0.48 residue: pdb=" N ASP A1113 " occ=0.69 ... (6 atoms not shown) pdb=" OD2 ASP A1113 " occ=0.64 residue: pdb=" N GLN A1120 " occ=0.79 ... (7 atoms not shown) pdb=" NE2 GLN A1120 " occ=0.78 residue: pdb=" N SER A1160 " occ=0.14 ... (4 atoms not shown) pdb=" OG SER A1160 " occ=0.65 ... (remaining 4 not shown) Time building chain proxies: 7.40, per 1000 atoms: 0.60 Number of scatterers: 12389 At special positions: 0 Unit cell: (103.5, 116.1, 148.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 2378 8.00 N 2197 7.00 C 7779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.7 seconds 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2942 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 11 sheets defined 56.3% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 5 through 22 Processing helix chain 'A' and resid 35 through 55 Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.536A pdb=" N GLN A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 93 through 132 Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 147 through 170 removed outlier: 4.413A pdb=" N ALA A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 202 Processing helix chain 'A' and resid 203 through 216 removed outlier: 4.640A pdb=" N ALA A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ALA A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 296 through 301 removed outlier: 4.122A pdb=" N ARG A 300 " --> pdb=" O PRO A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 321 removed outlier: 3.529A pdb=" N TYR A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 4.093A pdb=" N VAL A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 390 Processing helix chain 'A' and resid 399 through 405 Processing helix chain 'A' and resid 418 through 425 Processing helix chain 'A' and resid 465 through 489 removed outlier: 3.816A pdb=" N SER A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 517 removed outlier: 3.808A pdb=" N ARG A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 541 through 558 Processing helix chain 'A' and resid 561 through 573 removed outlier: 3.523A pdb=" N ARG A 567 " --> pdb=" O PRO A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 577 removed outlier: 6.218A pdb=" N ALA A 577 " --> pdb=" O LYS A 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 574 through 577' Processing helix chain 'A' and resid 578 through 583 removed outlier: 4.157A pdb=" N LEU A 582 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 578 through 583' Processing helix chain 'A' and resid 586 through 589 Processing helix chain 'A' and resid 590 through 598 Processing helix chain 'A' and resid 598 through 623 removed outlier: 4.244A pdb=" N GLU A 611 " --> pdb=" O THR A 607 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU A 613 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR A 614 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 615 " --> pdb=" O GLU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 653 Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 659 through 664 Processing helix chain 'A' and resid 665 through 674 removed outlier: 3.544A pdb=" N LEU A 674 " --> pdb=" O GLU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 698 removed outlier: 3.948A pdb=" N LEU A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS A 688 " --> pdb=" O GLN A 684 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG A 691 " --> pdb=" O PHE A 687 " (cutoff:3.500A) Proline residue: A 692 - end of helix removed outlier: 3.571A pdb=" N PHE A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 731 Processing helix chain 'A' and resid 735 through 740 removed outlier: 3.573A pdb=" N ARG A 740 " --> pdb=" O GLN A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 756 Processing helix chain 'A' and resid 763 through 773 Processing helix chain 'A' and resid 781 through 789 Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 800 through 818 Processing helix chain 'A' and resid 823 through 834 removed outlier: 4.915A pdb=" N VAL A 829 " --> pdb=" O GLU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 857 removed outlier: 3.673A pdb=" N GLU A 855 " --> pdb=" O LYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 878 removed outlier: 3.922A pdb=" N ARG A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) Proline residue: A 875 - end of helix Processing helix chain 'A' and resid 879 through 881 No H-bonds generated for 'chain 'A' and resid 879 through 881' Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 930 through 937 Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 949 through 953 Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 1052 through 1056 Processing helix chain 'A' and resid 1065 through 1070 removed outlier: 3.908A pdb=" N TYR A1069 " --> pdb=" O ASP A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1152 removed outlier: 3.953A pdb=" N GLN A1133 " --> pdb=" O ARG A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1175 No H-bonds generated for 'chain 'A' and resid 1173 through 1175' Processing helix chain 'A' and resid 1176 through 1209 removed outlier: 3.624A pdb=" N ILE A1190 " --> pdb=" O VAL A1186 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP A1193 " --> pdb=" O ARG A1189 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN A1196 " --> pdb=" O ALA A1192 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A1197 " --> pdb=" O ASP A1193 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A1200 " --> pdb=" O GLN A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1259 removed outlier: 4.129A pdb=" N ILE A1217 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN A1219 " --> pdb=" O ASP A1215 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLN A1220 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A1221 " --> pdb=" O ILE A1217 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR A1237 " --> pdb=" O ALA A1233 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL A1238 " --> pdb=" O GLN A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1263 Processing helix chain 'A' and resid 1281 through 1289 Processing helix chain 'A' and resid 1298 through 1308 removed outlier: 4.304A pdb=" N SER A1302 " --> pdb=" O GLY A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1331 Processing helix chain 'A' and resid 1335 through 1358 Processing helix chain 'A' and resid 1361 through 1373 removed outlier: 3.852A pdb=" N PHE A1365 " --> pdb=" O GLN A1361 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER A1366 " --> pdb=" O THR A1362 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU A1367 " --> pdb=" O ALA A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1396 removed outlier: 3.950A pdb=" N GLY A1395 " --> pdb=" O ASP A1391 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG A1396 " --> pdb=" O ARG A1392 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1391 through 1396' Processing helix chain 'A' and resid 1396 through 1429 removed outlier: 3.759A pdb=" N ARG A1402 " --> pdb=" O TYR A1398 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A1406 " --> pdb=" O ARG A1402 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N GLU A1413 " --> pdb=" O ALA A1409 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ALA A1414 " --> pdb=" O SER A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1443 Processing helix chain 'A' and resid 1448 through 1453 Processing helix chain 'A' and resid 1463 through 1473 Processing helix chain 'A' and resid 1515 through 1528 removed outlier: 3.529A pdb=" N GLN A1525 " --> pdb=" O ARG A1521 " (cutoff:3.500A) Processing helix chain 'A' and resid 1531 through 1536 Processing helix chain 'A' and resid 1553 through 1558 removed outlier: 3.765A pdb=" N ALA A1558 " --> pdb=" O THR A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1576 through 1589 Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 236 removed outlier: 7.640A pdb=" N GLU A 234 " --> pdb=" O ARG A 241 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG A 241 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 236 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASN A 274 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLY A 271 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL A 363 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU A 273 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE A 361 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 339 removed outlier: 5.357A pdb=" N ILE A 361 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU A 273 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL A 363 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLY A 271 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASN A 274 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 307 " --> pdb=" O ILE A 398 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 261 Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA5, first strand: chain 'A' and resid 450 through 454 Processing sheet with id=AA6, first strand: chain 'A' and resid 720 through 722 Processing sheet with id=AA7, first strand: chain 'A' and resid 946 through 948 removed outlier: 6.729A pdb=" N LEU A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE A1022 " --> pdb=" O PRO A 992 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR A1025 " --> pdb=" O ALA A1081 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ALA A1081 " --> pdb=" O THR A1025 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 946 through 948 removed outlier: 6.729A pdb=" N LEU A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE A1022 " --> pdb=" O PRO A 992 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR A1025 " --> pdb=" O ALA A1081 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ALA A1081 " --> pdb=" O THR A1025 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1009 through 1014 removed outlier: 6.609A pdb=" N SER A1037 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL A1060 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1376 through 1379 removed outlier: 4.286A pdb=" N PHE A1376 " --> pdb=" O ALA A1512 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1457 through 1462 removed outlier: 5.020A pdb=" N GLY A1459 " --> pdb=" O LEU A1549 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A1549 " --> pdb=" O GLY A1459 " (cutoff:3.500A) 703 hydrogen bonds defined for protein. 2019 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.38 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4230 1.34 - 1.46: 2258 1.46 - 1.57: 6061 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 12618 Sorted by residual: bond pdb=" CD ARG A1530 " pdb=" NE ARG A1530 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.53e+00 bond pdb=" CD ARG A1209 " pdb=" NE ARG A1209 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.45e+00 bond pdb=" CA ARG A1530 " pdb=" CB ARG A1530 " ideal model delta sigma weight residual 1.529 1.507 0.022 1.40e-02 5.10e+03 2.38e+00 bond pdb=" C TYR A1398 " pdb=" N PRO A1399 " ideal model delta sigma weight residual 1.336 1.319 0.017 1.20e-02 6.94e+03 2.05e+00 bond pdb=" CB TRP A 805 " pdb=" CG TRP A 805 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.01e+00 ... (remaining 12613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 15635 1.37 - 2.75: 1166 2.75 - 4.12: 219 4.12 - 5.49: 48 5.49 - 6.87: 12 Bond angle restraints: 17080 Sorted by residual: angle pdb=" N VAL A 969 " pdb=" CA VAL A 969 " pdb=" C VAL A 969 " ideal model delta sigma weight residual 113.71 109.85 3.86 9.50e-01 1.11e+00 1.65e+01 angle pdb=" C GLU A1206 " pdb=" N ASN A1207 " pdb=" CA ASN A1207 " ideal model delta sigma weight residual 121.52 115.83 5.69 1.84e+00 2.95e-01 9.56e+00 angle pdb=" CA ARG A1214 " pdb=" CB ARG A1214 " pdb=" CG ARG A1214 " ideal model delta sigma weight residual 114.10 120.09 -5.99 2.00e+00 2.50e-01 8.97e+00 angle pdb=" N SER A 301 " pdb=" CA SER A 301 " pdb=" C SER A 301 " ideal model delta sigma weight residual 109.81 115.95 -6.14 2.21e+00 2.05e-01 7.71e+00 angle pdb=" CA GLN A 65 " pdb=" CB GLN A 65 " pdb=" CG GLN A 65 " ideal model delta sigma weight residual 114.10 119.61 -5.51 2.00e+00 2.50e-01 7.59e+00 ... (remaining 17075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7066 17.95 - 35.89: 471 35.89 - 53.84: 63 53.84 - 71.79: 36 71.79 - 89.74: 15 Dihedral angle restraints: 7651 sinusoidal: 3078 harmonic: 4573 Sorted by residual: dihedral pdb=" CA PRO A1014 " pdb=" C PRO A1014 " pdb=" N LYS A1015 " pdb=" CA LYS A1015 " ideal model delta harmonic sigma weight residual 180.00 151.40 28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ASN A 984 " pdb=" C ASN A 984 " pdb=" N ASP A 985 " pdb=" CA ASP A 985 " ideal model delta harmonic sigma weight residual 180.00 151.45 28.55 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA SER A 394 " pdb=" C SER A 394 " pdb=" N PHE A 395 " pdb=" CA PHE A 395 " ideal model delta harmonic sigma weight residual 180.00 151.77 28.23 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 7648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1373 0.050 - 0.100: 423 0.100 - 0.149: 91 0.149 - 0.199: 5 0.199 - 0.249: 1 Chirality restraints: 1893 Sorted by residual: chirality pdb=" CA ARG A1209 " pdb=" N ARG A1209 " pdb=" C ARG A1209 " pdb=" CB ARG A1209 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA LYS A1357 " pdb=" N LYS A1357 " pdb=" C LYS A1357 " pdb=" CB LYS A1357 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA PHE A 827 " pdb=" N PHE A 827 " pdb=" C PHE A 827 " pdb=" CB PHE A 827 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 1890 not shown) Planarity restraints: 2259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A1578 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C SER A1578 " 0.067 2.00e-02 2.50e+03 pdb=" O SER A1578 " -0.025 2.00e-02 2.50e+03 pdb=" N SER A1579 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1408 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C LEU A1408 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU A1408 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA A1409 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1405 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C THR A1405 " -0.058 2.00e-02 2.50e+03 pdb=" O THR A1405 " 0.021 2.00e-02 2.50e+03 pdb=" N VAL A1406 " 0.020 2.00e-02 2.50e+03 ... (remaining 2256 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 215 2.67 - 3.23: 12886 3.23 - 3.79: 18643 3.79 - 4.34: 25100 4.34 - 4.90: 40789 Nonbonded interactions: 97633 Sorted by model distance: nonbonded pdb=" O LEU A 144 " pdb=" OH TYR A 196 " model vdw 2.113 3.040 nonbonded pdb=" OG SER A1054 " pdb=" OD2 ASP A1065 " model vdw 2.165 3.040 nonbonded pdb=" OH TYR A1137 " pdb=" OE2 GLU A1241 " model vdw 2.178 3.040 nonbonded pdb=" OG SER A 500 " pdb=" OE1 GLU A 502 " model vdw 2.194 3.040 nonbonded pdb=" OD1 ASN A 13 " pdb=" NH1 ARG A 37 " model vdw 2.257 3.120 ... (remaining 97628 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=0.00 max=1.00 mean=0.97 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.640 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 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 : 0.006 0.044 12618 Z= 0.289 Angle : 0.827 6.865 17080 Z= 0.472 Chirality : 0.048 0.249 1893 Planarity : 0.009 0.101 2259 Dihedral : 13.504 89.737 4709 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -1.93 (0.19), residues: 1570 helix: -1.25 (0.16), residues: 786 sheet: -0.49 (0.38), residues: 160 loop : -1.33 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A1251 HIS 0.008 0.002 HIS A1370 PHE 0.022 0.002 PHE A 30 TYR 0.026 0.005 TYR A 820 ARG 0.022 0.003 ARG A 817 Details of bonding type rmsd hydrogen bonds : bond 0.16011 ( 671) hydrogen bonds : angle 7.02184 ( 2019) covalent geometry : bond 0.00637 (12618) covalent geometry : angle 0.82672 (17080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.3325 time to fit residues: 57.2960 Evaluate side-chains 62 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 20.0000 chunk 80 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 47 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 52 GLN A 288 GLN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 GLN A1052 ASN A1446 HIS A1486 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.080984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.054700 restraints weight = 55455.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.056681 restraints weight = 28319.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.057965 restraints weight = 19444.083| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 109 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 98 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12618 Z= 0.151 Angle : 0.658 8.935 17080 Z= 0.345 Chirality : 0.041 0.156 1893 Planarity : 0.005 0.037 2259 Dihedral : 5.642 21.240 1737 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.68 % Allowed : 4.89 % Favored : 94.43 % 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: 0.20 (0.21), residues: 1570 helix: 0.73 (0.18), residues: 807 sheet: -0.26 (0.39), residues: 162 loop : -0.43 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 605 HIS 0.008 0.001 HIS A 63 PHE 0.018 0.001 PHE A 395 TYR 0.020 0.002 TYR A1046 ARG 0.008 0.001 ARG A1584 Details of bonding type rmsd hydrogen bonds : bond 0.05017 ( 671) hydrogen bonds : angle 5.03050 ( 2019) covalent geometry : bond 0.00282 (12618) covalent geometry : angle 0.65840 (17080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.9803 (tt) cc_final: 0.9444 (mp) REVERT: A 233 MET cc_start: 0.8846 (mmm) cc_final: 0.8629 (mmm) REVERT: A 265 LEU cc_start: 0.9194 (mp) cc_final: 0.8904 (pp) REVERT: A 1062 MET cc_start: 0.8997 (mtt) cc_final: 0.8656 (mpp) REVERT: A 1176 ILE cc_start: 0.9721 (pt) cc_final: 0.9427 (mm) REVERT: A 1215 ASP cc_start: 0.8803 (t0) cc_final: 0.8551 (m-30) REVERT: A 1222 LYS cc_start: 0.9375 (mmtt) cc_final: 0.9106 (mttp) REVERT: A 1392 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8110 (mtp85) outliers start: 9 outliers final: 4 residues processed: 86 average time/residue: 0.2867 time to fit residues: 35.9006 Evaluate side-chains 63 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1064 VAL Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1392 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 67 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 862 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.076258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.049566 restraints weight = 54181.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.051344 restraints weight = 27819.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.052514 restraints weight = 19240.182| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 98 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 100 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12618 Z= 0.173 Angle : 0.627 10.615 17080 Z= 0.326 Chirality : 0.040 0.183 1893 Planarity : 0.004 0.041 2259 Dihedral : 5.080 22.137 1737 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.56 % Rotamer: Outliers : 0.98 % Allowed : 6.25 % Favored : 92.77 % 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: 0.65 (0.22), residues: 1570 helix: 1.23 (0.19), residues: 804 sheet: -0.27 (0.39), residues: 162 loop : -0.35 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 124 HIS 0.008 0.001 HIS A 63 PHE 0.016 0.001 PHE A 395 TYR 0.016 0.002 TYR A1046 ARG 0.009 0.001 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.04436 ( 671) hydrogen bonds : angle 4.72809 ( 2019) covalent geometry : bond 0.00379 (12618) covalent geometry : angle 0.62693 (17080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.9110 (mtp) cc_final: 0.8874 (mtp) REVERT: A 233 MET cc_start: 0.8813 (mmm) cc_final: 0.8534 (mmm) REVERT: A 242 MET cc_start: 0.8729 (tmm) cc_final: 0.8308 (tpt) REVERT: A 265 LEU cc_start: 0.9231 (mp) cc_final: 0.8888 (pp) REVERT: A 1062 MET cc_start: 0.9024 (mtt) cc_final: 0.8664 (mpp) REVERT: A 1176 ILE cc_start: 0.9751 (pt) cc_final: 0.9410 (mm) REVERT: A 1222 LYS cc_start: 0.9440 (mmtt) cc_final: 0.9182 (mttt) REVERT: A 1404 MET cc_start: 0.8950 (ttm) cc_final: 0.8684 (ttm) outliers start: 13 outliers final: 8 residues processed: 73 average time/residue: 0.2342 time to fit residues: 27.1213 Evaluate side-chains 65 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1064 VAL Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1392 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 116 optimal weight: 4.9990 chunk 30 optimal weight: 30.0000 chunk 105 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.077001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.050724 restraints weight = 53556.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.052511 restraints weight = 27401.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.053668 restraints weight = 18911.413| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 100 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 114 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12618 Z= 0.118 Angle : 0.560 8.964 17080 Z= 0.289 Chirality : 0.039 0.168 1893 Planarity : 0.004 0.043 2259 Dihedral : 4.711 21.212 1737 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 0.90 % Allowed : 7.23 % Favored : 91.87 % 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: 0.94 (0.22), residues: 1570 helix: 1.53 (0.19), residues: 796 sheet: -0.17 (0.40), residues: 156 loop : -0.29 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 605 HIS 0.009 0.001 HIS A 63 PHE 0.013 0.001 PHE A 395 TYR 0.015 0.001 TYR A1046 ARG 0.006 0.000 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 671) hydrogen bonds : angle 4.44414 ( 2019) covalent geometry : bond 0.00251 (12618) covalent geometry : angle 0.56013 (17080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.9287 (tp) cc_final: 0.9048 (tt) REVERT: A 166 LEU cc_start: 0.9799 (tt) cc_final: 0.9444 (mp) REVERT: A 233 MET cc_start: 0.8814 (mmm) cc_final: 0.8515 (mmm) REVERT: A 265 LEU cc_start: 0.9221 (mp) cc_final: 0.8867 (pp) REVERT: A 652 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8847 (mp) REVERT: A 1062 MET cc_start: 0.9076 (mtt) cc_final: 0.8706 (mpp) REVERT: A 1176 ILE cc_start: 0.9737 (pt) cc_final: 0.9414 (mm) REVERT: A 1222 LYS cc_start: 0.9428 (mmtt) cc_final: 0.9152 (mttt) REVERT: A 1392 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8223 (mtp85) REVERT: A 1404 MET cc_start: 0.9046 (ttm) cc_final: 0.8793 (ttm) REVERT: A 1478 MET cc_start: 0.8710 (mmm) cc_final: 0.8305 (mmt) outliers start: 12 outliers final: 9 residues processed: 72 average time/residue: 0.2278 time to fit residues: 25.6672 Evaluate side-chains 70 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1392 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 76 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 144 optimal weight: 8.9990 chunk 90 optimal weight: 0.0870 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 GLN A 664 GLN A1130 ASN A1252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.077989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.051939 restraints weight = 52828.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.053761 restraints weight = 26941.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.054956 restraints weight = 18544.920| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 114 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 118 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12618 Z= 0.114 Angle : 0.545 9.539 17080 Z= 0.280 Chirality : 0.038 0.176 1893 Planarity : 0.004 0.043 2259 Dihedral : 4.450 21.699 1737 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 1.28 % Allowed : 7.83 % Favored : 90.89 % 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: 1.13 (0.22), residues: 1570 helix: 1.70 (0.19), residues: 802 sheet: -0.06 (0.39), residues: 157 loop : -0.24 (0.27), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 124 HIS 0.005 0.001 HIS A 119 PHE 0.012 0.001 PHE A 395 TYR 0.016 0.001 TYR A 768 ARG 0.005 0.000 ARG A1392 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 671) hydrogen bonds : angle 4.31637 ( 2019) covalent geometry : bond 0.00242 (12618) covalent geometry : angle 0.54471 (17080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.9789 (tt) cc_final: 0.9458 (mp) REVERT: A 233 MET cc_start: 0.8827 (mmm) cc_final: 0.8500 (mmm) REVERT: A 265 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8851 (pp) REVERT: A 1062 MET cc_start: 0.9152 (mtt) cc_final: 0.8816 (mpp) REVERT: A 1176 ILE cc_start: 0.9725 (pt) cc_final: 0.9408 (mm) REVERT: A 1203 LYS cc_start: 0.9609 (OUTLIER) cc_final: 0.9354 (tppp) REVERT: A 1222 LYS cc_start: 0.9435 (mmtt) cc_final: 0.9129 (mttt) REVERT: A 1392 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8375 (mtp85) REVERT: A 1404 MET cc_start: 0.9065 (ttm) cc_final: 0.8794 (ttm) outliers start: 17 outliers final: 8 residues processed: 75 average time/residue: 0.2659 time to fit residues: 30.6928 Evaluate side-chains 73 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1392 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 120 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 34 optimal weight: 30.0000 chunk 68 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.077510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.050781 restraints weight = 55028.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.052622 restraints weight = 28108.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.053803 restraints weight = 19346.167| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 118 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 117 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12618 Z= 0.148 Angle : 0.559 9.930 17080 Z= 0.285 Chirality : 0.039 0.172 1893 Planarity : 0.004 0.043 2259 Dihedral : 4.393 20.597 1737 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.13 % Rotamer: Outliers : 1.05 % Allowed : 8.96 % Favored : 89.98 % 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: 1.15 (0.22), residues: 1570 helix: 1.74 (0.19), residues: 802 sheet: -0.17 (0.39), residues: 162 loop : -0.23 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 124 HIS 0.004 0.001 HIS A 63 PHE 0.010 0.001 PHE A 497 TYR 0.016 0.001 TYR A1046 ARG 0.005 0.000 ARG A1392 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 671) hydrogen bonds : angle 4.32718 ( 2019) covalent geometry : bond 0.00324 (12618) covalent geometry : angle 0.55914 (17080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.9786 (tt) cc_final: 0.9476 (mp) REVERT: A 233 MET cc_start: 0.8827 (mmm) cc_final: 0.8505 (mmm) REVERT: A 265 LEU cc_start: 0.9231 (mp) cc_final: 0.8895 (pp) REVERT: A 652 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8881 (mp) REVERT: A 1062 MET cc_start: 0.9199 (mtt) cc_final: 0.8858 (mpp) REVERT: A 1176 ILE cc_start: 0.9714 (pt) cc_final: 0.9394 (mm) REVERT: A 1203 LYS cc_start: 0.9602 (OUTLIER) cc_final: 0.9344 (tppp) REVERT: A 1222 LYS cc_start: 0.9440 (mmtt) cc_final: 0.9133 (mttt) REVERT: A 1392 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8190 (mtp85) REVERT: A 1404 MET cc_start: 0.9080 (ttm) cc_final: 0.8807 (ttm) REVERT: A 1478 MET cc_start: 0.8717 (mmm) cc_final: 0.8328 (mmt) outliers start: 14 outliers final: 9 residues processed: 73 average time/residue: 0.2345 time to fit residues: 26.6707 Evaluate side-chains 73 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1392 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 35 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 chunk 129 optimal weight: 0.9980 chunk 96 optimal weight: 0.0870 chunk 62 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.078466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.051888 restraints weight = 54296.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.053747 restraints weight = 27626.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.054988 restraints weight = 18986.978| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 117 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12618 Z= 0.097 Angle : 0.535 10.717 17080 Z= 0.270 Chirality : 0.038 0.165 1893 Planarity : 0.003 0.043 2259 Dihedral : 4.213 21.172 1737 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.74 % Favored : 97.20 % Rotamer: Outliers : 0.98 % Allowed : 9.26 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.22), residues: 1570 helix: 1.82 (0.19), residues: 802 sheet: -0.21 (0.38), residues: 168 loop : -0.14 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 556 HIS 0.004 0.001 HIS A 119 PHE 0.019 0.001 PHE A 395 TYR 0.015 0.001 TYR A1046 ARG 0.005 0.000 ARG A1392 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 671) hydrogen bonds : angle 4.20485 ( 2019) covalent geometry : bond 0.00203 (12618) covalent geometry : angle 0.53507 (17080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.9774 (tt) cc_final: 0.9415 (mt) REVERT: A 233 MET cc_start: 0.8798 (mmm) cc_final: 0.8457 (mmm) REVERT: A 265 LEU cc_start: 0.9203 (mp) cc_final: 0.8881 (pp) REVERT: A 652 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8799 (mp) REVERT: A 1062 MET cc_start: 0.9193 (mtt) cc_final: 0.8844 (mpp) REVERT: A 1176 ILE cc_start: 0.9716 (pt) cc_final: 0.9436 (mm) REVERT: A 1203 LYS cc_start: 0.9602 (OUTLIER) cc_final: 0.9349 (tppp) REVERT: A 1222 LYS cc_start: 0.9429 (mmtt) cc_final: 0.9116 (mttt) REVERT: A 1392 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8180 (mtp85) REVERT: A 1441 SER cc_start: 0.9645 (m) cc_final: 0.9428 (t) REVERT: A 1478 MET cc_start: 0.8719 (mmm) cc_final: 0.8284 (mmt) outliers start: 13 outliers final: 6 residues processed: 74 average time/residue: 0.2360 time to fit residues: 27.1895 Evaluate side-chains 70 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1392 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 30 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 138 optimal weight: 0.8980 chunk 20 optimal weight: 30.0000 chunk 133 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.077496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.050759 restraints weight = 54683.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.052625 restraints weight = 27951.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.053815 restraints weight = 19260.913| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 118 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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 0.029 12618 Z= 0.151 Angle : 0.569 11.182 17080 Z= 0.288 Chirality : 0.039 0.165 1893 Planarity : 0.004 0.043 2259 Dihedral : 4.260 23.047 1737 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.01 % Rotamer: Outliers : 0.90 % Allowed : 9.79 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.22), residues: 1570 helix: 1.85 (0.19), residues: 801 sheet: -0.25 (0.38), residues: 167 loop : -0.17 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 124 HIS 0.004 0.001 HIS A 63 PHE 0.029 0.001 PHE A 335 TYR 0.015 0.001 TYR A1046 ARG 0.006 0.000 ARG A 666 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 671) hydrogen bonds : angle 4.26408 ( 2019) covalent geometry : bond 0.00332 (12618) covalent geometry : angle 0.56912 (17080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.9784 (tt) cc_final: 0.9447 (mp) REVERT: A 233 MET cc_start: 0.8824 (mmm) cc_final: 0.8476 (mmm) REVERT: A 265 LEU cc_start: 0.9212 (mp) cc_final: 0.8915 (pp) REVERT: A 652 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8887 (mp) REVERT: A 1062 MET cc_start: 0.9210 (mtt) cc_final: 0.8846 (mpp) REVERT: A 1203 LYS cc_start: 0.9597 (OUTLIER) cc_final: 0.9342 (tppp) REVERT: A 1222 LYS cc_start: 0.9447 (mmtt) cc_final: 0.9125 (mttt) REVERT: A 1392 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8171 (mtp85) REVERT: A 1478 MET cc_start: 0.8751 (mmm) cc_final: 0.8287 (mmt) outliers start: 12 outliers final: 6 residues processed: 69 average time/residue: 0.2528 time to fit residues: 27.8334 Evaluate side-chains 70 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1392 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 83 optimal weight: 0.8980 chunk 155 optimal weight: 0.1980 chunk 156 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 113 optimal weight: 0.0050 chunk 44 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 62 optimal weight: 0.0050 overall best weight: 0.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 GLN A1535 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.078875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.052347 restraints weight = 53911.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.054251 restraints weight = 27193.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.055480 restraints weight = 18660.697| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 118 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 124 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12618 Z= 0.096 Angle : 0.568 12.591 17080 Z= 0.278 Chirality : 0.038 0.164 1893 Planarity : 0.003 0.043 2259 Dihedral : 4.169 23.639 1737 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 0.75 % Allowed : 9.64 % Favored : 89.61 % 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: 1.27 (0.23), residues: 1570 helix: 1.86 (0.19), residues: 802 sheet: -0.28 (0.38), residues: 169 loop : -0.13 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 556 HIS 0.002 0.000 HIS A 821 PHE 0.022 0.001 PHE A 395 TYR 0.015 0.001 TYR A1046 ARG 0.005 0.000 ARG A1392 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 671) hydrogen bonds : angle 4.20762 ( 2019) covalent geometry : bond 0.00192 (12618) covalent geometry : angle 0.56760 (17080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.9779 (tt) cc_final: 0.9443 (mp) REVERT: A 233 MET cc_start: 0.8798 (mmm) cc_final: 0.8440 (mmm) REVERT: A 265 LEU cc_start: 0.9210 (mp) cc_final: 0.8907 (pp) REVERT: A 652 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8810 (mp) REVERT: A 1222 LYS cc_start: 0.9426 (mmtt) cc_final: 0.9110 (mttt) REVERT: A 1392 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8185 (mtp85) REVERT: A 1478 MET cc_start: 0.8732 (mmm) cc_final: 0.8291 (mmt) outliers start: 10 outliers final: 6 residues processed: 74 average time/residue: 0.2277 time to fit residues: 26.1983 Evaluate side-chains 71 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1392 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 8 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 9 optimal weight: 0.0970 chunk 101 optimal weight: 0.8980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.077994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.051946 restraints weight = 52757.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.053792 restraints weight = 26862.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.054959 restraints weight = 18447.111| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 124 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 127 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12618 Z= 0.120 Angle : 0.566 11.915 17080 Z= 0.280 Chirality : 0.038 0.155 1893 Planarity : 0.003 0.042 2259 Dihedral : 4.122 23.434 1737 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.68 % Favored : 97.26 % Rotamer: Outliers : 0.68 % Allowed : 9.79 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.23), residues: 1570 helix: 1.91 (0.19), residues: 802 sheet: -0.18 (0.39), residues: 169 loop : -0.14 (0.28), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1251 HIS 0.004 0.001 HIS A 63 PHE 0.012 0.001 PHE A 335 TYR 0.015 0.001 TYR A1046 ARG 0.005 0.000 ARG A1392 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 671) hydrogen bonds : angle 4.22260 ( 2019) covalent geometry : bond 0.00263 (12618) covalent geometry : angle 0.56558 (17080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.9784 (tt) cc_final: 0.9456 (mp) REVERT: A 233 MET cc_start: 0.8849 (mmm) cc_final: 0.8475 (mmm) REVERT: A 265 LEU cc_start: 0.9212 (mp) cc_final: 0.8904 (pp) REVERT: A 324 TYR cc_start: 0.7846 (t80) cc_final: 0.7339 (m-80) REVERT: A 652 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8881 (mp) REVERT: A 715 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8066 (mt) REVERT: A 1222 LYS cc_start: 0.9440 (mmtt) cc_final: 0.9123 (mttt) REVERT: A 1392 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8213 (mtp85) REVERT: A 1478 MET cc_start: 0.8746 (mmm) cc_final: 0.8278 (mmt) outliers start: 9 outliers final: 6 residues processed: 68 average time/residue: 0.2322 time to fit residues: 24.5716 Evaluate side-chains 69 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1392 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 83 optimal weight: 0.0570 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.077684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.051047 restraints weight = 54192.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.052878 restraints weight = 27637.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.054080 restraints weight = 19097.855| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 127 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 124 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12618 Z= 0.138 Angle : 0.581 11.737 17080 Z= 0.289 Chirality : 0.038 0.153 1893 Planarity : 0.003 0.042 2259 Dihedral : 4.127 23.101 1737 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 0.75 % Allowed : 10.02 % Favored : 89.23 % 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: 1.32 (0.23), residues: 1570 helix: 1.92 (0.19), residues: 802 sheet: -0.25 (0.39), residues: 171 loop : -0.15 (0.28), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1251 HIS 0.004 0.001 HIS A 63 PHE 0.021 0.001 PHE A 395 TYR 0.015 0.001 TYR A1046 ARG 0.005 0.000 ARG A1392 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 671) hydrogen bonds : angle 4.23448 ( 2019) covalent geometry : bond 0.00306 (12618) covalent geometry : angle 0.58131 (17080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4782.98 seconds wall clock time: 84 minutes 40.66 seconds (5080.66 seconds total)