Starting phenix.real_space_refine on Sun Nov 17 01:31:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p51_17436/11_2024/8p51_17436.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p51_17436/11_2024/8p51_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p51_17436/11_2024/8p51_17436.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p51_17436/11_2024/8p51_17436.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p51_17436/11_2024/8p51_17436.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p51_17436/11_2024/8p51_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-5513/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: 7.65, per 1000 atoms: 0.62 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: 3.06 Conformation dependent library (CDL) restraints added in 1.6 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: 1.67 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: 5.85 Time building geometry restraints manager: 3.58 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 31.890 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.530 ------------------------------------------------------------------------------- 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= 0.414 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 *********************** 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 : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.3487 time to fit residues: 59.5784 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 : 1.484 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 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= 0.181 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 *********************** 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 : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1176 ILE cc_start: 0.9752 (pt) cc_final: 0.9371 (mm) outliers start: 9 outliers final: 4 residues processed: 86 average time/residue: 0.2784 time to fit residues: 34.7694 Evaluate side-chains 60 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2431 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= 0.173 Angle : 0.608 11.093 17080 Z= 0.312 Chirality : 0.040 0.174 1893 Planarity : 0.004 0.042 2259 Dihedral : 5.025 22.129 1737 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.69 % Rotamer: Outliers : 0.68 % Allowed : 6.17 % Favored : 93.15 % 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: 0.71 (0.22), residues: 1570 helix: 1.27 (0.19), residues: 804 sheet: -0.21 (0.39), residues: 162 loop : -0.32 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 124 HIS 0.008 0.001 HIS A 63 PHE 0.016 0.001 PHE A 395 TYR 0.016 0.001 TYR A1046 ARG 0.008 0.001 ARG A 125 *********************** 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 75 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1176 ILE cc_start: 0.9732 (pt) cc_final: 0.9303 (mm) outliers start: 9 outliers final: 5 residues processed: 72 average time/residue: 0.2168 time to fit residues: 25.3134 Evaluate side-chains 62 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 1045 VAL Chi-restraints excluded: chain A residue 1203 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 95 optimal weight: 0.2980 chunk 143 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 GLN A1130 ASN ** A1218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12618 Z= 0.160 Angle : 0.561 9.078 17080 Z= 0.289 Chirality : 0.039 0.171 1893 Planarity : 0.004 0.044 2259 Dihedral : 4.690 20.992 1737 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.55 % Favored : 97.39 % Rotamer: Outliers : 0.98 % Allowed : 6.63 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.93 (0.22), residues: 1570 helix: 1.50 (0.19), residues: 798 sheet: -0.04 (0.40), residues: 158 loop : -0.28 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 605 HIS 0.008 0.001 HIS A 63 PHE 0.012 0.001 PHE A 395 TYR 0.018 0.001 TYR A 473 ARG 0.003 0.000 ARG A 125 *********************** 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 79 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1176 ILE cc_start: 0.9724 (pt) cc_final: 0.9309 (mm) outliers start: 13 outliers final: 9 residues processed: 73 average time/residue: 0.2327 time to fit residues: 27.2283 Evaluate side-chains 67 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 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 1203 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12618 Z= 0.218 Angle : 0.588 13.416 17080 Z= 0.300 Chirality : 0.039 0.173 1893 Planarity : 0.004 0.044 2259 Dihedral : 4.541 21.451 1737 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.94 % Rotamer: Outliers : 1.20 % Allowed : 7.91 % 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: 1.02 (0.22), residues: 1570 helix: 1.58 (0.19), residues: 800 sheet: -0.07 (0.40), residues: 157 loop : -0.23 (0.27), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 124 HIS 0.009 0.001 HIS A 63 PHE 0.012 0.001 PHE A 480 TYR 0.015 0.001 TYR A1046 ARG 0.003 0.000 ARG A 125 *********************** 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 78 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 652 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8179 (mp) REVERT: A 1176 ILE cc_start: 0.9727 (pt) cc_final: 0.9319 (mm) outliers start: 16 outliers final: 11 residues processed: 73 average time/residue: 0.2471 time to fit residues: 27.9867 Evaluate side-chains 71 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 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 766 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1203 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 0.3980 chunk 29 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 0.0030 chunk 146 optimal weight: 4.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3124 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= 0.133 Angle : 0.566 13.239 17080 Z= 0.283 Chirality : 0.038 0.173 1893 Planarity : 0.004 0.044 2259 Dihedral : 4.401 20.838 1737 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.13 % Rotamer: Outliers : 1.13 % Allowed : 8.28 % Favored : 90.59 % 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: 1.12 (0.22), residues: 1570 helix: 1.67 (0.19), residues: 800 sheet: -0.11 (0.39), residues: 162 loop : -0.19 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 124 HIS 0.009 0.001 HIS A 63 PHE 0.016 0.001 PHE A 395 TYR 0.015 0.001 TYR A1046 ARG 0.004 0.000 ARG A1213 *********************** 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 81 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.7602 (mmm) cc_final: 0.7356 (mmm) REVERT: A 652 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8128 (mp) REVERT: A 1176 ILE cc_start: 0.9719 (pt) cc_final: 0.9317 (mm) outliers start: 15 outliers final: 9 residues processed: 76 average time/residue: 0.2366 time to fit residues: 28.8595 Evaluate side-chains 71 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 893 THR Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1203 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 387 ASN A1196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3239 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= 0.196 Angle : 0.587 14.975 17080 Z= 0.293 Chirality : 0.039 0.166 1893 Planarity : 0.003 0.043 2259 Dihedral : 4.317 20.478 1737 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.94 % Rotamer: Outliers : 1.05 % Allowed : 9.19 % 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: 1.16 (0.22), residues: 1570 helix: 1.71 (0.19), residues: 800 sheet: -0.17 (0.39), residues: 164 loop : -0.16 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1251 HIS 0.008 0.001 HIS A 63 PHE 0.009 0.001 PHE A 64 TYR 0.015 0.001 TYR A1046 ARG 0.002 0.000 ARG A 531 *********************** 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 79 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 652 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8154 (mp) REVERT: A 1176 ILE cc_start: 0.9714 (pt) cc_final: 0.9348 (mm) REVERT: A 1203 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8839 (tppp) outliers start: 14 outliers final: 9 residues processed: 75 average time/residue: 0.2313 time to fit residues: 27.2452 Evaluate side-chains 74 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 9.9990 chunk 90 optimal weight: 0.0170 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 0.0040 chunk 96 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 overall best weight: 2.2036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12618 Z= 0.234 Angle : 0.603 11.586 17080 Z= 0.301 Chirality : 0.040 0.163 1893 Planarity : 0.003 0.043 2259 Dihedral : 4.332 22.025 1737 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.06 % Favored : 96.88 % Rotamer: Outliers : 1.20 % Allowed : 9.41 % Favored : 89.38 % 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: 800 sheet: -0.19 (0.40), residues: 160 loop : -0.21 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1251 HIS 0.008 0.001 HIS A 63 PHE 0.021 0.001 PHE A 395 TYR 0.014 0.001 TYR A1046 ARG 0.002 0.000 ARG A 531 *********************** 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 76 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 652 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8210 (mp) REVERT: A 1203 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8829 (tppp) outliers start: 16 outliers final: 11 residues processed: 71 average time/residue: 0.2274 time to fit residues: 25.6595 Evaluate side-chains 71 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 1.537 ------------------------------------------------------------------------------- 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 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 947 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1203 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 127 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12618 Z= 0.190 Angle : 0.591 11.752 17080 Z= 0.294 Chirality : 0.039 0.157 1893 Planarity : 0.003 0.043 2259 Dihedral : 4.305 24.673 1737 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 0.98 % Allowed : 9.56 % Favored : 89.46 % 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: 1.18 (0.22), residues: 1570 helix: 1.76 (0.19), residues: 801 sheet: -0.25 (0.39), residues: 169 loop : -0.16 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1251 HIS 0.008 0.001 HIS A 63 PHE 0.022 0.001 PHE A 335 TYR 0.015 0.001 TYR A1046 ARG 0.004 0.000 ARG A 125 *********************** 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 76 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 652 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8206 (mp) REVERT: A 1203 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8834 (tppp) outliers start: 13 outliers final: 8 residues processed: 72 average time/residue: 0.2587 time to fit residues: 29.1378 Evaluate side-chains 70 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 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 947 VAL Chi-restraints excluded: chain A residue 1203 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12618 Z= 0.275 Angle : 0.652 13.329 17080 Z= 0.322 Chirality : 0.040 0.156 1893 Planarity : 0.004 0.043 2259 Dihedral : 4.402 24.452 1737 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.01 % Rotamer: Outliers : 0.90 % Allowed : 9.86 % 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: 1.11 (0.22), residues: 1570 helix: 1.75 (0.19), residues: 794 sheet: -0.43 (0.39), residues: 166 loop : -0.20 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1251 HIS 0.005 0.001 HIS A 63 PHE 0.022 0.001 PHE A 335 TYR 0.015 0.001 TYR A1046 ARG 0.003 0.000 ARG A 125 ********************** 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: 12 poor density : 59 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 652 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8310 (mp) REVERT: A 1203 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8822 (tppp) outliers start: 12 outliers final: 10 residues processed: 68 average time/residue: 0.2467 time to fit residues: 26.7976 Evaluate side-chains 70 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 107 ILE 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 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 947 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1203 LYS 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 38 optimal weight: 0.9980 chunk 114 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.080000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.053541 restraints weight = 55251.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.055496 restraints weight = 28402.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.056771 restraints weight = 19590.814| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 109 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 97 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12618 Z= 0.163 Angle : 0.610 12.098 17080 Z= 0.298 Chirality : 0.039 0.159 1893 Planarity : 0.003 0.042 2259 Dihedral : 4.287 24.481 1737 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.74 % Favored : 97.20 % Rotamer: Outliers : 0.98 % Allowed : 9.71 % 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: 1.16 (0.22), residues: 1570 helix: 1.79 (0.19), residues: 796 sheet: -0.38 (0.39), residues: 171 loop : -0.18 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 805 HIS 0.003 0.001 HIS A 63 PHE 0.010 0.001 PHE A 335 TYR 0.016 0.001 TYR A1046 ARG 0.003 0.000 ARG A1351 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2214.27 seconds wall clock time: 41 minutes 29.96 seconds (2489.96 seconds total)