Starting phenix.real_space_refine on Wed Dec 13 00:16:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezj_28743/12_2023/8ezj_28743_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezj_28743/12_2023/8ezj_28743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezj_28743/12_2023/8ezj_28743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezj_28743/12_2023/8ezj_28743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezj_28743/12_2023/8ezj_28743_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ezj_28743/12_2023/8ezj_28743_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 80 5.16 5 C 14868 2.51 5 N 3780 2.21 5 O 4481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 23215 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 10319 Classifications: {'peptide': 1285} Link IDs: {'PTRANS': 39, 'TRANS': 1245} Chain breaks: 5 Chain: "B" Number of atoms: 10248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1276, 10248 Classifications: {'peptide': 1276} Link IDs: {'PTRANS': 39, 'TRANS': 1236} Chain breaks: 5 Chain: "C" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1292 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain: "D" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1292 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.52, per 1000 atoms: 0.54 Number of scatterers: 23215 At special positions: 0 Unit cell: (123.372, 143.244, 305.532, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 6 15.00 O 4481 8.00 N 3780 7.00 C 14868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.99 Conformation dependent library (CDL) restraints added in 4.8 seconds 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 140 helices and 5 sheets defined 60.9% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.02 Creating SS restraints... Processing helix chain 'A' and resid 11 through 29 Processing helix chain 'A' and resid 71 through 84 Processing helix chain 'A' and resid 94 through 106 Proline residue: A 100 - end of helix Processing helix chain 'A' and resid 112 through 128 Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 159 through 178 Processing helix chain 'A' and resid 180 through 183 No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 187 through 201 Processing helix chain 'A' and resid 208 through 231 removed outlier: 3.860A pdb=" N THR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 343 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 353 through 370 Processing helix chain 'A' and resid 378 through 385 Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 402 through 418 Processing helix chain 'A' and resid 420 through 422 No H-bonds generated for 'chain 'A' and resid 420 through 422' Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 456 through 471 removed outlier: 4.628A pdb=" N LEU A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TRP A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR A 471 " --> pdb=" O SER A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 No H-bonds generated for 'chain 'A' and resid 507 through 510' Processing helix chain 'A' and resid 517 through 536 removed outlier: 3.599A pdb=" N MET A 536 " --> pdb=" O MET A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 Processing helix chain 'A' and resid 552 through 572 removed outlier: 4.024A pdb=" N ARG A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N THR A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU A 562 " --> pdb=" O ASP A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 608 through 614 Processing helix chain 'A' and resid 618 through 630 removed outlier: 4.588A pdb=" N SER A 622 " --> pdb=" O ASP A 619 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A 624 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 648 removed outlier: 4.449A pdb=" N LYS A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 696 through 712 removed outlier: 3.529A pdb=" N THR A 710 " --> pdb=" O ILE A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 730 No H-bonds generated for 'chain 'A' and resid 728 through 730' Processing helix chain 'A' and resid 734 through 736 No H-bonds generated for 'chain 'A' and resid 734 through 736' Processing helix chain 'A' and resid 741 through 752 Processing helix chain 'A' and resid 769 through 776 Processing helix chain 'A' and resid 794 through 796 No H-bonds generated for 'chain 'A' and resid 794 through 796' Processing helix chain 'A' and resid 799 through 827 Proline residue: A 815 - end of helix Processing helix chain 'A' and resid 831 through 851 Processing helix chain 'A' and resid 854 through 868 Processing helix chain 'A' and resid 907 through 913 Processing helix chain 'A' and resid 916 through 931 Processing helix chain 'A' and resid 940 through 955 Processing helix chain 'A' and resid 965 through 970 Processing helix chain 'A' and resid 1011 through 1025 Processing helix chain 'A' and resid 1028 through 1032 Processing helix chain 'A' and resid 1041 through 1049 Processing helix chain 'A' and resid 1060 through 1080 removed outlier: 4.015A pdb=" N PHE A1063 " --> pdb=" O SER A1060 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU A1064 " --> pdb=" O ARG A1061 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA A1065 " --> pdb=" O TYR A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1099 Processing helix chain 'A' and resid 1106 through 1122 Processing helix chain 'A' and resid 1127 through 1140 removed outlier: 3.533A pdb=" N LYS A1140 " --> pdb=" O ASP A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1150 No H-bonds generated for 'chain 'A' and resid 1148 through 1150' Processing helix chain 'A' and resid 1155 through 1165 Processing helix chain 'A' and resid 1173 through 1176 No H-bonds generated for 'chain 'A' and resid 1173 through 1176' Processing helix chain 'A' and resid 1180 through 1190 Processing helix chain 'A' and resid 1195 through 1208 Processing helix chain 'A' and resid 1218 through 1229 Processing helix chain 'A' and resid 1232 through 1246 removed outlier: 4.114A pdb=" N GLU A1241 " --> pdb=" O HIS A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1275 Processing helix chain 'A' and resid 1285 through 1298 Processing helix chain 'A' and resid 1303 through 1319 Processing helix chain 'A' and resid 1331 through 1345 removed outlier: 4.683A pdb=" N LEU A1340 " --> pdb=" O GLU A1336 " (cutoff:3.500A) Proline residue: A1341 - end of helix removed outlier: 3.733A pdb=" N SER A1345 " --> pdb=" O PRO A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1372 removed outlier: 4.003A pdb=" N ILE A1354 " --> pdb=" O ASP A1351 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR A1370 " --> pdb=" O TYR A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1390 Processing helix chain 'A' and resid 1396 through 1416 Processing helix chain 'B' and resid 12 through 29 Processing helix chain 'B' and resid 71 through 83 Processing helix chain 'B' and resid 94 through 106 Proline residue: B 100 - end of helix Processing helix chain 'B' and resid 112 through 127 Processing helix chain 'B' and resid 138 through 151 removed outlier: 3.625A pdb=" N HIS B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 177 Processing helix chain 'B' and resid 180 through 183 No H-bonds generated for 'chain 'B' and resid 180 through 183' Processing helix chain 'B' and resid 187 through 201 Processing helix chain 'B' and resid 209 through 231 removed outlier: 4.057A pdb=" N THR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 342 Processing helix chain 'B' and resid 353 through 370 Processing helix chain 'B' and resid 378 through 385 Processing helix chain 'B' and resid 387 through 397 Processing helix chain 'B' and resid 402 through 418 Processing helix chain 'B' and resid 425 through 438 Processing helix chain 'B' and resid 457 through 470 removed outlier: 4.964A pdb=" N LEU B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TRP B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 484 removed outlier: 3.764A pdb=" N PHE B 477 " --> pdb=" O PRO B 474 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 484 " --> pdb=" O PHE B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 504 Processing helix chain 'B' and resid 507 through 510 No H-bonds generated for 'chain 'B' and resid 507 through 510' Processing helix chain 'B' and resid 517 through 535 Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 552 through 572 removed outlier: 3.926A pdb=" N ARG B 559 " --> pdb=" O LYS B 555 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N THR B 561 " --> pdb=" O ARG B 557 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU B 562 " --> pdb=" O ASP B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 583 Proline residue: B 579 - end of helix Processing helix chain 'B' and resid 592 through 600 Processing helix chain 'B' and resid 608 through 615 Processing helix chain 'B' and resid 622 through 629 Processing helix chain 'B' and resid 638 through 648 removed outlier: 4.198A pdb=" N LYS B 648 " --> pdb=" O ILE B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 672 Processing helix chain 'B' and resid 697 through 712 Processing helix chain 'B' and resid 723 through 729 Processing helix chain 'B' and resid 741 through 753 Processing helix chain 'B' and resid 768 through 777 Processing helix chain 'B' and resid 793 through 796 removed outlier: 3.637A pdb=" N LYS B 796 " --> pdb=" O VAL B 793 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 793 through 796' Processing helix chain 'B' and resid 799 through 827 Proline residue: B 815 - end of helix Processing helix chain 'B' and resid 831 through 850 Processing helix chain 'B' and resid 854 through 868 Processing helix chain 'B' and resid 907 through 913 Processing helix chain 'B' and resid 916 through 931 Processing helix chain 'B' and resid 940 through 955 Processing helix chain 'B' and resid 965 through 971 Processing helix chain 'B' and resid 1011 through 1026 Processing helix chain 'B' and resid 1029 through 1032 No H-bonds generated for 'chain 'B' and resid 1029 through 1032' Processing helix chain 'B' and resid 1041 through 1049 Processing helix chain 'B' and resid 1063 through 1080 Processing helix chain 'B' and resid 1085 through 1099 Processing helix chain 'B' and resid 1106 through 1122 Processing helix chain 'B' and resid 1127 through 1136 Processing helix chain 'B' and resid 1147 through 1150 No H-bonds generated for 'chain 'B' and resid 1147 through 1150' Processing helix chain 'B' and resid 1153 through 1166 Processing helix chain 'B' and resid 1172 through 1177 removed outlier: 3.720A pdb=" N GLY B1177 " --> pdb=" O GLY B1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1189 Processing helix chain 'B' and resid 1195 through 1208 Processing helix chain 'B' and resid 1210 through 1212 No H-bonds generated for 'chain 'B' and resid 1210 through 1212' Processing helix chain 'B' and resid 1218 through 1231 Processing helix chain 'B' and resid 1234 through 1248 removed outlier: 4.729A pdb=" N SER B1248 " --> pdb=" O LYS B1244 " (cutoff:3.500A) Processing helix chain 'B' and resid 1259 through 1276 Processing helix chain 'B' and resid 1285 through 1298 Processing helix chain 'B' and resid 1304 through 1319 Processing helix chain 'B' and resid 1331 through 1343 Proline residue: B1341 - end of helix Processing helix chain 'B' and resid 1350 through 1373 removed outlier: 4.129A pdb=" N ILE B1354 " --> pdb=" O GLU B1350 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B1373 " --> pdb=" O HIS B1369 " (cutoff:3.500A) Processing helix chain 'B' and resid 1379 through 1390 Processing helix chain 'B' and resid 1395 through 1416 Processing helix chain 'C' and resid 31 through 39 Processing helix chain 'C' and resid 76 through 82 Processing helix chain 'C' and resid 98 through 113 removed outlier: 3.978A pdb=" N SER C 102 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 137 through 143 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 167 through 181 Processing helix chain 'D' and resid 31 through 39 Processing helix chain 'D' and resid 76 through 82 Processing helix chain 'D' and resid 98 through 114 removed outlier: 4.286A pdb=" N SER D 102 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN D 113 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 137 through 143 Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 166 through 181 Processing sheet with id= A, first strand: chain 'A' and resid 892 through 894 Processing sheet with id= B, first strand: chain 'B' and resid 892 through 896 Processing sheet with id= C, first strand: chain 'C' and resid 88 through 92 removed outlier: 3.738A pdb=" N VAL C 92 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLY C 25 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 88 through 92 removed outlier: 5.321A pdb=" N GLY D 25 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 121 through 124 removed outlier: 6.190A pdb=" N SER D 153 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N VAL D 124 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER D 155 " --> pdb=" O VAL D 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= E 1191 hydrogen bonds defined for protein. 3300 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: 7.92 Time building geometry restraints manager: 10.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7450 1.34 - 1.46: 4454 1.46 - 1.58: 11564 1.58 - 1.69: 10 1.69 - 1.81: 124 Bond restraints: 23602 Sorted by residual: bond pdb=" C TRP A1220 " pdb=" N VAL A1221 " ideal model delta sigma weight residual 1.334 1.380 -0.046 1.26e-02 6.30e+03 1.34e+01 bond pdb=" N SER A 974 " pdb=" CA SER A 974 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.07e+00 bond pdb=" N TYR D 78 " pdb=" CA TYR D 78 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.77e+00 bond pdb=" N ASN A 326 " pdb=" CA ASN A 326 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.32e-02 5.74e+03 4.65e+00 bond pdb=" N ALA A 695 " pdb=" CA ALA A 695 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.09e+00 ... (remaining 23597 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.39: 440 106.39 - 113.28: 13430 113.28 - 120.18: 8521 120.18 - 127.08: 9355 127.08 - 133.98: 167 Bond angle restraints: 31913 Sorted by residual: angle pdb=" C ILE A 644 " pdb=" CA ILE A 644 " pdb=" CB ILE A 644 " ideal model delta sigma weight residual 111.77 103.27 8.50 2.27e+00 1.94e-01 1.40e+01 angle pdb=" C ASN A 326 " pdb=" N TYR A 327 " pdb=" CA TYR A 327 " ideal model delta sigma weight residual 122.09 117.15 4.94 1.48e+00 4.57e-01 1.11e+01 angle pdb=" C ILE B 232 " pdb=" CA ILE B 232 " pdb=" CB ILE B 232 " ideal model delta sigma weight residual 110.91 114.76 -3.85 1.24e+00 6.50e-01 9.63e+00 angle pdb=" CA TRP D 79 " pdb=" CB TRP D 79 " pdb=" CG TRP D 79 " ideal model delta sigma weight residual 113.60 119.42 -5.82 1.90e+00 2.77e-01 9.38e+00 angle pdb=" C ILE B 219 " pdb=" CA ILE B 219 " pdb=" CB ILE B 219 " ideal model delta sigma weight residual 112.14 108.02 4.12 1.35e+00 5.49e-01 9.32e+00 ... (remaining 31908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.77: 14268 33.77 - 67.54: 164 67.54 - 101.32: 3 101.32 - 135.09: 0 135.09 - 168.86: 2 Dihedral angle restraints: 14437 sinusoidal: 5917 harmonic: 8520 Sorted by residual: dihedral pdb=" O3B GTP D 301 " pdb=" O3A GTP D 301 " pdb=" PB GTP D 301 " pdb=" PA GTP D 301 " ideal model delta sinusoidal sigma weight residual -68.92 99.94 -168.86 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O3B GTP C 301 " pdb=" O3A GTP C 301 " pdb=" PB GTP C 301 " pdb=" PA GTP C 301 " ideal model delta sinusoidal sigma weight residual 291.08 141.31 149.77 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" C8 GTP D 301 " pdb=" C1' GTP D 301 " pdb=" N9 GTP D 301 " pdb=" O4' GTP D 301 " ideal model delta sinusoidal sigma weight residual 104.59 18.73 85.86 1 2.00e+01 2.50e-03 2.23e+01 ... (remaining 14434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2339 0.032 - 0.064: 1033 0.064 - 0.097: 290 0.097 - 0.129: 96 0.129 - 0.161: 8 Chirality restraints: 3766 Sorted by residual: chirality pdb=" CA ILE A 644 " pdb=" N ILE A 644 " pdb=" C ILE A 644 " pdb=" CB ILE A 644 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA THR A 869 " pdb=" N THR A 869 " pdb=" C THR A 869 " pdb=" CB THR A 869 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA GLN A 99 " pdb=" N GLN A 99 " pdb=" C GLN A 99 " pdb=" CB GLN A 99 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 3763 not shown) Planarity restraints: 4009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A1179 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C GLU A1179 " -0.044 2.00e-02 2.50e+03 pdb=" O GLU A1179 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN A1180 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B1284 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" C LYS B1284 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS B1284 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN B1285 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1010 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C GLU A1010 " 0.040 2.00e-02 2.50e+03 pdb=" O GLU A1010 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A1011 " -0.013 2.00e-02 2.50e+03 ... (remaining 4006 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2276 2.74 - 3.28: 25491 3.28 - 3.82: 38534 3.82 - 4.36: 44867 4.36 - 4.90: 75598 Nonbonded interactions: 186766 Sorted by model distance: nonbonded pdb=" O ASN B1056 " pdb=" OG SER B1060 " model vdw 2.195 2.440 nonbonded pdb=" O GLU B1204 " pdb=" OG1 THR B1208 " model vdw 2.216 2.440 nonbonded pdb=" O SER B 509 " pdb=" OG1 THR B 513 " model vdw 2.216 2.440 nonbonded pdb=" O LEU B1339 " pdb=" N LEU B1343 " model vdw 2.217 2.520 nonbonded pdb=" OG1 THR B1009 " pdb=" OE2 GLU B1011 " model vdw 2.217 2.440 ... (remaining 186761 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 871 or resid 888 through 1417)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 27.140 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 64.730 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.130 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:3.020 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23602 Z= 0.283 Angle : 0.554 8.499 31913 Z= 0.300 Chirality : 0.040 0.161 3766 Planarity : 0.004 0.051 4009 Dihedral : 11.204 168.859 8869 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.23 % Allowed : 7.90 % Favored : 91.88 % 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: 0.57 (0.16), residues: 2863 helix: 1.59 (0.12), residues: 1879 sheet: -0.97 (0.58), residues: 94 loop : -2.23 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 470 HIS 0.003 0.001 HIS A 762 PHE 0.011 0.001 PHE B 926 TYR 0.027 0.001 TYR D 78 ARG 0.003 0.000 ARG A 605 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 643 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 647 average time/residue: 0.3823 time to fit residues: 383.7479 Evaluate side-chains 562 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 559 time to evaluate : 2.983 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2793 time to fit residues: 5.5380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 1.9990 chunk 217 optimal weight: 0.2980 chunk 120 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 chunk 146 optimal weight: 0.2980 chunk 116 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 87 optimal weight: 0.0050 chunk 136 optimal weight: 0.9990 chunk 167 optimal weight: 0.2980 chunk 260 optimal weight: 3.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 547 GLN ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1147 GLN ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 GLN ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 571 ASN ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN ** B1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 23602 Z= 0.181 Angle : 0.561 11.275 31913 Z= 0.289 Chirality : 0.039 0.258 3766 Planarity : 0.004 0.046 4009 Dihedral : 6.669 166.908 3078 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.13 % Favored : 92.84 % Rotamer: Outliers : 1.69 % Allowed : 14.40 % Favored : 83.90 % 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: 0.58 (0.16), residues: 2863 helix: 1.59 (0.12), residues: 1877 sheet: -0.91 (0.59), residues: 94 loop : -2.20 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 173 HIS 0.009 0.001 HIS B1369 PHE 0.029 0.002 PHE A1069 TYR 0.020 0.001 TYR D 78 ARG 0.005 0.000 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 570 time to evaluate : 2.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 22 residues processed: 591 average time/residue: 0.3581 time to fit residues: 326.2072 Evaluate side-chains 566 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 544 time to evaluate : 2.582 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2610 time to fit residues: 13.7033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 144 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 216 optimal weight: 0.9990 chunk 177 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 261 optimal weight: 0.6980 chunk 282 optimal weight: 1.9990 chunk 232 optimal weight: 0.2980 chunk 258 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 209 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 ASN A 919 GLN ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN ** B1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1217 ASN ** B1369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23602 Z= 0.251 Angle : 0.577 11.277 31913 Z= 0.297 Chirality : 0.041 0.223 3766 Planarity : 0.004 0.047 4009 Dihedral : 6.706 168.511 3078 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.14 % Favored : 91.83 % Rotamer: Outliers : 1.69 % Allowed : 16.13 % Favored : 82.17 % 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: 0.37 (0.16), residues: 2863 helix: 1.42 (0.12), residues: 1867 sheet: -1.10 (0.57), residues: 94 loop : -2.19 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 173 HIS 0.008 0.001 HIS B1369 PHE 0.027 0.002 PHE A1069 TYR 0.018 0.001 TYR A 327 ARG 0.009 0.000 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 564 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 26 residues processed: 585 average time/residue: 0.3683 time to fit residues: 333.5459 Evaluate side-chains 569 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 543 time to evaluate : 2.767 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2534 time to fit residues: 15.5092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 257 optimal weight: 6.9990 chunk 196 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 chunk 28 optimal weight: 0.0670 chunk 124 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 chunk 277 optimal weight: 0.7980 chunk 136 optimal weight: 0.0370 chunk 248 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 ASN A1147 GLN ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1147 GLN ** B1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1292 GLN B1296 HIS B1297 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23602 Z= 0.211 Angle : 0.575 11.889 31913 Z= 0.292 Chirality : 0.040 0.211 3766 Planarity : 0.004 0.046 4009 Dihedral : 6.696 167.555 3078 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.68 % Favored : 92.28 % Rotamer: Outliers : 1.28 % Allowed : 17.56 % Favored : 81.16 % 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: 0.38 (0.16), residues: 2863 helix: 1.43 (0.12), residues: 1868 sheet: -1.20 (0.56), residues: 94 loop : -2.20 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 173 HIS 0.007 0.001 HIS B1369 PHE 0.027 0.001 PHE A1069 TYR 0.016 0.001 TYR A1201 ARG 0.008 0.000 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 553 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 570 average time/residue: 0.3711 time to fit residues: 326.9354 Evaluate side-chains 556 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 539 time to evaluate : 2.633 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2242 time to fit residues: 11.0869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 231 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 236 optimal weight: 0.3980 chunk 191 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 ASN ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN B1147 GLN ** B1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23602 Z= 0.301 Angle : 0.617 13.175 31913 Z= 0.314 Chirality : 0.042 0.224 3766 Planarity : 0.004 0.048 4009 Dihedral : 6.780 168.844 3078 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.56 % Favored : 91.41 % Rotamer: Outliers : 1.69 % Allowed : 18.16 % Favored : 80.14 % 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 (0.16), residues: 2863 helix: 1.26 (0.12), residues: 1868 sheet: -1.29 (0.53), residues: 104 loop : -2.17 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 173 HIS 0.007 0.001 HIS B1369 PHE 0.049 0.002 PHE B1388 TYR 0.023 0.001 TYR A 327 ARG 0.009 0.000 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 559 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 22 residues processed: 582 average time/residue: 0.3646 time to fit residues: 329.3600 Evaluate side-chains 566 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 544 time to evaluate : 2.520 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2222 time to fit residues: 12.6913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 93 optimal weight: 0.5980 chunk 249 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 162 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 277 optimal weight: 0.5980 chunk 230 optimal weight: 0.2980 chunk 128 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 91 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 ASN ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 421 ASN ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN ** B1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23602 Z= 0.225 Angle : 0.608 12.891 31913 Z= 0.306 Chirality : 0.041 0.222 3766 Planarity : 0.004 0.047 4009 Dihedral : 6.751 167.631 3078 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.96 % Favored : 92.00 % Rotamer: Outliers : 1.09 % Allowed : 19.33 % Favored : 79.58 % 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: 0.29 (0.16), residues: 2863 helix: 1.38 (0.12), residues: 1859 sheet: -1.39 (0.52), residues: 104 loop : -2.21 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 173 HIS 0.008 0.001 HIS B1369 PHE 0.060 0.002 PHE C 91 TYR 0.042 0.001 TYR A1201 ARG 0.008 0.000 ARG A1061 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 547 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 561 average time/residue: 0.3851 time to fit residues: 335.0645 Evaluate side-chains 553 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 535 time to evaluate : 2.558 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2295 time to fit residues: 11.4542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 267 optimal weight: 0.0020 chunk 31 optimal weight: 0.7980 chunk 158 optimal weight: 0.6980 chunk 202 optimal weight: 0.6980 chunk 157 optimal weight: 0.9980 chunk 233 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 276 optimal weight: 0.0060 chunk 173 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 ASN A 948 ASN ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 804 ASN ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN ** B1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1292 GLN ** B1369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23602 Z= 0.217 Angle : 0.610 14.129 31913 Z= 0.306 Chirality : 0.040 0.257 3766 Planarity : 0.004 0.047 4009 Dihedral : 6.731 167.615 3078 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.21 % Favored : 91.76 % Rotamer: Outliers : 0.94 % Allowed : 19.93 % Favored : 79.13 % 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: 0.32 (0.16), residues: 2863 helix: 1.38 (0.12), residues: 1855 sheet: -1.42 (0.52), residues: 104 loop : -2.12 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 173 HIS 0.009 0.001 HIS B1369 PHE 0.047 0.002 PHE C 91 TYR 0.043 0.001 TYR A1201 ARG 0.009 0.000 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 539 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 550 average time/residue: 0.3728 time to fit residues: 317.6547 Evaluate side-chains 542 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 532 time to evaluate : 2.586 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2327 time to fit residues: 8.0340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 171 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 217 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 804 ASN ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN ** B1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23602 Z= 0.232 Angle : 0.628 14.921 31913 Z= 0.314 Chirality : 0.041 0.242 3766 Planarity : 0.004 0.052 4009 Dihedral : 6.753 167.756 3078 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.21 % Favored : 91.76 % Rotamer: Outliers : 0.79 % Allowed : 21.06 % Favored : 78.15 % 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: 0.24 (0.16), residues: 2863 helix: 1.32 (0.12), residues: 1861 sheet: -1.42 (0.52), residues: 104 loop : -2.18 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 173 HIS 0.008 0.001 HIS B1369 PHE 0.056 0.002 PHE B1388 TYR 0.059 0.001 TYR A1201 ARG 0.010 0.000 ARG A1061 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 549 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 561 average time/residue: 0.3751 time to fit residues: 326.5390 Evaluate side-chains 551 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 541 time to evaluate : 2.862 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2590 time to fit residues: 8.4909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 251 optimal weight: 0.0570 chunk 265 optimal weight: 1.9990 chunk 241 optimal weight: 0.7980 chunk 257 optimal weight: 10.0000 chunk 264 optimal weight: 0.0370 chunk 155 optimal weight: 0.5980 chunk 112 optimal weight: 0.0770 chunk 202 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 chunk 232 optimal weight: 0.4980 chunk 243 optimal weight: 0.7980 overall best weight: 0.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN ** B1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23602 Z= 0.178 Angle : 0.627 15.448 31913 Z= 0.310 Chirality : 0.040 0.253 3766 Planarity : 0.004 0.043 4009 Dihedral : 6.698 166.388 3078 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.75 % Favored : 92.21 % Rotamer: Outliers : 0.53 % Allowed : 21.70 % Favored : 77.77 % 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: 0.37 (0.16), residues: 2863 helix: 1.46 (0.12), residues: 1852 sheet: -1.45 (0.52), residues: 104 loop : -2.19 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 173 HIS 0.008 0.001 HIS B1369 PHE 0.058 0.002 PHE B1388 TYR 0.050 0.001 TYR A1201 ARG 0.010 0.000 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 549 time to evaluate : 2.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 555 average time/residue: 0.3787 time to fit residues: 329.2392 Evaluate side-chains 541 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 534 time to evaluate : 2.644 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2814 time to fit residues: 7.1056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 256 optimal weight: 5.9990 chunk 169 optimal weight: 0.6980 chunk 272 optimal weight: 0.9990 chunk 166 optimal weight: 0.0670 chunk 129 optimal weight: 0.9980 chunk 189 optimal weight: 0.0670 chunk 285 optimal weight: 5.9990 chunk 263 optimal weight: 0.8980 chunk 227 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 175 optimal weight: 0.8980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 GLN B 347 ASN ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN ** B1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23602 Z= 0.217 Angle : 0.647 15.879 31913 Z= 0.323 Chirality : 0.041 0.311 3766 Planarity : 0.004 0.044 4009 Dihedral : 6.722 167.250 3078 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.17 % Favored : 91.79 % Rotamer: Outliers : 0.26 % Allowed : 22.26 % Favored : 77.47 % 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: 0.33 (0.16), residues: 2863 helix: 1.42 (0.12), residues: 1852 sheet: -1.48 (0.53), residues: 102 loop : -2.18 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 173 HIS 0.010 0.001 HIS B1369 PHE 0.057 0.002 PHE B1388 TYR 0.026 0.001 TYR A1001 ARG 0.009 0.000 ARG B 807 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 538 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 540 average time/residue: 0.3732 time to fit residues: 312.9208 Evaluate side-chains 532 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 528 time to evaluate : 2.673 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2361 time to fit residues: 5.5640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 139 optimal weight: 0.0770 chunk 180 optimal weight: 0.5980 chunk 242 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 209 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 228 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 234 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 GLN B 347 ASN ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN ** B1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.154671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.131950 restraints weight = 41258.910| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.58 r_work: 0.3534 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23602 Z= 0.245 Angle : 0.664 15.728 31913 Z= 0.332 Chirality : 0.042 0.284 3766 Planarity : 0.004 0.057 4009 Dihedral : 6.774 167.458 3078 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.17 % Favored : 91.79 % Rotamer: Outliers : 0.41 % Allowed : 22.56 % Favored : 77.02 % 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: 0.24 (0.16), residues: 2863 helix: 1.32 (0.12), residues: 1854 sheet: -1.52 (0.53), residues: 102 loop : -2.15 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 173 HIS 0.010 0.001 HIS B1369 PHE 0.056 0.002 PHE B1388 TYR 0.025 0.001 TYR A1001 ARG 0.010 0.000 ARG A1110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7136.37 seconds wall clock time: 129 minutes 15.86 seconds (7755.86 seconds total)