Starting phenix.real_space_refine on Sun Jul 21 17:09:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t76_41085/07_2024/8t76_41085.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t76_41085/07_2024/8t76_41085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t76_41085/07_2024/8t76_41085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t76_41085/07_2024/8t76_41085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t76_41085/07_2024/8t76_41085.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t76_41085/07_2024/8t76_41085.cif" } resolution = 3.42 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= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4884 atoms to isotropic. 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 111 5.49 5 S 17 5.16 5 C 6629 2.51 5 N 1932 2.21 5 O 2360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 39": "OD1" <-> "OD2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 353": "OD1" <-> "OD2" Residue "A TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A GLU 952": "OE1" <-> "OE2" Residue "A TYR 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1108": "OE1" <-> "OE2" Residue "A GLU 1150": "OE1" <-> "OE2" Residue "A GLU 1225": "OE1" <-> "OE2" Residue "A ASP 1267": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11049 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8689 Classifications: {'peptide': 1088} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 30, 'TRANS': 1057} Chain breaks: 5 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1887 Classifications: {'RNA': 88} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 46, 'rna3p_pyr': 31} Link IDs: {'rna2p': 10, 'rna3p': 77} Chain: "C" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Time building chain proxies: 7.67, per 1000 atoms: 0.69 Number of scatterers: 11049 At special positions: 0 Unit cell: (87.486, 120.814, 121.647, 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 17 16.00 P 111 15.00 O 2360 8.00 N 1932 7.00 C 6629 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: 4.88 Conformation dependent library (CDL) restraints added in 1.5 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 56.6% alpha, 10.9% beta 35 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 4.14 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.611A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.919A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 180 through 197 removed outlier: 4.168A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 236 through 245 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 286 through 305 Processing helix chain 'A' and resid 308 through 312 removed outlier: 4.260A pdb=" N ILE A 312 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 removed outlier: 4.837A pdb=" N LYS A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.836A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.200A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.585A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.546A pdb=" N GLU A 480 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.704A pdb=" N ILE A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 4.265A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 652 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 703 through 713 removed outlier: 3.575A pdb=" N ALA A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.545A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 940 removed outlier: 4.548A pdb=" N ILE A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU A 935 " --> pdb=" O VAL A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 980 through 1000 removed outlier: 4.501A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.813A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1240 Processing helix chain 'A' and resid 1248 through 1261 Processing helix chain 'A' and resid 1264 through 1281 removed outlier: 4.034A pdb=" N GLU A1271 " --> pdb=" O ASP A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1317 removed outlier: 3.534A pdb=" N GLN A1305 " --> pdb=" O PRO A1301 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A1310 " --> pdb=" O ALA A1306 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N THR A1314 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU A1315 " --> pdb=" O HIS A1311 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR A1316 " --> pdb=" O LEU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.510A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1340 through 1344' Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 959 removed outlier: 7.073A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N LEU A 9 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 9.954A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 529 through 530 Processing sheet with id=AA4, first strand: chain 'A' and resid 1106 through 1111 removed outlier: 6.449A pdb=" N LYS A1107 " --> pdb=" O PRO A1137 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N SER A1109 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU A1135 " --> pdb=" O SER A1109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 4.030A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A1158 " --> pdb=" O VAL A1149 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 4.030A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A1158 " --> pdb=" O VAL A1149 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 87 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 5.30 Time building geometry restraints manager: 5.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2660 1.33 - 1.46: 2907 1.46 - 1.58: 5674 1.58 - 1.70: 219 1.70 - 1.82: 32 Bond restraints: 11492 Sorted by residual: bond pdb=" CB ASP A1344 " pdb=" CG ASP A1344 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.62e+00 bond pdb=" C ASN A 199 " pdb=" O ASN A 199 " ideal model delta sigma weight residual 1.238 1.214 0.024 1.28e-02 6.10e+03 3.47e+00 bond pdb=" CA ARG A 457 " pdb=" CB ARG A 457 " ideal model delta sigma weight residual 1.528 1.554 -0.026 1.39e-02 5.18e+03 3.40e+00 bond pdb=" CA ILE A 201 " pdb=" CB ILE A 201 " ideal model delta sigma weight residual 1.528 1.552 -0.025 1.34e-02 5.57e+03 3.35e+00 bond pdb=" CA VAL A 27 " pdb=" C VAL A 27 " ideal model delta sigma weight residual 1.526 1.512 0.014 7.90e-03 1.60e+04 3.23e+00 ... (remaining 11487 not shown) Histogram of bond angle deviations from ideal: 97.67 - 104.93: 588 104.93 - 112.20: 5721 112.20 - 119.47: 4106 119.47 - 126.74: 5213 126.74 - 134.01: 414 Bond angle restraints: 16042 Sorted by residual: angle pdb=" CA LYS A 929 " pdb=" CB LYS A 929 " pdb=" CG LYS A 929 " ideal model delta sigma weight residual 114.10 127.25 -13.15 2.00e+00 2.50e-01 4.33e+01 angle pdb=" CA ARG A 457 " pdb=" CB ARG A 457 " pdb=" CG ARG A 457 " ideal model delta sigma weight residual 114.10 125.25 -11.15 2.00e+00 2.50e-01 3.11e+01 angle pdb=" CB LYS A 755 " pdb=" CG LYS A 755 " pdb=" CD LYS A 755 " ideal model delta sigma weight residual 111.30 123.47 -12.17 2.30e+00 1.89e-01 2.80e+01 angle pdb=" CA LEU A 156 " pdb=" CB LEU A 156 " pdb=" CG LEU A 156 " ideal model delta sigma weight residual 116.30 133.43 -17.13 3.50e+00 8.16e-02 2.39e+01 angle pdb=" CA LYS A1158 " pdb=" CB LYS A1158 " pdb=" CG LYS A1158 " ideal model delta sigma weight residual 114.10 123.38 -9.28 2.00e+00 2.50e-01 2.15e+01 ... (remaining 16037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.75: 6387 29.75 - 59.50: 490 59.50 - 89.25: 93 89.25 - 119.00: 1 119.00 - 148.75: 1 Dihedral angle restraints: 6972 sinusoidal: 3772 harmonic: 3200 Sorted by residual: dihedral pdb=" CA GLU A1099 " pdb=" C GLU A1099 " pdb=" N VAL A1100 " pdb=" CA VAL A1100 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA PRO A 200 " pdb=" C PRO A 200 " pdb=" N ILE A 201 " pdb=" CA ILE A 201 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PHE A 498 " pdb=" C PHE A 498 " pdb=" N ASP A 499 " pdb=" CA ASP A 499 " ideal model delta harmonic sigma weight residual -180.00 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 6969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1575 0.064 - 0.129: 259 0.129 - 0.193: 35 0.193 - 0.257: 6 0.257 - 0.321: 3 Chirality restraints: 1878 Sorted by residual: chirality pdb=" CG LEU A 156 " pdb=" CB LEU A 156 " pdb=" CD1 LEU A 156 " pdb=" CD2 LEU A 156 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C3' A B 38 " pdb=" C4' A B 38 " pdb=" O3' A B 38 " pdb=" C2' A B 38 " both_signs ideal model delta sigma weight residual False -2.48 -2.22 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE A 201 " pdb=" CA ILE A 201 " pdb=" CG1 ILE A 201 " pdb=" CG2 ILE A 201 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1875 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 499 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.69e+00 pdb=" CG ASP A 499 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASP A 499 " 0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP A 499 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 936 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.70e+00 pdb=" CG ASP A 936 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP A 936 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 936 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1166 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.32e+00 pdb=" C ILE A1166 " 0.043 2.00e-02 2.50e+03 pdb=" O ILE A1166 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A1167 " -0.015 2.00e-02 2.50e+03 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2726 2.80 - 3.33: 10104 3.33 - 3.85: 20021 3.85 - 4.38: 22954 4.38 - 4.90: 35813 Nonbonded interactions: 91618 Sorted by model distance: nonbonded pdb=" OD2 ASP A 110 " pdb=" OH TYR A1131 " model vdw 2.278 2.440 nonbonded pdb=" OG SER A 6 " pdb=" OD1 ASN A 758 " model vdw 2.307 2.440 nonbonded pdb=" OD1 ASN A 14 " pdb=" OG SER A 55 " model vdw 2.308 2.440 nonbonded pdb=" OD2 ASP A 596 " pdb=" OH TYR A 656 " model vdw 2.310 2.440 nonbonded pdb=" OG SER A 541 " pdb=" OE1 GLN A 544 " model vdw 2.312 2.440 ... (remaining 91613 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=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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 38.280 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11492 Z= 0.295 Angle : 1.021 17.128 16042 Z= 0.517 Chirality : 0.050 0.321 1878 Planarity : 0.007 0.060 1638 Dihedral : 18.986 148.749 4896 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.32 % Allowed : 21.30 % Favored : 78.38 % 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: -1.23 (0.24), residues: 1076 helix: -0.88 (0.20), residues: 524 sheet: -0.30 (0.51), residues: 102 loop : -0.62 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 464 HIS 0.022 0.002 HIS A1297 PHE 0.025 0.003 PHE A 518 TYR 0.037 0.003 TYR A 517 ARG 0.013 0.001 ARG A1317 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 1.040 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8304 (m-80) cc_final: 0.7738 (m-80) REVERT: A 631 MET cc_start: 0.6515 (tpt) cc_final: 0.6288 (tpt) REVERT: A 763 MET cc_start: -0.1591 (mmm) cc_final: -0.1836 (mmm) REVERT: A 939 MET cc_start: 0.8749 (mmp) cc_final: 0.8052 (mmt) REVERT: A 1124 LYS cc_start: 0.9168 (tppt) cc_final: 0.8849 (ptpp) REVERT: A 1225 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7163 (mm-30) outliers start: 3 outliers final: 1 residues processed: 94 average time/residue: 0.2707 time to fit residues: 35.6861 Evaluate side-chains 72 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1166 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 0.0980 chunk 47 optimal weight: 0.4980 chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 0.0170 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 129 HIS A 190 GLN ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11492 Z= 0.205 Angle : 0.569 7.411 16042 Z= 0.302 Chirality : 0.037 0.168 1878 Planarity : 0.004 0.042 1638 Dihedral : 19.018 152.945 2768 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.81 % Allowed : 16.65 % Favored : 80.54 % 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 (0.25), residues: 1076 helix: 0.15 (0.22), residues: 537 sheet: -0.19 (0.54), residues: 97 loop : -0.36 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1136 HIS 0.007 0.001 HIS A 129 PHE 0.014 0.002 PHE A 693 TYR 0.014 0.001 TYR A 517 ARG 0.006 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 77 time to evaluate : 1.059 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 revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8389 (m-80) cc_final: 0.7767 (m-80) REVERT: A 220 ARG cc_start: 0.9518 (mmp-170) cc_final: 0.9289 (mpp-170) REVERT: A 625 LEU cc_start: 0.8926 (mt) cc_final: 0.8712 (mt) REVERT: A 631 MET cc_start: 0.6847 (tpt) cc_final: 0.6475 (tpp) REVERT: A 976 ARG cc_start: 0.8070 (mmt90) cc_final: 0.7795 (mmt-90) REVERT: A 1170 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7920 (pt0) outliers start: 26 outliers final: 12 residues processed: 99 average time/residue: 0.2535 time to fit residues: 35.8396 Evaluate side-chains 79 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1299 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 ASN ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 11492 Z= 0.392 Angle : 0.752 6.207 16042 Z= 0.398 Chirality : 0.044 0.227 1878 Planarity : 0.005 0.043 1638 Dihedral : 19.915 156.456 2768 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.11 % Allowed : 16.86 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.24), residues: 1076 helix: -0.09 (0.21), residues: 537 sheet: -0.23 (0.55), residues: 88 loop : -0.93 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 464 HIS 0.011 0.002 HIS A 160 PHE 0.023 0.003 PHE A1276 TYR 0.021 0.002 TYR A1187 ARG 0.009 0.001 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 70 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8629 (m-80) cc_final: 0.7751 (m-80) REVERT: A 220 ARG cc_start: 0.9473 (mmp-170) cc_final: 0.9236 (mtm110) REVERT: A 356 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8445 (mmmt) REVERT: A 462 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: A 761 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7458 (tt) REVERT: A 763 MET cc_start: 0.0516 (mmt) cc_final: 0.0207 (mmm) REVERT: A 939 MET cc_start: 0.8540 (mmp) cc_final: 0.7867 (mmt) outliers start: 38 outliers final: 22 residues processed: 103 average time/residue: 0.2507 time to fit residues: 36.9891 Evaluate side-chains 79 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 55 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1317 ARG Chi-restraints excluded: chain A residue 1330 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 HIS ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11492 Z= 0.264 Angle : 0.597 8.423 16042 Z= 0.316 Chirality : 0.039 0.190 1878 Planarity : 0.004 0.038 1638 Dihedral : 19.749 153.667 2768 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.24 % Allowed : 18.92 % Favored : 77.84 % 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 (0.25), residues: 1076 helix: 0.30 (0.22), residues: 538 sheet: -0.06 (0.58), residues: 83 loop : -0.78 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1136 HIS 0.005 0.001 HIS A 160 PHE 0.012 0.002 PHE A1105 TYR 0.014 0.002 TYR A 450 ARG 0.007 0.001 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 66 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8694 (m-80) cc_final: 0.7664 (m-80) REVERT: A 462 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7686 (m-80) REVERT: A 631 MET cc_start: 0.6880 (tpt) cc_final: 0.6469 (tpp) REVERT: A 643 PHE cc_start: 0.6592 (OUTLIER) cc_final: 0.5203 (p90) REVERT: A 659 TRP cc_start: 0.8502 (m100) cc_final: 0.8194 (m100) REVERT: A 737 ILE cc_start: 0.9585 (mm) cc_final: 0.9291 (mt) REVERT: A 761 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7373 (tt) REVERT: A 763 MET cc_start: 0.0590 (mmt) cc_final: 0.0147 (mmm) REVERT: A 939 MET cc_start: 0.8577 (mmp) cc_final: 0.8005 (mmt) REVERT: A 1170 GLU cc_start: 0.8442 (pt0) cc_final: 0.8108 (mm-30) REVERT: A 1332 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7677 (p0) outliers start: 30 outliers final: 23 residues processed: 91 average time/residue: 0.2397 time to fit residues: 32.0504 Evaluate side-chains 84 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 57 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1258 PHE Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1317 ARG Chi-restraints excluded: chain A residue 1330 THR Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain A residue 1355 LEU Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11492 Z= 0.310 Angle : 0.630 9.242 16042 Z= 0.331 Chirality : 0.040 0.179 1878 Planarity : 0.004 0.041 1638 Dihedral : 19.828 154.549 2768 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.89 % Allowed : 19.89 % Favored : 76.22 % 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: -0.43 (0.25), residues: 1076 helix: 0.31 (0.22), residues: 538 sheet: -0.61 (0.55), residues: 95 loop : -0.84 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1136 HIS 0.006 0.001 HIS A 160 PHE 0.014 0.002 PHE A1105 TYR 0.015 0.002 TYR A 521 ARG 0.006 0.001 ARG A1084 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 63 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8746 (m-80) cc_final: 0.8244 (m-80) REVERT: A 462 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: A 659 TRP cc_start: 0.8413 (m100) cc_final: 0.8159 (m100) REVERT: A 761 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7512 (tt) REVERT: A 763 MET cc_start: 0.0829 (mmt) cc_final: 0.0601 (mmm) REVERT: A 939 MET cc_start: 0.8642 (mmp) cc_final: 0.8020 (mmt) REVERT: A 951 ARG cc_start: 0.8452 (mmm160) cc_final: 0.8035 (tpt170) REVERT: A 1105 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.6206 (p90) REVERT: A 1170 GLU cc_start: 0.8389 (pt0) cc_final: 0.8018 (mm-30) outliers start: 36 outliers final: 24 residues processed: 94 average time/residue: 0.2471 time to fit residues: 33.9521 Evaluate side-chains 85 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 58 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1330 THR Chi-restraints excluded: chain A residue 1355 LEU Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11492 Z= 0.272 Angle : 0.597 7.738 16042 Z= 0.316 Chirality : 0.039 0.185 1878 Planarity : 0.004 0.041 1638 Dihedral : 19.738 153.617 2768 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.89 % Allowed : 19.68 % Favored : 76.43 % 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: -0.39 (0.25), residues: 1076 helix: 0.36 (0.22), residues: 540 sheet: -0.60 (0.56), residues: 95 loop : -0.84 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1136 HIS 0.006 0.001 HIS A 160 PHE 0.018 0.002 PHE A1105 TYR 0.016 0.002 TYR A 521 ARG 0.005 0.001 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 62 time to evaluate : 1.307 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: A 25 TYR cc_start: 0.8731 (m-80) cc_final: 0.7688 (m-80) REVERT: A 220 ARG cc_start: 0.9458 (mmp-170) cc_final: 0.9216 (mtm180) REVERT: A 357 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7417 (t0) REVERT: A 462 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: A 631 MET cc_start: 0.6923 (tpt) cc_final: 0.6717 (tpt) REVERT: A 659 TRP cc_start: 0.8423 (m100) cc_final: 0.8163 (m100) REVERT: A 761 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7613 (tt) REVERT: A 763 MET cc_start: 0.0735 (mmt) cc_final: 0.0443 (mmm) REVERT: A 939 MET cc_start: 0.8676 (mmp) cc_final: 0.8074 (mmt) REVERT: A 1105 PHE cc_start: 0.6410 (OUTLIER) cc_final: 0.6175 (p90) REVERT: A 1170 GLU cc_start: 0.8359 (pt0) cc_final: 0.8019 (mm-30) REVERT: A 1332 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7873 (p0) outliers start: 36 outliers final: 25 residues processed: 92 average time/residue: 0.2482 time to fit residues: 33.1454 Evaluate side-chains 89 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 59 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1330 THR Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain A residue 1355 LEU Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11492 Z= 0.327 Angle : 0.654 7.699 16042 Z= 0.345 Chirality : 0.041 0.196 1878 Planarity : 0.004 0.068 1638 Dihedral : 19.908 155.178 2768 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.78 % Allowed : 20.43 % Favored : 75.78 % 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 (0.25), residues: 1076 helix: 0.21 (0.22), residues: 540 sheet: -0.36 (0.59), residues: 90 loop : -1.03 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1136 HIS 0.006 0.001 HIS A1264 PHE 0.019 0.002 PHE A1105 TYR 0.014 0.002 TYR A 450 ARG 0.012 0.001 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 63 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8808 (m-80) cc_final: 0.7767 (m-80) REVERT: A 161 MET cc_start: 0.7915 (ttm) cc_final: 0.7628 (ttp) REVERT: A 356 LYS cc_start: 0.8743 (mmtt) cc_final: 0.8262 (mtmt) REVERT: A 357 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.7479 (t0) REVERT: A 462 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7661 (m-80) REVERT: A 629 ARG cc_start: 0.8875 (ttp80) cc_final: 0.8536 (ptp-170) REVERT: A 763 MET cc_start: 0.0675 (mmt) cc_final: 0.0347 (mmm) REVERT: A 939 MET cc_start: 0.8648 (mmp) cc_final: 0.7933 (mmt) REVERT: A 1105 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.6411 (p90) REVERT: A 1170 GLU cc_start: 0.8417 (pt0) cc_final: 0.8124 (mm-30) REVERT: A 1332 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8068 (p0) outliers start: 35 outliers final: 27 residues processed: 90 average time/residue: 0.2665 time to fit residues: 34.0360 Evaluate side-chains 89 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 58 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1317 ARG Chi-restraints excluded: chain A residue 1330 THR Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain A residue 1355 LEU Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11492 Z= 0.148 Angle : 0.536 8.515 16042 Z= 0.276 Chirality : 0.036 0.178 1878 Planarity : 0.003 0.040 1638 Dihedral : 19.555 149.519 2768 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.05 % Allowed : 22.92 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.26), residues: 1076 helix: 0.61 (0.22), residues: 548 sheet: -0.46 (0.57), residues: 95 loop : -0.55 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1136 HIS 0.003 0.001 HIS A 160 PHE 0.011 0.001 PHE A 478 TYR 0.018 0.001 TYR A 521 ARG 0.006 0.000 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8673 (m-80) cc_final: 0.7576 (m-80) REVERT: A 220 ARG cc_start: 0.9453 (mmp-170) cc_final: 0.9214 (mtm180) REVERT: A 321 MET cc_start: 0.8010 (mmp) cc_final: 0.7753 (mmp) REVERT: A 556 ASN cc_start: 0.9375 (OUTLIER) cc_final: 0.9106 (p0) REVERT: A 629 ARG cc_start: 0.8863 (ttp80) cc_final: 0.8617 (ptp-170) REVERT: A 631 MET cc_start: 0.6693 (tpt) cc_final: 0.6318 (tpt) REVERT: A 659 TRP cc_start: 0.8528 (m100) cc_final: 0.8272 (m100) REVERT: A 763 MET cc_start: 0.0450 (mmt) cc_final: 0.0082 (mmm) REVERT: A 939 MET cc_start: 0.8622 (mmp) cc_final: 0.7902 (mmt) REVERT: A 1170 GLU cc_start: 0.8131 (pt0) cc_final: 0.7897 (mm-30) outliers start: 19 outliers final: 12 residues processed: 81 average time/residue: 0.2778 time to fit residues: 31.5478 Evaluate side-chains 73 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1330 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.6043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11492 Z= 0.376 Angle : 0.695 8.701 16042 Z= 0.363 Chirality : 0.042 0.203 1878 Planarity : 0.004 0.041 1638 Dihedral : 19.832 155.175 2766 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 25.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.81 % Allowed : 22.38 % Favored : 74.81 % 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: -0.48 (0.25), residues: 1076 helix: 0.36 (0.22), residues: 540 sheet: -0.68 (0.56), residues: 95 loop : -0.98 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A1126 HIS 0.008 0.002 HIS A 160 PHE 0.022 0.002 PHE A1105 TYR 0.019 0.002 TYR A 521 ARG 0.007 0.001 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 60 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8910 (m-80) cc_final: 0.7855 (m-80) REVERT: A 161 MET cc_start: 0.7895 (ttm) cc_final: 0.7648 (ttp) REVERT: A 356 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8260 (mtmt) REVERT: A 357 ASN cc_start: 0.7833 (OUTLIER) cc_final: 0.7485 (t0) REVERT: A 556 ASN cc_start: 0.9473 (OUTLIER) cc_final: 0.9204 (p0) REVERT: A 629 ARG cc_start: 0.8890 (ttp80) cc_final: 0.8596 (ptp-170) REVERT: A 763 MET cc_start: 0.0756 (mmt) cc_final: 0.0314 (mmm) REVERT: A 939 MET cc_start: 0.8642 (mmp) cc_final: 0.7933 (mmt) REVERT: A 1105 PHE cc_start: 0.7228 (OUTLIER) cc_final: 0.6710 (p90) REVERT: A 1108 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7528 (mp0) REVERT: A 1124 LYS cc_start: 0.9014 (tppt) cc_final: 0.8519 (mtmm) REVERT: A 1170 GLU cc_start: 0.8402 (pt0) cc_final: 0.8056 (mm-30) outliers start: 26 outliers final: 16 residues processed: 82 average time/residue: 0.2650 time to fit residues: 30.9179 Evaluate side-chains 77 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 58 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1330 THR Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 GLN A 556 ASN ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11492 Z= 0.182 Angle : 0.579 9.863 16042 Z= 0.297 Chirality : 0.038 0.272 1878 Planarity : 0.003 0.040 1638 Dihedral : 19.625 151.082 2766 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.73 % Allowed : 23.89 % Favored : 74.38 % 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: -0.09 (0.26), residues: 1076 helix: 0.59 (0.22), residues: 547 sheet: -0.64 (0.55), residues: 95 loop : -0.62 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1136 HIS 0.003 0.001 HIS A 160 PHE 0.017 0.001 PHE A1105 TYR 0.015 0.001 TYR A 521 ARG 0.007 0.000 ARG A 629 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8781 (m-80) cc_final: 0.7688 (m-80) REVERT: A 220 ARG cc_start: 0.9450 (mmp-170) cc_final: 0.9232 (mtm180) REVERT: A 321 MET cc_start: 0.8065 (mmp) cc_final: 0.7782 (mmp) REVERT: A 737 ILE cc_start: 0.9473 (mm) cc_final: 0.9131 (mt) REVERT: A 763 MET cc_start: 0.0603 (mmt) cc_final: 0.0210 (mmm) REVERT: A 939 MET cc_start: 0.8662 (mmp) cc_final: 0.7947 (mmt) REVERT: A 1105 PHE cc_start: 0.6378 (OUTLIER) cc_final: 0.6043 (p90) REVERT: A 1108 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7492 (mp0) REVERT: A 1124 LYS cc_start: 0.9018 (tppt) cc_final: 0.8577 (mtmm) REVERT: A 1170 GLU cc_start: 0.8197 (pt0) cc_final: 0.7938 (mm-30) outliers start: 16 outliers final: 12 residues processed: 75 average time/residue: 0.2736 time to fit residues: 29.0893 Evaluate side-chains 71 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1330 THR Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 96 optimal weight: 0.0060 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 HIS ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.080532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.057703 restraints weight = 51666.655| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 4.91 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11492 Z= 0.151 Angle : 0.553 9.055 16042 Z= 0.284 Chirality : 0.036 0.166 1878 Planarity : 0.003 0.039 1638 Dihedral : 19.361 149.322 2766 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.51 % Allowed : 23.78 % Favored : 74.70 % 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: 0.22 (0.26), residues: 1076 helix: 0.87 (0.23), residues: 542 sheet: -0.51 (0.55), residues: 95 loop : -0.50 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1136 HIS 0.002 0.001 HIS A 930 PHE 0.013 0.001 PHE A1105 TYR 0.013 0.001 TYR A 521 ARG 0.004 0.000 ARG A1084 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2178.59 seconds wall clock time: 40 minutes 10.00 seconds (2410.00 seconds total)