Starting phenix.real_space_refine on Sun Jul 21 09:52:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzz_41775/07_2024/8tzz_41775_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzz_41775/07_2024/8tzz_41775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzz_41775/07_2024/8tzz_41775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzz_41775/07_2024/8tzz_41775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzz_41775/07_2024/8tzz_41775_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzz_41775/07_2024/8tzz_41775_neut.cif" } resolution = 3.56 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= 0.002 sd= 0.045 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: 6 Type Number sf(0) Gaussians P 144 5.49 5 Mg 5 5.21 5 S 22 5.16 5 C 8375 2.51 5 N 2458 2.21 5 O 3008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A ASP 144": "OD1" <-> "OD2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 331": "OD1" <-> "OD2" Residue "A TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 644": "OD1" <-> "OD2" Residue "A ASP 699": "OD1" <-> "OD2" Residue "A ASP 700": "OD1" <-> "OD2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A GLU 779": "OE1" <-> "OE2" Residue "A GLU 790": "OE1" <-> "OE2" Residue "A TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 827": "OE1" <-> "OE2" Residue "A ASP 868": "OD1" <-> "OD2" Residue "A PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 947": "OD1" <-> "OD2" Residue "A GLU 952": "OE1" <-> "OE2" Residue "A ASP 965": "OD1" <-> "OD2" Residue "A PHE 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 977": "OE1" <-> "OE2" Residue "A TYR 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1005": "OE1" <-> "OE2" Residue "A TYR 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1049": "OE1" <-> "OE2" Residue "A GLU 1068": "OE1" <-> "OE2" Residue "A GLU 1150": "OE1" <-> "OE2" Residue "A GLU 1170": "OE1" <-> "OE2" Residue "A TYR 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1193": "OD1" <-> "OD2" Residue "A PHE 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1225": "OE1" <-> "OE2" Residue "A TYR 1237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1271": "OE1" <-> "OE2" Residue "A GLU 1275": "OE1" <-> "OE2" Residue "A ASP 1328": "OD1" <-> "OD2" Residue "A ASP 1332": "OD1" <-> "OD2" Residue "A GLU 1341": "OE1" <-> "OE2" 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: 14012 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 10962 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1336, 10951 Classifications: {'peptide': 1336} Link IDs: {'PTRANS': 35, 'TRANS': 1300} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1336, 10951 Classifications: {'peptide': 1336} Link IDs: {'PTRANS': 35, 'TRANS': 1300} Chain breaks: 3 bond proxies already assigned to first conformer: 11134 Chain: "B" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2103 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 53, 'rna3p_pyr': 34} Link IDs: {'rna2p': 10, 'rna3p': 87} Chain: "C" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "c" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 341 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "D" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "c" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 783 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 783 " occ=0.50 Time building chain proxies: 13.30, per 1000 atoms: 0.95 Number of scatterers: 14012 At special positions: 0 Unit cell: (87.465, 129.115, 120.785, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 144 15.00 Mg 5 11.99 O 3008 8.00 N 2458 7.00 C 8375 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: 6.06 Conformation dependent library (CDL) restraints added in 3.8 seconds 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2548 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 8 sheets defined 55.5% alpha, 7.9% beta 49 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 5.39 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.055A pdb=" N LYS A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 144 Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 175 through 179 removed outlier: 3.613A pdb=" N ASN A 178 " --> pdb=" O ASN A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.953A pdb=" N GLN A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 238 through 244 removed outlier: 3.847A pdb=" N ALA A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 290 through 306 removed outlier: 4.414A pdb=" N LYS A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN A 295 " --> pdb=" O LEU A 291 " (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 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.524A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.038A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.863A 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 482 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.593A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 553 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 609 removed outlier: 3.589A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 643 removed outlier: 4.965A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 711 Processing helix chain 'A' and resid 719 through 727 Processing helix chain 'A' and resid 732 through 751 removed outlier: 4.059A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 779 through 792 removed outlier: 3.751A pdb=" N GLY A 787 " --> pdb=" O AARG A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 804 through 807 Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 829 through 834 removed outlier: 5.608A pdb=" N SER A 834 " --> pdb=" O ASN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 860 through 866 Processing helix chain 'A' and resid 872 through 889 removed outlier: 5.191A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 902 through 906 removed outlier: 3.797A pdb=" N GLY A 906 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 Processing helix chain 'A' and resid 917 through 940 removed outlier: 4.143A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 922 " --> pdb=" O LYS A 918 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 981 through 1001 Processing helix chain 'A' and resid 1002 through 1005 removed outlier: 3.682A pdb=" N GLU A1005 " --> pdb=" O PRO A1002 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1002 through 1005' Processing helix chain 'A' and resid 1033 through 1042 removed outlier: 3.604A pdb=" N ILE A1042 " --> pdb=" O PHE A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1046 removed outlier: 3.526A pdb=" N PHE A1046 " --> pdb=" O MET A1043 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1043 through 1046' Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.721A 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 1191 through 1195 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 1262 Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1310 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 4.026A pdb=" N THR A1316 " --> pdb=" O LEU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.672A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) 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: 7.313A pdb=" N TYR A 5 " --> pdb=" O ASN A 758 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N VAL A 760 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 8.072A 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: 4.685A pdb=" N GLU A1357 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA4, first strand: chain 'A' and resid 836 through 840 Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 4.233A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 5.369A pdb=" N LYS A1156 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU A1150 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LYS A1158 " --> pdb=" O LYS A1148 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS A1148 " --> pdb=" O LYS A1158 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL A1160 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL A1146 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU A1162 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU A1144 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A1164 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER A1142 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1324 through 1325 487 hydrogen bonds defined for protein. 1411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 115 hydrogen bonds 218 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 7.04 Time building geometry restraints manager: 6.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2075 1.31 - 1.44: 4532 1.44 - 1.56: 7627 1.56 - 1.69: 284 1.69 - 1.81: 42 Bond restraints: 14560 Sorted by residual: bond pdb=" CA SER A1216 " pdb=" CB SER A1216 " ideal model delta sigma weight residual 1.530 1.457 0.073 1.69e-02 3.50e+03 1.87e+01 bond pdb=" C PRO A1137 " pdb=" O PRO A1137 " ideal model delta sigma weight residual 1.233 1.186 0.047 1.12e-02 7.97e+03 1.76e+01 bond pdb=" N LEU A1214 " pdb=" CA LEU A1214 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.22e-02 6.72e+03 1.40e+01 bond pdb=" C PRO A1199 " pdb=" O PRO A1199 " ideal model delta sigma weight residual 1.235 1.192 0.043 1.30e-02 5.92e+03 1.09e+01 bond pdb=" CA ALA A1217 " pdb=" CB ALA A1217 " ideal model delta sigma weight residual 1.533 1.483 0.050 1.63e-02 3.76e+03 9.33e+00 ... (remaining 14555 not shown) Histogram of bond angle deviations from ideal: 90.65 - 99.37: 4 99.37 - 108.08: 1670 108.08 - 116.80: 9250 116.80 - 125.52: 8741 125.52 - 134.23: 606 Bond angle restraints: 20271 Sorted by residual: angle pdb=" N ALA A1217 " pdb=" CA ALA A1217 " pdb=" C ALA A1217 " ideal model delta sigma weight residual 113.02 105.12 7.90 1.49e+00 4.50e-01 2.81e+01 angle pdb=" O3' DG C 17 " pdb=" C3' DG C 17 " pdb=" C2' DG C 17 " ideal model delta sigma weight residual 111.50 103.83 7.67 1.50e+00 4.44e-01 2.61e+01 angle pdb=" CG MET A 383 " pdb=" SD MET A 383 " pdb=" CE MET A 383 " ideal model delta sigma weight residual 100.90 90.65 10.25 2.20e+00 2.07e-01 2.17e+01 angle pdb=" N TYR A1326 " pdb=" CA TYR A1326 " pdb=" C TYR A1326 " ideal model delta sigma weight residual 110.17 103.51 6.66 1.51e+00 4.39e-01 1.95e+01 angle pdb=" N GLN A 190 " pdb=" CA GLN A 190 " pdb=" CB GLN A 190 " ideal model delta sigma weight residual 110.28 116.83 -6.55 1.55e+00 4.16e-01 1.79e+01 ... (remaining 20266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.57: 8312 33.57 - 67.14: 478 67.14 - 100.70: 40 100.70 - 134.27: 1 134.27 - 167.84: 5 Dihedral angle restraints: 8836 sinusoidal: 4901 harmonic: 3935 Sorted by residual: dihedral pdb=" O4' U B 59 " pdb=" C1' U B 59 " pdb=" N1 U B 59 " pdb=" C2 U B 59 " ideal model delta sinusoidal sigma weight residual 200.00 32.16 167.84 1 1.50e+01 4.44e-03 8.44e+01 dihedral pdb=" O4' C B 70 " pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sinusoidal sigma weight residual 200.00 33.20 166.80 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" CA TYR A1326 " pdb=" C TYR A1326 " pdb=" N PHE A1327 " pdb=" CA PHE A1327 " ideal model delta harmonic sigma weight residual 180.00 -153.09 -26.91 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 8833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2152 0.087 - 0.173: 153 0.173 - 0.260: 13 0.260 - 0.347: 3 0.347 - 0.434: 1 Chirality restraints: 2322 Sorted by residual: chirality pdb=" P DT c 23 " pdb=" OP1 DT c 23 " pdb=" OP2 DT c 23 " pdb=" O5' DT c 23 " both_signs ideal model delta sigma weight residual True 2.35 -2.78 -0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" C3' DG C 17 " pdb=" C4' DG C 17 " pdb=" O3' DG C 17 " pdb=" C2' DG C 17 " both_signs ideal model delta sigma weight residual False -2.66 -2.97 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA LYS A1222 " pdb=" N LYS A1222 " pdb=" C LYS A1222 " pdb=" CB LYS A1222 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2319 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 730 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO A 731 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 731 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 731 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1228 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO A1229 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A1229 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A1229 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 549 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C VAL A 549 " 0.035 2.00e-02 2.50e+03 pdb=" O VAL A 549 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP A 550 " -0.012 2.00e-02 2.50e+03 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 3 2.13 - 2.82: 4064 2.82 - 3.51: 19523 3.51 - 4.21: 35299 4.21 - 4.90: 57477 Nonbonded interactions: 116366 Sorted by model distance: nonbonded pdb="MG MG A1401 " pdb="MG MG A1402 " model vdw 1.432 1.300 nonbonded pdb=" OP2 DT c 23 " pdb="MG MG c 101 " model vdw 1.995 2.170 nonbonded pdb=" OP2 A B 65 " pdb="MG MG B 101 " model vdw 2.013 2.170 nonbonded pdb=" O3' DG C 22 " pdb="MG MG c 101 " model vdw 2.137 2.170 nonbonded pdb=" OG SER A 860 " pdb=" NH1 ARG A 864 " model vdw 2.138 2.520 ... (remaining 116361 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 52.020 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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 : 0.007 0.073 14560 Z= 0.428 Angle : 0.857 10.629 20271 Z= 0.494 Chirality : 0.050 0.434 2322 Planarity : 0.004 0.064 2066 Dihedral : 18.892 167.840 6288 Min Nonbonded Distance : 1.432 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.66 % Allowed : 0.25 % Favored : 99.09 % 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: -0.59 (0.22), residues: 1331 helix: 0.01 (0.20), residues: 633 sheet: -0.54 (0.47), residues: 128 loop : -0.67 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1136 HIS 0.009 0.002 HIS A 328 PHE 0.018 0.002 PHE A 643 TYR 0.026 0.003 TYR A1326 ARG 0.018 0.001 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.273 Fit side-chains REVERT: A 221 ARG cc_start: 0.7705 (mtt180) cc_final: 0.7358 (ttt-90) REVERT: A 311 GLU cc_start: 0.5489 (mp0) cc_final: 0.5279 (mp0) REVERT: A 383 MET cc_start: 0.6979 (ttt) cc_final: 0.6200 (ttt) REVERT: A 919 ARG cc_start: 0.8498 (ttp-170) cc_final: 0.8126 (ttp80) REVERT: A 1006 SER cc_start: 0.8563 (t) cc_final: 0.8224 (m) outliers start: 8 outliers final: 1 residues processed: 99 average time/residue: 0.3080 time to fit residues: 43.4360 Evaluate side-chains 63 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1332 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** 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: 0.8254 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14560 Z= 0.214 Angle : 0.590 7.076 20271 Z= 0.314 Chirality : 0.040 0.190 2322 Planarity : 0.004 0.052 2066 Dihedral : 20.044 168.852 3432 Min Nonbonded Distance : 1.331 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.75 % Allowed : 4.07 % Favored : 95.18 % 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: -0.07 (0.22), residues: 1331 helix: 0.52 (0.20), residues: 644 sheet: -0.05 (0.48), residues: 123 loop : -0.59 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 PHE 0.026 0.001 PHE A1045 TYR 0.021 0.001 TYR A1326 ARG 0.010 0.001 ARG A1333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 1.283 Fit side-chains REVERT: A 919 ARG cc_start: 0.8503 (ttp-170) cc_final: 0.8165 (ttp80) outliers start: 9 outliers final: 3 residues processed: 75 average time/residue: 0.3018 time to fit residues: 33.2702 Evaluate side-chains 62 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 1082 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 0.0170 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 14560 Z= 0.155 Angle : 0.518 6.358 20271 Z= 0.277 Chirality : 0.038 0.201 2322 Planarity : 0.004 0.047 2066 Dihedral : 19.723 163.974 3430 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.58 % Allowed : 5.90 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.23), residues: 1331 helix: 0.91 (0.21), residues: 639 sheet: 0.22 (0.50), residues: 118 loop : -0.46 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 PHE 0.023 0.001 PHE A1045 TYR 0.019 0.001 TYR A1326 ARG 0.008 0.001 ARG A1303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 1.340 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 0.3071 time to fit residues: 37.0537 Evaluate side-chains 68 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 1038 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 0.0070 chunk 62 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14560 Z= 0.221 Angle : 0.533 6.553 20271 Z= 0.282 Chirality : 0.039 0.260 2322 Planarity : 0.004 0.049 2066 Dihedral : 19.579 164.969 3430 Min Nonbonded Distance : 1.089 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.75 % Allowed : 7.56 % Favored : 91.69 % 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 (0.23), residues: 1331 helix: 0.95 (0.20), residues: 649 sheet: 0.06 (0.48), residues: 125 loop : -0.44 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1136 HIS 0.009 0.001 HIS A1262 PHE 0.021 0.001 PHE A1045 TYR 0.012 0.001 TYR A1326 ARG 0.007 0.000 ARG A1303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 1.440 Fit side-chains REVERT: A 1091 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8452 (tm-30) outliers start: 9 outliers final: 6 residues processed: 68 average time/residue: 0.3612 time to fit residues: 35.7896 Evaluate side-chains 68 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1038 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 96 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14560 Z= 0.281 Angle : 0.560 6.938 20271 Z= 0.295 Chirality : 0.040 0.225 2322 Planarity : 0.004 0.048 2066 Dihedral : 19.541 166.738 3430 Min Nonbonded Distance : 1.087 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.08 % Allowed : 7.89 % Favored : 91.03 % 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: 0.25 (0.23), residues: 1331 helix: 0.82 (0.20), residues: 653 sheet: -0.09 (0.48), residues: 125 loop : -0.45 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1136 HIS 0.007 0.001 HIS A 328 PHE 0.021 0.002 PHE A1045 TYR 0.011 0.002 TYR A 136 ARG 0.008 0.001 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 1.363 Fit side-chains REVERT: A 1091 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8635 (tm-30) outliers start: 13 outliers final: 9 residues processed: 73 average time/residue: 0.2977 time to fit residues: 32.0102 Evaluate side-chains 70 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1038 PHE Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1332 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14560 Z= 0.158 Angle : 0.489 6.430 20271 Z= 0.261 Chirality : 0.037 0.257 2322 Planarity : 0.003 0.047 2066 Dihedral : 19.373 164.861 3430 Min Nonbonded Distance : 1.158 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.75 % Allowed : 8.47 % Favored : 90.78 % 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: 0.60 (0.23), residues: 1331 helix: 1.13 (0.21), residues: 645 sheet: 0.06 (0.49), residues: 124 loop : -0.28 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1136 HIS 0.004 0.001 HIS A 328 PHE 0.019 0.001 PHE A1045 TYR 0.012 0.001 TYR A 155 ARG 0.008 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 1.660 Fit side-chains REVERT: A 1091 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8557 (tm-30) outliers start: 9 outliers final: 7 residues processed: 69 average time/residue: 0.3086 time to fit residues: 31.8126 Evaluate side-chains 67 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1224 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 5.9990 chunk 15 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14560 Z= 0.208 Angle : 0.511 6.829 20271 Z= 0.271 Chirality : 0.038 0.234 2322 Planarity : 0.003 0.045 2066 Dihedral : 19.364 164.995 3430 Min Nonbonded Distance : 1.102 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.91 % Allowed : 9.14 % Favored : 89.95 % 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: 0.55 (0.23), residues: 1331 helix: 1.13 (0.20), residues: 650 sheet: 0.03 (0.49), residues: 124 loop : -0.38 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 883 HIS 0.006 0.001 HIS A 328 PHE 0.033 0.001 PHE A 606 TYR 0.009 0.001 TYR A 521 ARG 0.006 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 1.214 Fit side-chains REVERT: A 1038 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.7318 (t80) REVERT: A 1091 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8575 (tm-30) outliers start: 11 outliers final: 9 residues processed: 68 average time/residue: 0.2872 time to fit residues: 29.4773 Evaluate side-chains 69 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1038 PHE Chi-restraints excluded: chain A residue 1224 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14560 Z= 0.217 Angle : 0.517 6.626 20271 Z= 0.274 Chirality : 0.038 0.223 2322 Planarity : 0.003 0.046 2066 Dihedral : 19.362 165.218 3430 Min Nonbonded Distance : 1.100 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.16 % Allowed : 8.97 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.23), residues: 1331 helix: 1.12 (0.20), residues: 650 sheet: -0.00 (0.49), residues: 124 loop : -0.36 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 PHE 0.022 0.001 PHE A 606 TYR 0.010 0.001 TYR A 521 ARG 0.008 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 1.477 Fit side-chains REVERT: A 1038 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.7182 (t80) REVERT: A 1091 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8588 (tm-30) outliers start: 14 outliers final: 12 residues processed: 66 average time/residue: 0.2704 time to fit residues: 27.7694 Evaluate side-chains 70 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1038 PHE Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1224 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 9.9990 chunk 130 optimal weight: 0.0870 chunk 133 optimal weight: 7.9990 chunk 78 optimal weight: 0.0370 chunk 56 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 117 optimal weight: 0.0970 chunk 123 optimal weight: 8.9990 chunk 129 optimal weight: 0.0770 chunk 85 optimal weight: 1.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14560 Z= 0.133 Angle : 0.474 6.681 20271 Z= 0.253 Chirality : 0.036 0.243 2322 Planarity : 0.003 0.043 2066 Dihedral : 19.211 163.040 3430 Min Nonbonded Distance : 1.175 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.66 % Allowed : 9.39 % Favored : 89.95 % 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: 0.86 (0.23), residues: 1331 helix: 1.42 (0.21), residues: 642 sheet: 0.13 (0.49), residues: 124 loop : -0.23 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.005 0.001 HIS A 328 PHE 0.017 0.001 PHE A 606 TYR 0.013 0.001 TYR A 521 ARG 0.006 0.000 ARG A1303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 1.422 Fit side-chains REVERT: A 822 MET cc_start: 0.7989 (mmm) cc_final: 0.7743 (mmm) REVERT: A 1038 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.6813 (t80) REVERT: A 1091 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8518 (tm-30) outliers start: 8 outliers final: 5 residues processed: 65 average time/residue: 0.2815 time to fit residues: 27.7710 Evaluate side-chains 65 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1038 PHE Chi-restraints excluded: chain A residue 1224 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 95 optimal weight: 0.0570 chunk 144 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 115 optimal weight: 0.0870 chunk 11 optimal weight: 0.2980 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.0278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14560 Z= 0.176 Angle : 0.490 7.649 20271 Z= 0.260 Chirality : 0.037 0.222 2322 Planarity : 0.003 0.045 2066 Dihedral : 19.217 163.709 3430 Min Nonbonded Distance : 1.109 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.58 % Allowed : 9.47 % Favored : 89.95 % 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: 0.80 (0.23), residues: 1331 helix: 1.35 (0.21), residues: 648 sheet: 0.08 (0.49), residues: 124 loop : -0.25 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 PHE 0.018 0.001 PHE A1045 TYR 0.012 0.001 TYR A1010 ARG 0.006 0.000 ARG A1303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 1.363 Fit side-chains REVERT: A 1038 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.6762 (t80) REVERT: A 1091 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8558 (tm-30) outliers start: 7 outliers final: 6 residues processed: 63 average time/residue: 0.2652 time to fit residues: 25.8060 Evaluate side-chains 65 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1038 PHE Chi-restraints excluded: chain A residue 1224 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 115 optimal weight: 0.0870 chunk 48 optimal weight: 0.4980 chunk 118 optimal weight: 3.9990 chunk 14 optimal weight: 0.0980 chunk 21 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.107879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.081073 restraints weight = 61252.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.083266 restraints weight = 30090.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.084725 restraints weight = 18268.367| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14560 Z= 0.158 Angle : 0.481 7.413 20271 Z= 0.255 Chirality : 0.036 0.221 2322 Planarity : 0.003 0.045 2066 Dihedral : 19.181 163.606 3430 Min Nonbonded Distance : 1.143 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.58 % Allowed : 9.72 % Favored : 89.70 % 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: 0.88 (0.24), residues: 1331 helix: 1.40 (0.21), residues: 648 sheet: 0.10 (0.50), residues: 124 loop : -0.18 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 18 HIS 0.005 0.001 HIS A 328 PHE 0.018 0.001 PHE A1045 TYR 0.012 0.001 TYR A1010 ARG 0.006 0.000 ARG A1303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2301.18 seconds wall clock time: 43 minutes 22.27 seconds (2602.27 seconds total)