Starting phenix.real_space_refine (version: dev) on Mon Feb 20 20:47:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yn9_33955/02_2023/7yn9_33955.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yn9_33955/02_2023/7yn9_33955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yn9_33955/02_2023/7yn9_33955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yn9_33955/02_2023/7yn9_33955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yn9_33955/02_2023/7yn9_33955.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yn9_33955/02_2023/7yn9_33955.pdb" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 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 Process input model Symmetric amino acids flipped Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 108": "NH1" <-> "NH2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A GLU 605": "OE1" <-> "OE2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A GLU 666": "OE1" <-> "OE2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A PHE 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 787": "OE1" <-> "OE2" Residue "A GLU 839": "OE1" <-> "OE2" Residue "A GLU 853": "OE1" <-> "OE2" Residue "A GLU 869": "OE1" <-> "OE2" Residue "A GLU 926": "OE1" <-> "OE2" Residue "A ARG 967": "NH1" <-> "NH2" Residue "A ARG 978": "NH1" <-> "NH2" Residue "A ARG 994": "NH1" <-> "NH2" Residue "A GLU 1007": "OE1" <-> "OE2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A ARG 1066": "NH1" <-> "NH2" Residue "A GLU 1109": "OE1" <-> "OE2" Residue "A ARG 1122": "NH1" <-> "NH2" Residue "A ARG 1125": "NH1" <-> "NH2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A GLU 1202": "OE1" <-> "OE2" Residue "A GLU 1224": "OE1" <-> "OE2" Residue "A GLU 1227": "OE1" <-> "OE2" Residue "A ARG 1260": "NH1" <-> "NH2" Residue "A GLU 1267": "OE1" <-> "OE2" Residue "A ARG 1356": "NH1" <-> "NH2" Residue "A GLU 1392": "OE1" <-> "OE2" Residue "A ARG 1393": "NH1" <-> "NH2" Residue "A PHE 1460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1537": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13068 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1514, 12258 Classifications: {'peptide': 1514} Link IDs: {'PTRANS': 83, 'TRANS': 1430} Chain breaks: 4 Chain: "B" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 810 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 6, 'rna3p_pur': 7, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 17} Time building chain proxies: 8.13, per 1000 atoms: 0.62 Number of scatterers: 13068 At special positions: 0 Unit cell: (106.24, 171.81, 128.65, 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 56 16.00 P 38 15.00 O 2531 8.00 N 2329 7.00 C 8114 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: 5.62 Conformation dependent library (CDL) restraints added in 1.9 seconds 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2816 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 20 sheets defined 20.9% alpha, 15.9% beta 0 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 58 through 74 removed outlier: 3.891A pdb=" N THR A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 261 through 275 removed outlier: 3.610A pdb=" N ALA A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ILE A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 272 " --> pdb=" O GLN A 268 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A 273 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.745A pdb=" N ILE A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 293 removed outlier: 3.693A pdb=" N ARG A 293 " --> pdb=" O ARG A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 290 through 293' Processing helix chain 'A' and resid 295 through 299 removed outlier: 3.534A pdb=" N LEU A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 344 through 357 removed outlier: 4.437A pdb=" N GLU A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 removed outlier: 4.223A pdb=" N LEU A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 357 through 362' Processing helix chain 'A' and resid 443 through 459 removed outlier: 3.797A pdb=" N VAL A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 555 removed outlier: 3.903A pdb=" N THR A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 585 through 594 removed outlier: 3.990A pdb=" N ASN A 589 " --> pdb=" O GLU A 585 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP A 590 " --> pdb=" O ASN A 586 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 607 removed outlier: 3.595A pdb=" N GLU A 604 " --> pdb=" O GLU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 649 removed outlier: 3.643A pdb=" N VAL A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 691 removed outlier: 3.507A pdb=" N PHE A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 690 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS A 691 " --> pdb=" O VAL A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 removed outlier: 3.831A pdb=" N ILE A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 755 removed outlier: 4.148A pdb=" N LYS A 755 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 787 through 802 removed outlier: 3.515A pdb=" N ALA A 791 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 795 " --> pdb=" O ALA A 791 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 799 " --> pdb=" O ALA A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.654A pdb=" N ILE A 812 " --> pdb=" O LYS A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.882A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 956 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 957 " --> pdb=" O MET A 953 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 962 " --> pdb=" O TYR A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 Processing helix chain 'A' and resid 1232 through 1247 removed outlier: 3.859A pdb=" N LYS A1237 " --> pdb=" O LYS A1233 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR A1238 " --> pdb=" O ALA A1234 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A1242 " --> pdb=" O TYR A1238 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG A1243 " --> pdb=" O LYS A1239 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A1244 " --> pdb=" O GLU A1240 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A1245 " --> pdb=" O LEU A1241 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN A1246 " --> pdb=" O LEU A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1264 Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 3.837A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1347 removed outlier: 3.517A pdb=" N ARG A1346 " --> pdb=" O CYS A1342 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A1347 " --> pdb=" O PRO A1343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1342 through 1347' Processing helix chain 'A' and resid 1420 through 1425 removed outlier: 3.550A pdb=" N ILE A1424 " --> pdb=" O ALA A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1476 removed outlier: 3.607A pdb=" N GLY A1469 " --> pdb=" O GLU A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1517 No H-bonds generated for 'chain 'A' and resid 1515 through 1517' Processing helix chain 'A' and resid 1518 through 1526 removed outlier: 3.904A pdb=" N GLY A1524 " --> pdb=" O PRO A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1534 removed outlier: 3.926A pdb=" N PHE A1534 " --> pdb=" O LEU A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1539 No H-bonds generated for 'chain 'A' and resid 1537 through 1539' Processing helix chain 'A' and resid 1540 through 1545 Processing helix chain 'A' and resid 1575 through 1579 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 5.876A pdb=" N GLU A 201 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU A 153 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLU A 203 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 3 removed outlier: 3.573A pdb=" N GLY A 202 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 7 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 10 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 3.871A pdb=" N ARG A 171 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 485 removed outlier: 3.649A pdb=" N GLY A 408 " --> pdb=" O PHE A 530 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 485 removed outlier: 3.649A pdb=" N GLY A 408 " --> pdb=" O PHE A 530 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 497 through 498 removed outlier: 3.544A pdb=" N GLU A 497 " --> pdb=" O VAL A 521 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 501 through 504 removed outlier: 9.986A pdb=" N ARG A 501 " --> pdb=" O GLY A 514 " (cutoff:3.500A) removed outlier: 10.328A pdb=" N GLY A 514 " --> pdb=" O ARG A 501 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ARG A 503 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 576 through 577 removed outlier: 3.702A pdb=" N TYR A 577 " --> pdb=" O ASN A 611 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 611 " --> pdb=" O TYR A 577 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 723 through 725 removed outlier: 3.728A pdb=" N VAL A 630 " --> pdb=" O GLY A 774 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 823 " --> pdb=" O ASN A 629 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 659 through 663 Processing sheet with id=AB2, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AB3, first strand: chain 'A' and resid 944 through 945 Processing sheet with id=AB4, first strand: chain 'A' and resid 944 through 945 removed outlier: 3.841A pdb=" N PHE A1456 " --> pdb=" O CYS A 897 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR A 892 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU A1505 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS A 894 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL A1503 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG A 896 " --> pdb=" O GLU A1501 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1227 through 1229 Processing sheet with id=AB6, first strand: chain 'A' and resid 1007 through 1012 removed outlier: 4.122A pdb=" N GLU A1007 " --> pdb=" O PHE A1220 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A1220 " --> pdb=" O GLU A1007 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1130 removed outlier: 3.727A pdb=" N TYR A1126 " --> pdb=" O ARG A1041 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG A1041 " --> pdb=" O TYR A1126 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LYS A1128 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL A1039 " --> pdb=" O LYS A1128 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE A1130 " --> pdb=" O MET A1037 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N MET A1037 " --> pdb=" O PHE A1130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A1146 " --> pdb=" O VAL A1035 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1086 Processing sheet with id=AB9, first strand: chain 'A' and resid 1187 through 1188 removed outlier: 4.098A pdb=" N ASP A1187 " --> pdb=" O VAL A1198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1200 through 1202 removed outlier: 3.672A pdb=" N CYS A1201 " --> pdb=" O TYR A1209 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1278 through 1280 removed outlier: 6.625A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) 249 hydrogen bonds defined for protein. 675 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 6.01 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: 3891 1.33 - 1.45: 2336 1.45 - 1.57: 7073 1.57 - 1.69: 75 1.69 - 1.81: 80 Bond restraints: 13455 Sorted by residual: bond pdb=" N CYS A 965 " pdb=" CA CYS A 965 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.22e-02 6.72e+03 6.57e+00 bond pdb=" N CYS A1312 " pdb=" CA CYS A1312 " ideal model delta sigma weight residual 1.456 1.486 -0.031 1.22e-02 6.72e+03 6.31e+00 bond pdb=" N CYS A 711 " pdb=" CA CYS A 711 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.35e-02 5.49e+03 5.61e+00 bond pdb=" N CYS A1345 " pdb=" CA CYS A1345 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.29e-02 6.01e+03 5.32e+00 bond pdb=" N CYS A 86 " pdb=" CA CYS A 86 " ideal model delta sigma weight residual 1.453 1.487 -0.035 1.51e-02 4.39e+03 5.25e+00 ... (remaining 13450 not shown) Histogram of bond angle deviations from ideal: 98.79 - 105.85: 499 105.85 - 112.92: 7032 112.92 - 119.98: 4763 119.98 - 127.04: 5764 127.04 - 134.11: 253 Bond angle restraints: 18311 Sorted by residual: angle pdb=" C ARG A 924 " pdb=" N LYS A 925 " pdb=" CA LYS A 925 " ideal model delta sigma weight residual 122.44 115.51 6.93 1.19e+00 7.06e-01 3.39e+01 angle pdb=" N CYS A1345 " pdb=" CA CYS A1345 " pdb=" C CYS A1345 " ideal model delta sigma weight residual 113.97 107.03 6.94 1.28e+00 6.10e-01 2.94e+01 angle pdb=" N VAL A 782 " pdb=" CA VAL A 782 " pdb=" C VAL A 782 " ideal model delta sigma weight residual 111.81 107.41 4.40 8.60e-01 1.35e+00 2.61e+01 angle pdb=" N ILE A 479 " pdb=" CA ILE A 479 " pdb=" C ILE A 479 " ideal model delta sigma weight residual 112.96 108.10 4.86 1.00e+00 1.00e+00 2.36e+01 angle pdb=" N VAL A1151 " pdb=" CA VAL A1151 " pdb=" C VAL A1151 " ideal model delta sigma weight residual 112.17 108.14 4.03 9.50e-01 1.11e+00 1.80e+01 ... (remaining 18306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 7888 35.49 - 70.97: 182 70.97 - 106.45: 15 106.45 - 141.94: 0 141.94 - 177.42: 1 Dihedral angle restraints: 8086 sinusoidal: 3719 harmonic: 4367 Sorted by residual: dihedral pdb=" CA TRP A1512 " pdb=" C TRP A1512 " pdb=" N ARG A1513 " pdb=" CA ARG A1513 " ideal model delta harmonic sigma weight residual 180.00 146.44 33.56 0 5.00e+00 4.00e-02 4.51e+01 dihedral pdb=" CA ALA A 425 " pdb=" C ALA A 425 " pdb=" N LYS A 426 " pdb=" CA LYS A 426 " ideal model delta harmonic sigma weight residual -180.00 -153.20 -26.80 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA PHE A 990 " pdb=" C PHE A 990 " pdb=" N LEU A 991 " pdb=" CA LEU A 991 " ideal model delta harmonic sigma weight residual 180.00 153.31 26.69 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 8083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1386 0.049 - 0.099: 448 0.099 - 0.148: 89 0.148 - 0.198: 10 0.198 - 0.247: 2 Chirality restraints: 1935 Sorted by residual: chirality pdb=" C3' U B -14 " pdb=" C4' U B -14 " pdb=" O3' U B -14 " pdb=" C2' U B -14 " both_signs ideal model delta sigma weight residual False -2.74 -2.50 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA CYS A 123 " pdb=" N CYS A 123 " pdb=" C CYS A 123 " pdb=" CB CYS A 123 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C1' A B -2 " pdb=" O4' A B -2 " pdb=" C2' A B -2 " pdb=" N9 A B -2 " both_signs ideal model delta sigma weight residual False 2.44 2.25 0.19 2.00e-01 2.50e+01 9.07e-01 ... (remaining 1932 not shown) Planarity restraints: 2255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 863 " 0.069 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO A 864 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 768 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.87e+00 pdb=" N PRO A 769 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 769 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 769 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 765 " -0.045 5.00e-02 4.00e+02 6.74e-02 7.28e+00 pdb=" N PRO A 766 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 766 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 766 " -0.038 5.00e-02 4.00e+02 ... (remaining 2252 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 643 2.70 - 3.25: 12390 3.25 - 3.80: 18833 3.80 - 4.35: 24617 4.35 - 4.90: 41635 Nonbonded interactions: 98118 Sorted by model distance: nonbonded pdb=" NE2 HIS A 865 " pdb=" OH TYR A1561 " model vdw 2.151 2.520 nonbonded pdb=" O SER A 211 " pdb=" NH1 ARG A 215 " model vdw 2.171 2.520 nonbonded pdb=" OH TYR A1014 " pdb=" OE2 GLU A1216 " model vdw 2.174 2.440 nonbonded pdb=" OD1 ASN A1088 " pdb=" OG1 THR A1092 " model vdw 2.212 2.440 nonbonded pdb=" NZ LYS A1004 " pdb=" O PHE A1005 " model vdw 2.218 2.520 ... (remaining 98113 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 38 5.49 5 S 56 5.16 5 C 8114 2.51 5 N 2329 2.21 5 O 2531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.420 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: 14.860 Check model and map are aligned: 0.210 Process input model: 40.750 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 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 0.062 13455 Z= 0.428 Angle : 0.830 10.399 18311 Z= 0.494 Chirality : 0.050 0.247 1935 Planarity : 0.006 0.105 2255 Dihedral : 15.336 177.424 5270 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 15.36 % Favored : 84.44 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -5.33 (0.16), residues: 1504 helix: -3.34 (0.23), residues: 274 sheet: -2.82 (0.30), residues: 250 loop : -4.07 (0.15), residues: 980 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 1.588 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 111 average time/residue: 0.3407 time to fit residues: 52.1194 Evaluate side-chains 71 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 1.561 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1179 time to fit residues: 2.3578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 64 optimal weight: 0.2980 chunk 39 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 518 ASN A 531 GLN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 ASN ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 ASN A1098 HIS A1168 ASN A1247 ASN A1382 HIS A1417 HIS A1418 HIS A1428 ASN A1452 ASN A1516 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 13455 Z= 0.220 Angle : 0.646 14.059 18311 Z= 0.337 Chirality : 0.045 0.228 1935 Planarity : 0.005 0.101 2255 Dihedral : 11.409 175.549 2111 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.50 % Favored : 87.30 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.47 (0.18), residues: 1504 helix: -2.16 (0.29), residues: 281 sheet: -2.26 (0.31), residues: 248 loop : -3.65 (0.16), residues: 975 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 1.720 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 96 average time/residue: 0.2619 time to fit residues: 38.3700 Evaluate side-chains 80 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 1.518 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1314 time to fit residues: 4.1850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 8.9990 chunk 43 optimal weight: 0.0270 chunk 116 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 124 optimal weight: 0.0170 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 GLN ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 13455 Z= 0.214 Angle : 0.612 12.325 18311 Z= 0.318 Chirality : 0.044 0.227 1935 Planarity : 0.005 0.096 2255 Dihedral : 11.208 174.684 2111 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.84 % Favored : 87.97 % Rotamer Outliers : 1.66 % 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: -4.07 (0.19), residues: 1504 helix: -1.65 (0.30), residues: 284 sheet: -2.02 (0.31), residues: 257 loop : -3.45 (0.16), residues: 963 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 1.563 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 95 average time/residue: 0.2597 time to fit residues: 37.5523 Evaluate side-chains 87 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 1.445 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1232 time to fit residues: 4.8943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 chunk 72 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1555 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 13455 Z= 0.391 Angle : 0.694 12.593 18311 Z= 0.360 Chirality : 0.047 0.245 1935 Planarity : 0.006 0.104 2255 Dihedral : 11.317 176.727 2111 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.90 % Favored : 85.90 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.98 (0.19), residues: 1504 helix: -1.51 (0.30), residues: 291 sheet: -1.92 (0.31), residues: 263 loop : -3.45 (0.16), residues: 950 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 76 time to evaluate : 1.610 Fit side-chains outliers start: 23 outliers final: 16 residues processed: 92 average time/residue: 0.2507 time to fit residues: 35.5739 Evaluate side-chains 88 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 1.491 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1308 time to fit residues: 5.8391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.0000 chunk 84 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 13455 Z= 0.205 Angle : 0.596 9.026 18311 Z= 0.310 Chirality : 0.043 0.228 1935 Planarity : 0.005 0.095 2255 Dihedral : 11.151 175.295 2111 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.57 % Favored : 88.23 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.76 (0.19), residues: 1504 helix: -1.27 (0.31), residues: 298 sheet: -1.72 (0.31), residues: 259 loop : -3.35 (0.17), residues: 947 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 1.572 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 85 average time/residue: 0.2608 time to fit residues: 34.1474 Evaluate side-chains 79 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 1.576 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1264 time to fit residues: 3.5840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 0.0870 chunk 149 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 13455 Z= 0.229 Angle : 0.610 12.679 18311 Z= 0.313 Chirality : 0.044 0.229 1935 Planarity : 0.005 0.098 2255 Dihedral : 11.059 174.953 2111 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.03 % Favored : 87.77 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.57 (0.19), residues: 1504 helix: -1.02 (0.31), residues: 298 sheet: -1.66 (0.31), residues: 261 loop : -3.24 (0.17), residues: 945 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 1.669 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 84 average time/residue: 0.2452 time to fit residues: 32.6811 Evaluate side-chains 81 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 1.439 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1303 time to fit residues: 3.6983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 13455 Z= 0.274 Angle : 0.631 12.948 18311 Z= 0.323 Chirality : 0.045 0.235 1935 Planarity : 0.005 0.096 2255 Dihedral : 11.091 175.751 2111 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.37 % Favored : 87.43 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.49 (0.20), residues: 1504 helix: -0.95 (0.31), residues: 298 sheet: -1.53 (0.32), residues: 253 loop : -3.20 (0.17), residues: 953 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 1.727 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 82 average time/residue: 0.2719 time to fit residues: 34.4910 Evaluate side-chains 80 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 1.638 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1907 time to fit residues: 4.6411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 13455 Z= 0.265 Angle : 0.626 11.307 18311 Z= 0.320 Chirality : 0.044 0.234 1935 Planarity : 0.005 0.098 2255 Dihedral : 11.092 175.868 2111 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.10 % Favored : 87.70 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.46 (0.20), residues: 1504 helix: -0.91 (0.31), residues: 303 sheet: -1.61 (0.32), residues: 266 loop : -3.18 (0.17), residues: 935 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 1.456 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 84 average time/residue: 0.2564 time to fit residues: 32.8573 Evaluate side-chains 78 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 1.549 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1364 time to fit residues: 3.3648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 13455 Z= 0.260 Angle : 0.632 12.344 18311 Z= 0.323 Chirality : 0.044 0.234 1935 Planarity : 0.005 0.097 2255 Dihedral : 11.091 175.782 2111 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.37 % Favored : 87.43 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.42 (0.20), residues: 1504 helix: -0.82 (0.31), residues: 303 sheet: -1.64 (0.31), residues: 275 loop : -3.17 (0.17), residues: 926 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 1.593 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 80 average time/residue: 0.2770 time to fit residues: 33.7869 Evaluate side-chains 78 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1354 time to fit residues: 2.8117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.0870 chunk 89 optimal weight: 0.1980 chunk 69 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 13455 Z= 0.151 Angle : 0.582 11.561 18311 Z= 0.296 Chirality : 0.042 0.219 1935 Planarity : 0.005 0.091 2255 Dihedral : 10.905 173.758 2111 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.70 % Favored : 89.16 % Rotamer Outliers : 0.30 % 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: -3.15 (0.20), residues: 1504 helix: -0.54 (0.32), residues: 303 sheet: -1.34 (0.32), residues: 257 loop : -3.04 (0.17), residues: 944 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 1.605 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 81 average time/residue: 0.2541 time to fit residues: 32.1162 Evaluate side-chains 75 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 1.596 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1855 time to fit residues: 2.4421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 4.9990 chunk 37 optimal weight: 0.4980 chunk 112 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 22 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 HIS ** A1280 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 = 0.3627 r_free = 0.3627 target = 0.119345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.090958 restraints weight = 24274.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.092666 restraints weight = 17528.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.093282 restraints weight = 12919.929| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 13455 Z= 0.198 Angle : 0.592 10.555 18311 Z= 0.302 Chirality : 0.043 0.225 1935 Planarity : 0.005 0.097 2255 Dihedral : 10.845 174.006 2111 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.90 % Favored : 88.90 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.20), residues: 1504 helix: -0.46 (0.32), residues: 303 sheet: -1.29 (0.32), residues: 257 loop : -3.00 (0.17), residues: 944 =============================================================================== Job complete usr+sys time: 2123.45 seconds wall clock time: 39 minutes 53.11 seconds (2393.11 seconds total)