Starting phenix.real_space_refine on Sat Mar 16 04:21:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0c_32238/03_2024/7w0c_32238_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0c_32238/03_2024/7w0c_32238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0c_32238/03_2024/7w0c_32238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0c_32238/03_2024/7w0c_32238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0c_32238/03_2024/7w0c_32238_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0c_32238/03_2024/7w0c_32238_updated.pdb" } resolution = 3.93 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= 0.004 sd= 0.042 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 73 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 8460 2.51 5 N 2338 2.21 5 O 2728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 3": "OD1" <-> "OD2" Residue "A TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 349": "OD1" <-> "OD2" Residue "A PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 715": "OD1" <-> "OD2" Residue "A PHE 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1480": "OD1" <-> "OD2" Residue "A PHE 1542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 345": "OD1" <-> "OD2" Residue "B GLU 355": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13663 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1476, 11967 Classifications: {'peptide': 1476} Link IDs: {'PTRANS': 60, 'TRANS': 1415} Chain breaks: 2 Chain: "B" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 143 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "C" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 748 Classifications: {'RNA': 35} Modifications used: {'5*END': 1, 'rna3p_pur': 20, 'rna3p_pyr': 15} Link IDs: {'rna3p': 34} Chain: "D" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 777 Classifications: {'RNA': 37} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 22} Link IDs: {'rna3p': 36} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.41, per 1000 atoms: 0.54 Number of scatterers: 13663 At special positions: 0 Unit cell: (105.002, 96.3425, 185.107, 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 63 16.00 P 73 15.00 Mg 1 11.99 O 2728 8.00 N 2338 7.00 C 8460 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: 6.45 Conformation dependent library (CDL) restraints added in 2.4 seconds 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2852 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 7 sheets defined 48.0% alpha, 6.6% beta 25 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 7.46 Creating SS restraints... Processing helix chain 'A' and resid 4 through 6 No H-bonds generated for 'chain 'A' and resid 4 through 6' Processing helix chain 'A' and resid 10 through 21 removed outlier: 3.513A pdb=" N LYS A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 45 removed outlier: 3.600A pdb=" N PHE A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 67 through 80 Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 116 through 124 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.610A pdb=" N LEU A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 209 through 214 removed outlier: 4.199A pdb=" N TYR A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 251 Processing helix chain 'A' and resid 272 through 291 removed outlier: 4.859A pdb=" N VAL A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 313 removed outlier: 4.011A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 344 removed outlier: 3.869A pdb=" N LYS A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 361 Processing helix chain 'A' and resid 365 through 378 removed outlier: 3.817A pdb=" N PHE A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 395 through 411 removed outlier: 3.824A pdb=" N LYS A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 446 through 452 Processing helix chain 'A' and resid 485 through 494 Processing helix chain 'A' and resid 511 through 534 Processing helix chain 'A' and resid 544 through 550 Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 568 through 581 removed outlier: 4.847A pdb=" N LEU A 572 " --> pdb=" O ASN A 569 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 580 " --> pdb=" O ARG A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'A' and resid 608 through 611 removed outlier: 4.173A pdb=" N LYS A 611 " --> pdb=" O VAL A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 608 through 611' Processing helix chain 'A' and resid 638 through 655 Processing helix chain 'A' and resid 668 through 679 removed outlier: 3.784A pdb=" N ALA A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 674 " --> pdb=" O GLU A 670 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 686 No H-bonds generated for 'chain 'A' and resid 684 through 686' Processing helix chain 'A' and resid 693 through 698 removed outlier: 4.117A pdb=" N ASP A 698 " --> pdb=" O ASN A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 748 removed outlier: 4.295A pdb=" N ASN A 747 " --> pdb=" O HIS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 809 removed outlier: 3.658A pdb=" N PHE A 807 " --> pdb=" O HIS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 Processing helix chain 'A' and resid 863 through 866 No H-bonds generated for 'chain 'A' and resid 863 through 866' Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 917 through 924 removed outlier: 3.630A pdb=" N LYS A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 929 No H-bonds generated for 'chain 'A' and resid 926 through 929' Processing helix chain 'A' and resid 963 through 967 Processing helix chain 'A' and resid 983 through 1016 removed outlier: 4.680A pdb=" N PHE A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) Proline residue: A 993 - end of helix removed outlier: 4.133A pdb=" N ARG A 998 " --> pdb=" O SER A 994 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A1001 " --> pdb=" O ASN A 997 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N HIS A1004 " --> pdb=" O TYR A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1027 No H-bonds generated for 'chain 'A' and resid 1025 through 1027' Processing helix chain 'A' and resid 1175 through 1181 Processing helix chain 'A' and resid 1183 through 1185 No H-bonds generated for 'chain 'A' and resid 1183 through 1185' Processing helix chain 'A' and resid 1191 through 1198 Processing helix chain 'A' and resid 1201 through 1203 No H-bonds generated for 'chain 'A' and resid 1201 through 1203' Processing helix chain 'A' and resid 1210 through 1231 removed outlier: 3.752A pdb=" N ILE A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1247 Processing helix chain 'A' and resid 1250 through 1258 Processing helix chain 'A' and resid 1263 through 1265 No H-bonds generated for 'chain 'A' and resid 1263 through 1265' Processing helix chain 'A' and resid 1286 through 1294 Processing helix chain 'A' and resid 1296 through 1299 No H-bonds generated for 'chain 'A' and resid 1296 through 1299' Processing helix chain 'A' and resid 1304 through 1309 Processing helix chain 'A' and resid 1314 through 1318 Processing helix chain 'A' and resid 1325 through 1338 Processing helix chain 'A' and resid 1349 through 1356 removed outlier: 3.867A pdb=" N ASN A1353 " --> pdb=" O SER A1349 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE A1354 " --> pdb=" O SER A1350 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N CYS A1355 " --> pdb=" O GLU A1351 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A1356 " --> pdb=" O VAL A1352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1349 through 1356' Processing helix chain 'A' and resid 1363 through 1392 removed outlier: 3.770A pdb=" N ASN A1380 " --> pdb=" O VAL A1376 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LEU A1383 " --> pdb=" O LYS A1379 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N GLN A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N HIS A1385 " --> pdb=" O TYR A1381 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A1386 " --> pdb=" O GLY A1382 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A1387 " --> pdb=" O LEU A1383 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS A1388 " --> pdb=" O GLN A1384 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET A1389 " --> pdb=" O HIS A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1407 Proline residue: A1403 - end of helix Processing helix chain 'A' and resid 1409 through 1412 No H-bonds generated for 'chain 'A' and resid 1409 through 1412' Processing helix chain 'A' and resid 1417 through 1420 Processing helix chain 'A' and resid 1424 through 1429 Processing helix chain 'A' and resid 1433 through 1440 Processing helix chain 'A' and resid 1448 through 1454 Processing helix chain 'A' and resid 1469 through 1490 removed outlier: 4.876A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1506 removed outlier: 4.081A pdb=" N ASP A1501 " --> pdb=" O GLY A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1509 through 1518 Processing helix chain 'A' and resid 1530 through 1545 removed outlier: 4.048A pdb=" N PHE A1542 " --> pdb=" O LYS A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1610 through 1627 removed outlier: 3.533A pdb=" N LEU A1616 " --> pdb=" O LEU A1612 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS A1627 " --> pdb=" O VAL A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1650 Proline residue: A1643 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 198 through 200 removed outlier: 3.648A pdb=" N GLY A 24 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 172 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU A 61 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N ASP A 139 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N MET A 63 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 114 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 219 through 225 Processing sheet with id= C, first strand: chain 'A' and resid 593 through 597 removed outlier: 4.854A pdb=" N VAL A 615 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 703 through 706 Processing sheet with id= E, first strand: chain 'A' and resid 786 through 789 Processing sheet with id= F, first strand: chain 'A' and resid 729 through 733 Processing sheet with id= G, first strand: chain 'A' and resid 897 through 899 removed outlier: 3.517A pdb=" N ILE A 940 " --> pdb=" O LEU A 971 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 6.53 Time building geometry restraints manager: 6.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4126 1.34 - 1.46: 2817 1.46 - 1.58: 6915 1.58 - 1.70: 144 1.70 - 1.82: 99 Bond restraints: 14101 Sorted by residual: bond pdb=" CB GLU A1472 " pdb=" CG GLU A1472 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.24e+00 bond pdb=" CA ARG A 873 " pdb=" CB ARG A 873 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.58e-02 4.01e+03 1.05e+00 bond pdb=" CB LYS B 352 " pdb=" CG LYS B 352 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.02e+00 bond pdb=" CG GLU A1472 " pdb=" CD GLU A1472 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 1.02e+00 bond pdb=" C4 ADP A1802 " pdb=" C5 ADP A1802 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.42e-01 ... (remaining 14096 not shown) Histogram of bond angle deviations from ideal: 98.20 - 105.80: 606 105.80 - 113.41: 7846 113.41 - 121.01: 7141 121.01 - 128.62: 3687 128.62 - 136.22: 145 Bond angle restraints: 19425 Sorted by residual: angle pdb=" CB LYS B 352 " pdb=" CG LYS B 352 " pdb=" CD LYS B 352 " ideal model delta sigma weight residual 111.30 119.03 -7.73 2.30e+00 1.89e-01 1.13e+01 angle pdb=" C LYS A 910 " pdb=" N ASN A 911 " pdb=" CA ASN A 911 " ideal model delta sigma weight residual 121.54 127.57 -6.03 1.91e+00 2.74e-01 9.96e+00 angle pdb=" C ASP A 350 " pdb=" N ASP A 351 " pdb=" CA ASP A 351 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.69e+00 angle pdb=" N GLN A 801 " pdb=" CA GLN A 801 " pdb=" CB GLN A 801 " ideal model delta sigma weight residual 110.28 114.54 -4.26 1.55e+00 4.16e-01 7.57e+00 angle pdb=" CB LYS A 441 " pdb=" CG LYS A 441 " pdb=" CD LYS A 441 " ideal model delta sigma weight residual 111.30 117.16 -5.86 2.30e+00 1.89e-01 6.50e+00 ... (remaining 19420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.96: 8062 25.96 - 51.91: 428 51.91 - 77.87: 120 77.87 - 103.82: 6 103.82 - 129.78: 1 Dihedral angle restraints: 8617 sinusoidal: 4219 harmonic: 4398 Sorted by residual: dihedral pdb=" C5' ADP A1802 " pdb=" O5' ADP A1802 " pdb=" PA ADP A1802 " pdb=" O2A ADP A1802 " ideal model delta sinusoidal sigma weight residual 300.00 170.22 129.78 1 2.00e+01 2.50e-03 3.94e+01 dihedral pdb=" O1B ADP A1802 " pdb=" O3A ADP A1802 " pdb=" PB ADP A1802 " pdb=" PA ADP A1802 " ideal model delta sinusoidal sigma weight residual -60.00 -153.70 93.70 1 2.00e+01 2.50e-03 2.55e+01 dihedral pdb=" CA ARG A 873 " pdb=" C ARG A 873 " pdb=" N PRO A 874 " pdb=" CA PRO A 874 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 8614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1564 0.034 - 0.068: 471 0.068 - 0.102: 150 0.102 - 0.136: 48 0.136 - 0.170: 4 Chirality restraints: 2237 Sorted by residual: chirality pdb=" CA TYR A 519 " pdb=" N TYR A 519 " pdb=" C TYR A 519 " pdb=" CB TYR A 519 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" CA ASP A 351 " pdb=" N ASP A 351 " pdb=" C ASP A 351 " pdb=" CB ASP A 351 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA PRO A 874 " pdb=" N PRO A 874 " pdb=" C PRO A 874 " pdb=" CB PRO A 874 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 2234 not shown) Planarity restraints: 2218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 768 " 0.048 5.00e-02 4.00e+02 7.33e-02 8.60e+00 pdb=" N PRO A 769 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 769 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 769 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1468 " 0.018 2.00e-02 2.50e+03 1.46e-02 4.24e+00 pdb=" CG TYR A1468 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A1468 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A1468 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A1468 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A1468 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A1468 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A1468 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1331 " 0.017 2.00e-02 2.50e+03 1.43e-02 3.57e+00 pdb=" CG PHE A1331 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A1331 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A1331 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A1331 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A1331 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A1331 " 0.003 2.00e-02 2.50e+03 ... (remaining 2215 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 311 2.66 - 3.22: 13728 3.22 - 3.78: 22965 3.78 - 4.34: 30896 4.34 - 4.90: 46458 Nonbonded interactions: 114358 Sorted by model distance: nonbonded pdb="MG MG A1801 " pdb=" O2A ADP A1802 " model vdw 2.105 2.170 nonbonded pdb=" O VAL A 608 " pdb=" NZ LYS A 611 " model vdw 2.177 2.520 nonbonded pdb=" OE1 GLN A 287 " pdb=" OG1 THR A 397 " model vdw 2.178 2.440 nonbonded pdb=" O GLU A1411 " pdb=" OH TYR A1624 " model vdw 2.194 2.440 nonbonded pdb=" O GLU A 512 " pdb=" NE2 GLN A 516 " model vdw 2.214 2.520 ... (remaining 114353 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=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: 1.540 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: 3.430 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 45.110 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 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 : 0.002 0.054 14101 Z= 0.154 Angle : 0.547 7.726 19425 Z= 0.289 Chirality : 0.039 0.170 2237 Planarity : 0.004 0.073 2218 Dihedral : 16.220 129.779 5765 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 0.07 % Allowed : 0.22 % Favored : 99.70 % 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: -0.14 (0.22), residues: 1484 helix: 0.34 (0.20), residues: 719 sheet: -0.45 (0.41), residues: 149 loop : -0.35 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1634 HIS 0.006 0.001 HIS A1004 PHE 0.033 0.001 PHE A1331 TYR 0.035 0.001 TYR A1468 ARG 0.009 0.001 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8206 (ppp) cc_final: 0.7986 (tmm) REVERT: A 263 LYS cc_start: 0.7766 (mmmt) cc_final: 0.7443 (tptp) REVERT: A 458 MET cc_start: 0.6039 (tpt) cc_final: 0.5732 (tpt) REVERT: A 762 LEU cc_start: 0.8899 (mm) cc_final: 0.8392 (mt) REVERT: A 827 ASN cc_start: 0.8389 (m-40) cc_final: 0.7766 (m-40) REVERT: A 1029 MET cc_start: 0.6760 (mmp) cc_final: 0.6256 (ppp) REVERT: A 1209 MET cc_start: 0.8434 (ppp) cc_final: 0.7861 (ppp) REVERT: A 1408 LEU cc_start: 0.7782 (pp) cc_final: 0.7381 (mm) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.2328 time to fit residues: 61.9144 Evaluate side-chains 136 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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: 5.9990 chunk 116 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 139 optimal weight: 0.0470 overall best weight: 3.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 HIS A 954 HIS A1217 ASN ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1476 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14101 Z= 0.324 Angle : 0.651 9.579 19425 Z= 0.327 Chirality : 0.042 0.149 2237 Planarity : 0.005 0.061 2218 Dihedral : 14.584 125.095 2748 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.39 % Favored : 94.54 % Rotamer: Outliers : 0.97 % Allowed : 9.38 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.22), residues: 1484 helix: 0.18 (0.20), residues: 707 sheet: -0.84 (0.41), residues: 153 loop : -0.60 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 593 HIS 0.012 0.002 HIS A1456 PHE 0.028 0.002 PHE A1481 TYR 0.016 0.002 TYR A1468 ARG 0.006 0.001 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7790 (mmmt) cc_final: 0.7408 (tptp) REVERT: A 827 ASN cc_start: 0.8649 (m-40) cc_final: 0.8008 (m110) REVERT: A 908 MET cc_start: 0.6286 (ttm) cc_final: 0.6070 (ttm) REVERT: A 939 MET cc_start: 0.6281 (mmp) cc_final: 0.5936 (mmp) REVERT: A 1029 MET cc_start: 0.7309 (mmp) cc_final: 0.6463 (ppp) REVERT: A 1331 PHE cc_start: 0.6189 (m-80) cc_final: 0.5720 (m-80) REVERT: A 1456 HIS cc_start: 0.7662 (t-90) cc_final: 0.7261 (t-90) outliers start: 13 outliers final: 8 residues processed: 145 average time/residue: 0.2354 time to fit residues: 52.6210 Evaluate side-chains 135 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 1376 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 ASN ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14101 Z= 0.183 Angle : 0.554 7.730 19425 Z= 0.278 Chirality : 0.040 0.142 2237 Planarity : 0.004 0.056 2218 Dihedral : 14.459 111.697 2748 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.58 % Favored : 95.35 % Rotamer: Outliers : 1.34 % Allowed : 13.18 % Favored : 85.48 % 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: -0.36 (0.22), residues: 1484 helix: 0.33 (0.20), residues: 706 sheet: -0.93 (0.40), residues: 153 loop : -0.57 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 593 HIS 0.018 0.001 HIS A 954 PHE 0.012 0.001 PHE A1481 TYR 0.015 0.001 TYR A 88 ARG 0.004 0.000 ARG A 662 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7272 (t0) cc_final: 0.6920 (m-30) REVERT: A 243 GLU cc_start: 0.7822 (tt0) cc_final: 0.7482 (tm-30) REVERT: A 263 LYS cc_start: 0.7748 (mmmt) cc_final: 0.7409 (tptp) REVERT: A 608 VAL cc_start: 0.7699 (OUTLIER) cc_final: 0.6695 (p) REVERT: A 625 MET cc_start: 0.7318 (pmm) cc_final: 0.6881 (pmm) REVERT: A 762 LEU cc_start: 0.8966 (mm) cc_final: 0.8717 (mm) REVERT: A 827 ASN cc_start: 0.8617 (m-40) cc_final: 0.7986 (m110) REVERT: A 908 MET cc_start: 0.6485 (ttm) cc_final: 0.6254 (ttm) REVERT: A 1029 MET cc_start: 0.7264 (mmp) cc_final: 0.6387 (ppp) REVERT: A 1209 MET cc_start: 0.8276 (ppp) cc_final: 0.8062 (ppp) REVERT: A 1331 PHE cc_start: 0.6089 (m-80) cc_final: 0.5834 (m-80) REVERT: A 1456 HIS cc_start: 0.7710 (t-90) cc_final: 0.7258 (t-90) REVERT: A 1480 ASP cc_start: 0.7204 (t0) cc_final: 0.6877 (t0) outliers start: 18 outliers final: 10 residues processed: 157 average time/residue: 0.2339 time to fit residues: 56.0660 Evaluate side-chains 140 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1471 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 HIS A 954 HIS ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14101 Z= 0.248 Angle : 0.598 11.542 19425 Z= 0.297 Chirality : 0.040 0.139 2237 Planarity : 0.004 0.058 2218 Dihedral : 14.379 105.668 2748 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.19 % Favored : 94.74 % Rotamer: Outliers : 2.01 % Allowed : 15.64 % Favored : 82.35 % 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: -0.45 (0.22), residues: 1484 helix: 0.27 (0.20), residues: 709 sheet: -0.98 (0.40), residues: 153 loop : -0.64 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 593 HIS 0.006 0.001 HIS A1004 PHE 0.029 0.002 PHE A 378 TYR 0.014 0.002 TYR A1468 ARG 0.005 0.000 ARG A1009 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 136 time to evaluate : 1.467 Fit side-chains revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7782 (mmmt) cc_final: 0.7372 (tptp) REVERT: A 312 ARG cc_start: 0.8541 (ttm-80) cc_final: 0.8118 (ttm-80) REVERT: A 608 VAL cc_start: 0.7898 (OUTLIER) cc_final: 0.7402 (m) REVERT: A 762 LEU cc_start: 0.8972 (mm) cc_final: 0.8726 (mm) REVERT: A 827 ASN cc_start: 0.8627 (m-40) cc_final: 0.7983 (m110) REVERT: A 908 MET cc_start: 0.6767 (ttm) cc_final: 0.6541 (ttm) REVERT: A 939 MET cc_start: 0.6165 (mmp) cc_final: 0.5814 (mmp) REVERT: A 1029 MET cc_start: 0.7186 (mmp) cc_final: 0.6184 (ppp) REVERT: A 1480 ASP cc_start: 0.7214 (t0) cc_final: 0.6911 (t0) outliers start: 27 outliers final: 17 residues processed: 154 average time/residue: 0.2421 time to fit residues: 56.9187 Evaluate side-chains 142 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1471 LEU Chi-restraints excluded: chain A residue 1476 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14101 Z= 0.227 Angle : 0.581 11.032 19425 Z= 0.291 Chirality : 0.040 0.162 2237 Planarity : 0.004 0.061 2218 Dihedral : 14.359 100.578 2748 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 2.16 % Allowed : 16.98 % Favored : 80.86 % 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: -0.44 (0.22), residues: 1484 helix: 0.30 (0.20), residues: 706 sheet: -0.83 (0.40), residues: 148 loop : -0.69 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 593 HIS 0.006 0.001 HIS A 954 PHE 0.023 0.001 PHE A 378 TYR 0.012 0.001 TYR A1468 ARG 0.012 0.000 ARG A1330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.537 Fit side-chains revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7780 (mmmt) cc_final: 0.7371 (tptp) REVERT: A 762 LEU cc_start: 0.8975 (mm) cc_final: 0.8722 (mm) REVERT: A 827 ASN cc_start: 0.8616 (m-40) cc_final: 0.7997 (m110) REVERT: A 908 MET cc_start: 0.6764 (ttm) cc_final: 0.6475 (ttm) REVERT: A 939 MET cc_start: 0.5999 (mmp) cc_final: 0.5766 (mmp) REVERT: A 1029 MET cc_start: 0.7172 (mmp) cc_final: 0.6156 (ppp) REVERT: A 1258 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.8077 (mt) REVERT: A 1480 ASP cc_start: 0.7363 (t0) cc_final: 0.7102 (t0) outliers start: 29 outliers final: 21 residues processed: 153 average time/residue: 0.2329 time to fit residues: 55.3821 Evaluate side-chains 147 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1471 LEU Chi-restraints excluded: chain A residue 1476 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 chunk 123 optimal weight: 0.2980 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN A 562 ASN ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14101 Z= 0.142 Angle : 0.536 11.701 19425 Z= 0.266 Chirality : 0.039 0.254 2237 Planarity : 0.004 0.056 2218 Dihedral : 14.208 92.801 2748 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 2.01 % Allowed : 18.47 % Favored : 79.52 % 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: -0.16 (0.22), residues: 1484 helix: 0.47 (0.20), residues: 705 sheet: -0.69 (0.41), residues: 149 loop : -0.48 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1634 HIS 0.004 0.001 HIS A 954 PHE 0.019 0.001 PHE A1331 TYR 0.016 0.001 TYR A 294 ARG 0.004 0.000 ARG A1330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7743 (mmmt) cc_final: 0.7409 (tptp) REVERT: A 312 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.8207 (ttm-80) REVERT: A 404 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7911 (tt) REVERT: A 458 MET cc_start: 0.6202 (tpt) cc_final: 0.5826 (tpt) REVERT: A 762 LEU cc_start: 0.8984 (mm) cc_final: 0.8737 (mm) REVERT: A 827 ASN cc_start: 0.8436 (m-40) cc_final: 0.7821 (m-40) REVERT: A 908 MET cc_start: 0.6676 (ttm) cc_final: 0.6413 (ttm) REVERT: A 939 MET cc_start: 0.5968 (mmp) cc_final: 0.5762 (mmp) REVERT: A 967 MET cc_start: -0.0058 (mmp) cc_final: -0.0452 (mmp) REVERT: A 1029 MET cc_start: 0.7036 (mmp) cc_final: 0.6090 (ppp) REVERT: A 1209 MET cc_start: 0.8669 (ppp) cc_final: 0.8467 (tmm) REVERT: A 1331 PHE cc_start: 0.6740 (m-10) cc_final: 0.6332 (m-80) outliers start: 27 outliers final: 15 residues processed: 158 average time/residue: 0.2309 time to fit residues: 56.5242 Evaluate side-chains 148 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1476 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 92 optimal weight: 0.1980 chunk 90 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14101 Z= 0.170 Angle : 0.560 11.796 19425 Z= 0.276 Chirality : 0.039 0.227 2237 Planarity : 0.004 0.056 2218 Dihedral : 14.134 93.254 2748 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.51 % Favored : 95.42 % Rotamer: Outliers : 1.79 % Allowed : 18.91 % Favored : 79.30 % 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: -0.16 (0.22), residues: 1484 helix: 0.50 (0.20), residues: 705 sheet: -0.72 (0.41), residues: 149 loop : -0.50 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 593 HIS 0.005 0.001 HIS A 954 PHE 0.028 0.001 PHE A 505 TYR 0.019 0.001 TYR A1000 ARG 0.004 0.000 ARG A1330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7759 (mmmt) cc_final: 0.7427 (tptp) REVERT: A 344 MET cc_start: 0.5898 (mpp) cc_final: 0.5395 (mmm) REVERT: A 372 MET cc_start: 0.7863 (mmm) cc_final: 0.7613 (mmm) REVERT: A 458 MET cc_start: 0.6153 (tpt) cc_final: 0.5767 (tpt) REVERT: A 762 LEU cc_start: 0.8986 (mm) cc_final: 0.8730 (mm) REVERT: A 827 ASN cc_start: 0.8473 (m-40) cc_final: 0.7880 (m-40) REVERT: A 908 MET cc_start: 0.6670 (ttm) cc_final: 0.6359 (ttm) REVERT: A 939 MET cc_start: 0.5785 (mmp) cc_final: 0.5557 (mmp) REVERT: A 1029 MET cc_start: 0.6996 (mmp) cc_final: 0.6014 (ppp) REVERT: A 1209 MET cc_start: 0.8669 (ppp) cc_final: 0.8465 (tmm) REVERT: A 1331 PHE cc_start: 0.6890 (m-10) cc_final: 0.6366 (m-80) outliers start: 24 outliers final: 19 residues processed: 156 average time/residue: 0.2304 time to fit residues: 56.1251 Evaluate side-chains 146 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1476 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.0020 chunk 28 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 101 optimal weight: 0.0040 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN A 623 ASN ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14101 Z= 0.144 Angle : 0.545 11.611 19425 Z= 0.272 Chirality : 0.038 0.217 2237 Planarity : 0.004 0.051 2218 Dihedral : 14.046 89.651 2748 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 1.49 % Allowed : 19.58 % Favored : 78.93 % 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 (0.23), residues: 1484 helix: 0.57 (0.20), residues: 713 sheet: -0.79 (0.40), residues: 155 loop : -0.43 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1634 HIS 0.005 0.001 HIS A 954 PHE 0.024 0.001 PHE A 505 TYR 0.018 0.001 TYR A 294 ARG 0.003 0.000 ARG A1041 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7715 (mmmt) cc_final: 0.7381 (tptp) REVERT: A 312 ARG cc_start: 0.8488 (ttm-80) cc_final: 0.7969 (ttm-80) REVERT: A 372 MET cc_start: 0.7844 (mmm) cc_final: 0.7618 (mmm) REVERT: A 458 MET cc_start: 0.6330 (tpt) cc_final: 0.5997 (tpt) REVERT: A 625 MET cc_start: 0.7115 (pmm) cc_final: 0.6732 (pmm) REVERT: A 827 ASN cc_start: 0.8455 (m-40) cc_final: 0.7959 (m110) REVERT: A 908 MET cc_start: 0.6618 (ttm) cc_final: 0.6324 (ttm) REVERT: A 939 MET cc_start: 0.5671 (mmp) cc_final: 0.5442 (mmp) REVERT: A 967 MET cc_start: -0.0149 (mmp) cc_final: -0.0452 (mmp) REVERT: A 1029 MET cc_start: 0.7088 (mmp) cc_final: 0.6117 (ppp) REVERT: A 1331 PHE cc_start: 0.6650 (m-10) cc_final: 0.6011 (m-80) outliers start: 20 outliers final: 16 residues processed: 157 average time/residue: 0.2401 time to fit residues: 57.8760 Evaluate side-chains 145 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 589 PHE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1476 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 108 optimal weight: 0.0040 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14101 Z= 0.151 Angle : 0.554 12.131 19425 Z= 0.274 Chirality : 0.038 0.198 2237 Planarity : 0.004 0.051 2218 Dihedral : 14.002 89.441 2748 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.62 % Rotamer: Outliers : 1.34 % Allowed : 20.25 % Favored : 78.41 % 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 (0.23), residues: 1484 helix: 0.53 (0.20), residues: 713 sheet: -0.79 (0.40), residues: 155 loop : -0.36 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 593 HIS 0.004 0.001 HIS A1004 PHE 0.024 0.001 PHE A 505 TYR 0.028 0.001 TYR A 294 ARG 0.007 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7714 (mmmt) cc_final: 0.7419 (tptp) REVERT: A 312 ARG cc_start: 0.8515 (ttm-80) cc_final: 0.8034 (ttm-80) REVERT: A 344 MET cc_start: 0.6046 (mpp) cc_final: 0.5657 (mmm) REVERT: A 360 MET cc_start: 0.8743 (tpp) cc_final: 0.8355 (mmm) REVERT: A 458 MET cc_start: 0.6235 (tpt) cc_final: 0.5976 (tpt) REVERT: A 625 MET cc_start: 0.7095 (pmm) cc_final: 0.6722 (pmm) REVERT: A 762 LEU cc_start: 0.8916 (mm) cc_final: 0.8597 (mt) REVERT: A 827 ASN cc_start: 0.8473 (m-40) cc_final: 0.7980 (m110) REVERT: A 908 MET cc_start: 0.6606 (ttm) cc_final: 0.6276 (ttm) REVERT: A 939 MET cc_start: 0.5642 (mmp) cc_final: 0.5411 (mmp) REVERT: A 967 MET cc_start: -0.0155 (mmp) cc_final: -0.0442 (mmp) REVERT: A 1029 MET cc_start: 0.6975 (mmp) cc_final: 0.6022 (ppp) REVERT: A 1331 PHE cc_start: 0.6539 (m-10) cc_final: 0.5917 (m-80) outliers start: 18 outliers final: 15 residues processed: 150 average time/residue: 0.2316 time to fit residues: 53.6114 Evaluate side-chains 148 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 589 PHE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1476 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.5980 chunk 89 optimal weight: 8.9990 chunk 69 optimal weight: 0.2980 chunk 101 optimal weight: 0.9980 chunk 153 optimal weight: 8.9990 chunk 141 optimal weight: 0.9980 chunk 122 optimal weight: 0.0050 chunk 12 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14101 Z= 0.147 Angle : 0.564 12.506 19425 Z= 0.275 Chirality : 0.038 0.190 2237 Planarity : 0.004 0.051 2218 Dihedral : 13.963 87.369 2748 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 1.34 % Allowed : 20.48 % Favored : 78.18 % 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: -0.04 (0.23), residues: 1484 helix: 0.57 (0.20), residues: 712 sheet: -0.71 (0.41), residues: 154 loop : -0.39 (0.27), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1634 HIS 0.003 0.001 HIS A1004 PHE 0.025 0.001 PHE A 505 TYR 0.027 0.001 TYR A 294 ARG 0.007 0.000 ARG A 269 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7770 (mmmt) cc_final: 0.7439 (tptp) REVERT: A 312 ARG cc_start: 0.8547 (ttm-80) cc_final: 0.8047 (ttm-80) REVERT: A 344 MET cc_start: 0.6035 (mpp) cc_final: 0.5652 (mmm) REVERT: A 360 MET cc_start: 0.8732 (tpp) cc_final: 0.8409 (mmm) REVERT: A 625 MET cc_start: 0.7067 (pmm) cc_final: 0.6733 (pmm) REVERT: A 762 LEU cc_start: 0.8892 (mm) cc_final: 0.8500 (mt) REVERT: A 827 ASN cc_start: 0.8454 (m-40) cc_final: 0.7933 (m-40) REVERT: A 908 MET cc_start: 0.6411 (ttm) cc_final: 0.6118 (ttm) REVERT: A 939 MET cc_start: 0.5617 (mmp) cc_final: 0.5403 (mmp) REVERT: A 1029 MET cc_start: 0.6901 (mmp) cc_final: 0.6001 (ppp) REVERT: A 1331 PHE cc_start: 0.6401 (m-10) cc_final: 0.5816 (m-80) outliers start: 18 outliers final: 14 residues processed: 155 average time/residue: 0.2365 time to fit residues: 56.9899 Evaluate side-chains 156 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1476 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 125 optimal weight: 0.4980 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 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 = 0.3968 r_free = 0.3968 target = 0.100146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.080906 restraints weight = 53405.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.082756 restraints weight = 32386.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.084025 restraints weight = 23164.240| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14101 Z= 0.147 Angle : 0.563 13.831 19425 Z= 0.275 Chirality : 0.038 0.181 2237 Planarity : 0.004 0.050 2218 Dihedral : 13.940 86.217 2748 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.25 % Favored : 95.69 % Rotamer: Outliers : 1.19 % Allowed : 21.07 % Favored : 77.74 % 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: -0.01 (0.23), residues: 1484 helix: 0.60 (0.20), residues: 712 sheet: -0.69 (0.40), residues: 154 loop : -0.40 (0.27), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1634 HIS 0.003 0.001 HIS A 323 PHE 0.026 0.001 PHE A 505 TYR 0.027 0.001 TYR A 294 ARG 0.007 0.000 ARG A 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2458.34 seconds wall clock time: 45 minutes 54.17 seconds (2754.17 seconds total)