Starting phenix.real_space_refine (version: dev) on Tue Dec 13 03:50:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0c_32238/12_2022/7w0c_32238_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0c_32238/12_2022/7w0c_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_32238/12_2022/7w0c_32238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0c_32238/12_2022/7w0c_32238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0c_32238/12_2022/7w0c_32238_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0c_32238/12_2022/7w0c_32238_updated.pdb" } resolution = 3.93 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= 0.004 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 Convert atoms to be neutral 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 7.95, per 1000 atoms: 0.58 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: 6.28 Conformation dependent library (CDL) restraints added in 1.8 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: 6.72 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: 7.28 Time building geometry restraints manager: 6.63 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: 7986 25.96 - 51.91: 346 51.91 - 77.87: 24 77.87 - 103.82: 6 103.82 - 129.78: 1 Dihedral angle restraints: 8363 sinusoidal: 3965 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 8360 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 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. 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: 0.890 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: 4.160 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.140 Process input model: 44.750 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 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 : 13.504 129.779 5511 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.18 % Favored : 95.75 % Rotamer Outliers : 0.07 % 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 *********************** 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 : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.2367 time to fit residues: 61.8207 Evaluate side-chains 135 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.454 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9279 ------------------------------------------------------------------------------- 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: 5.9990 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 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: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** 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 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 773 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 ** A1543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 14101 Z= 0.402 Angle : 0.724 10.258 19425 Z= 0.366 Chirality : 0.044 0.163 2237 Planarity : 0.005 0.062 2218 Dihedral : 6.908 128.273 2494 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 22.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.06 % Favored : 93.87 % Rotamer Outliers : 1.12 % 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: -0.76 (0.22), residues: 1484 helix: -0.08 (0.19), residues: 709 sheet: -0.79 (0.41), residues: 148 loop : -0.76 (0.26), residues: 627 *********************** 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 151 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 1.526 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 142 average time/residue: 0.2414 time to fit residues: 52.5647 Evaluate side-chains 130 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 1.663 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1876 time to fit residues: 5.1782 ------------------------------------------------------------------------------- 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: 7.9990 chunk 43 optimal weight: 0.0470 chunk 116 optimal weight: 5.9990 chunk 95 optimal weight: 0.0040 chunk 38 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 138 optimal weight: 0.0980 chunk 47 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 overall best weight: 0.3890 ------------------------------------------------------------------------------- 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 A 562 ASN ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 14101 Z= 0.141 Angle : 0.549 7.709 19425 Z= 0.274 Chirality : 0.039 0.142 2237 Planarity : 0.004 0.057 2218 Dihedral : 6.183 109.164 2494 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.91 % Favored : 96.02 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.22), residues: 1484 helix: 0.38 (0.20), residues: 703 sheet: -0.65 (0.41), residues: 149 loop : -0.48 (0.26), residues: 632 *********************** 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 170 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 162 average time/residue: 0.2433 time to fit residues: 60.3086 Evaluate side-chains 140 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1855 time to fit residues: 4.5105 ------------------------------------------------------------------------------- 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: 0.9980 chunk 105 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 148 optimal weight: 10.9990 chunk 73 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 257 GLN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 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 954 HIS ** 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: 0.7529 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 14101 Z= 0.296 Angle : 0.640 11.461 19425 Z= 0.319 Chirality : 0.041 0.146 2237 Planarity : 0.004 0.060 2218 Dihedral : 6.385 107.987 2494 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.59 % Favored : 94.34 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.22), residues: 1484 helix: 0.18 (0.20), residues: 709 sheet: -0.89 (0.40), residues: 148 loop : -0.72 (0.26), residues: 627 *********************** 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 152 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.597 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 146 average time/residue: 0.2401 time to fit residues: 54.1337 Evaluate side-chains 135 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 1.631 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1288 time to fit residues: 5.7484 ------------------------------------------------------------------------------- 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: 0.3980 chunk 84 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 127 optimal weight: 0.0770 chunk 102 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 76 optimal weight: 0.0000 chunk 133 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.3544 ------------------------------------------------------------------------------- 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 517 GLN ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 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: 0.7392 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 14101 Z= 0.140 Angle : 0.553 11.795 19425 Z= 0.275 Chirality : 0.039 0.252 2237 Planarity : 0.004 0.058 2218 Dihedral : 5.901 94.056 2494 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.64 % Favored : 96.29 % Rotamer Outliers : 0.74 % 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: -0.15 (0.22), residues: 1484 helix: 0.58 (0.20), residues: 697 sheet: -0.74 (0.41), residues: 149 loop : -0.58 (0.26), residues: 638 *********************** 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 156 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 152 average time/residue: 0.2531 time to fit residues: 59.0920 Evaluate side-chains 131 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 1.632 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1259 time to fit residues: 3.0761 ------------------------------------------------------------------------------- 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: 8.9990 chunk 134 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 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** ** A1456 HIS ** 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: 0.7413 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 14101 Z= 0.157 Angle : 0.556 11.956 19425 Z= 0.275 Chirality : 0.039 0.201 2237 Planarity : 0.004 0.056 2218 Dihedral : 5.746 92.332 2494 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer Outliers : 0.74 % 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: -0.08 (0.22), residues: 1484 helix: 0.60 (0.20), residues: 700 sheet: -0.70 (0.41), residues: 149 loop : -0.50 (0.26), residues: 635 *********************** 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 143 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 139 average time/residue: 0.2354 time to fit residues: 50.8437 Evaluate side-chains 131 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 1.578 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1262 time to fit residues: 3.0768 ------------------------------------------------------------------------------- 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: 8.9990 chunk 16 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 68 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 623 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** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1476 ASN ** 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: 0.7410 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 14101 Z= 0.158 Angle : 0.554 11.838 19425 Z= 0.273 Chirality : 0.039 0.171 2237 Planarity : 0.004 0.054 2218 Dihedral : 5.678 91.328 2494 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.22), residues: 1484 helix: 0.62 (0.20), residues: 701 sheet: -0.70 (0.41), residues: 149 loop : -0.51 (0.26), residues: 634 *********************** 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 146 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 1.554 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 142 average time/residue: 0.2335 time to fit residues: 51.3765 Evaluate side-chains 129 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 1.612 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1252 time to fit residues: 3.3235 ------------------------------------------------------------------------------- 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: 3.9990 chunk 88 optimal weight: 9.9990 chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 94 optimal weight: 8.9990 chunk 101 optimal weight: 0.0040 chunk 73 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 116 optimal weight: 0.0570 chunk 135 optimal weight: 2.9990 overall best weight: 0.3710 ------------------------------------------------------------------------------- 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** ** A1456 HIS ** 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: 0.7349 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 0.045 14101 Z= 0.142 Angle : 0.552 12.046 19425 Z= 0.270 Chirality : 0.038 0.163 2237 Planarity : 0.004 0.049 2218 Dihedral : 5.491 87.639 2494 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.82 % Rotamer Outliers : 0.52 % 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: 0.07 (0.23), residues: 1484 helix: 0.71 (0.20), residues: 701 sheet: -0.75 (0.41), residues: 155 loop : -0.36 (0.27), residues: 628 *********************** 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 151 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 149 average time/residue: 0.2453 time to fit residues: 56.2677 Evaluate side-chains 131 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 1.547 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1392 time to fit residues: 2.6838 ------------------------------------------------------------------------------- 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: 20.0000 chunk 129 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** 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: 0.7426 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 14101 Z= 0.191 Angle : 0.595 11.908 19425 Z= 0.290 Chirality : 0.039 0.164 2237 Planarity : 0.004 0.053 2218 Dihedral : 5.598 91.372 2494 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.78 % Favored : 95.15 % Rotamer Outliers : 0.74 % 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: -0.04 (0.23), residues: 1484 helix: 0.65 (0.20), residues: 702 sheet: -0.81 (0.40), residues: 155 loop : -0.47 (0.26), residues: 627 *********************** 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 144 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 139 average time/residue: 0.2535 time to fit residues: 53.7905 Evaluate side-chains 140 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1346 time to fit residues: 4.1885 ------------------------------------------------------------------------------- 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: 0.6980 chunk 89 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 97 optimal weight: 0.1980 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 A 954 HIS ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1327 ASN ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** 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: 0.7382 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 14101 Z= 0.156 Angle : 0.593 12.607 19425 Z= 0.286 Chirality : 0.039 0.163 2237 Planarity : 0.004 0.052 2218 Dihedral : 5.505 88.048 2494 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.62 % Rotamer Outliers : 0.37 % 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: -0.05 (0.23), residues: 1484 helix: 0.58 (0.20), residues: 699 sheet: -0.66 (0.41), residues: 154 loop : -0.43 (0.27), residues: 631 ********************** 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 138 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 137 average time/residue: 0.2614 time to fit residues: 54.7956 Evaluate side-chains 132 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.978 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1449 time to fit residues: 2.6177 ------------------------------------------------------------------------------- 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: 1.9990 chunk 37 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 122 optimal weight: 0.0670 chunk 51 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 overall best weight: 1.0124 ------------------------------------------------------------------------------- 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** ** A1456 HIS ** 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 = 0.3955 r_free = 0.3955 target = 0.099448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.080034 restraints weight = 54024.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.081875 restraints weight = 32918.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.083112 restraints weight = 23741.366| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 14101 Z= 0.168 Angle : 0.598 13.485 19425 Z= 0.289 Chirality : 0.039 0.159 2237 Planarity : 0.004 0.054 2218 Dihedral : 5.498 88.447 2494 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.85 % Favored : 95.08 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.61 (0.20), residues: 704 sheet: -0.64 (0.41), residues: 154 loop : -0.41 (0.27), residues: 626 =============================================================================== Job complete usr+sys time: 2348.73 seconds wall clock time: 44 minutes 17.70 seconds (2657.70 seconds total)