Starting phenix.real_space_refine on Sat Sep 12 09:22:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rqj_4983/09_2026/6rqj_4983.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rqj_4983/09_2026/6rqj_4983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rqj_4983/09_2026/6rqj_4983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rqj_4983/09_2026/6rqj_4983.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6rqj_4983/09_2026/6rqj_4983.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rqj_4983/09_2026/6rqj_4983.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rqj_4983/09_2026/6rqj_4983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rqj_4983/09_2026/6rqj_4983.map" } resolution = 3.5 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 79 5.16 5 C 9532 2.51 5 N 2475 2.21 5 O 2885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14971 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7768 Classifications: {'peptide': 981} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 945} Chain breaks: 2 Chain: "C" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1151 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 140} Chain: "D" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 324 Classifications: {'peptide': 46} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 43} Chain: "B" Number of atoms: 5080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5080 Classifications: {'peptide': 643} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 609} Chain breaks: 1 Chain: "E" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 620 Classifications: {'peptide': 82} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 74} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.30, per 1000 atoms: 0.22 Number of scatterers: 14971 At special positions: 0 Unit cell: (87.954, 179.196, 115.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 79 16.00 O 2885 8.00 N 2475 7.00 C 9532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 698 " - pdb=" SG CYS A 724 " distance=2.03 Simple disulfide: pdb=" SG CYS A 699 " - pdb=" SG CYS A 731 " distance=2.04 Simple disulfide: pdb=" SG CYS A 711 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A 810 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 856 " - pdb=" SG CYS A 883 " distance=2.04 Simple disulfide: pdb=" SG CYS A 866 " - pdb=" SG CYS A1527 " distance=2.03 Simple disulfide: pdb=" SG CYS A1101 " - pdb=" SG CYS A1159 " distance=2.02 Simple disulfide: pdb=" SG CYS A1375 " - pdb=" SG CYS A1505 " distance=2.05 Simple disulfide: pdb=" SG CYS A1405 " - pdb=" SG CYS A1474 " distance=2.03 Simple disulfide: pdb=" SG CYS A1520 " - pdb=" SG CYS A1525 " distance=2.03 Simple disulfide: pdb=" SG CYS A1532 " - pdb=" SG CYS A1606 " distance=2.03 Simple disulfide: pdb=" SG CYS A1553 " - pdb=" SG CYS A1676 " distance=2.03 Simple disulfide: pdb=" SG CYS A1654 " - pdb=" SG CYS A1657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 146 " distance=2.03 Simple disulfide: pdb=" SG CYS C 56 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS D 38 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 40 " distance=2.03 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 55 " distance=2.03 Simple disulfide: pdb=" SG CYS B 634 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 45 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 79 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 85 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG F 1 " - " ASN A 911 " Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 668.5 milliseconds 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3582 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 34 sheets defined 19.2% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 680 through 690 removed outlier: 4.510A pdb=" N ILE A 686 " --> pdb=" O LYS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 704 removed outlier: 4.665A pdb=" N CYS A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 715 Processing helix chain 'A' and resid 716 through 718 No H-bonds generated for 'chain 'A' and resid 716 through 718' Processing helix chain 'A' and resid 720 through 737 removed outlier: 3.937A pdb=" N CYS A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 758 Processing helix chain 'A' and resid 984 through 992 Processing helix chain 'A' and resid 1009 through 1014 Processing helix chain 'A' and resid 1015 through 1029 Processing helix chain 'A' and resid 1030 through 1034 Processing helix chain 'A' and resid 1039 through 1056 removed outlier: 3.777A pdb=" N SER A1055 " --> pdb=" O GLU A1051 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A1056 " --> pdb=" O GLY A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1060 removed outlier: 3.523A pdb=" N ARG A1060 " --> pdb=" O MET A1057 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1057 through 1060' Processing helix chain 'A' and resid 1075 through 1090 Processing helix chain 'A' and resid 1096 through 1111 Processing helix chain 'A' and resid 1132 through 1156 Processing helix chain 'A' and resid 1162 through 1179 Processing helix chain 'A' and resid 1184 through 1197 Processing helix chain 'A' and resid 1202 through 1214 Processing helix chain 'A' and resid 1244 through 1261 Processing helix chain 'A' and resid 1267 through 1278 Processing helix chain 'A' and resid 1286 through 1302 removed outlier: 3.501A pdb=" N THR A1290 " --> pdb=" O SER A1286 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A1291 " --> pdb=" O THR A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1445 removed outlier: 3.800A pdb=" N LEU A1439 " --> pdb=" O ASN A1435 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY A1445 " --> pdb=" O ALA A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1527 through 1532 removed outlier: 4.440A pdb=" N ASP A1531 " --> pdb=" O VAL A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1553 removed outlier: 3.617A pdb=" N CYS A1553 " --> pdb=" O LYS A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1657 through 1675 removed outlier: 4.574A pdb=" N PHE A1672 " --> pdb=" O ALA A1668 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU A1673 " --> pdb=" O GLU A1669 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN A1674 " --> pdb=" O ASP A1670 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A1675 " --> pdb=" O ILE A1671 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 40 removed outlier: 6.480A pdb=" N GLU C 38 " --> pdb=" O ALA C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 156 Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.712A pdb=" N LEU B 92 " --> pdb=" O PRO B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 307 Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'B' and resid 641 through 650 Processing sheet with id=AA1, first strand: chain 'A' and resid 764 through 765 Processing sheet with id=AA2, first strand: chain 'A' and resid 777 through 780 removed outlier: 3.807A pdb=" N TRP B 599 " --> pdb=" O ILE A 804 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 783 through 789 Processing sheet with id=AA4, first strand: chain 'A' and resid 815 through 818 Processing sheet with id=AA5, first strand: chain 'A' and resid 823 through 827 Processing sheet with id=AA6, first strand: chain 'A' and resid 832 through 834 removed outlier: 5.760A pdb=" N VAL A 833 " --> pdb=" O VAL A 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 919 " --> pdb=" O THR A 916 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET A 853 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 888 " --> pdb=" O MET A 853 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 839 through 840 Processing sheet with id=AA8, first strand: chain 'A' and resid 936 through 944 removed outlier: 3.632A pdb=" N LYS A 974 " --> pdb=" O VAL A1364 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 956 through 959 removed outlier: 3.930A pdb=" N VAL A1315 " --> pdb=" O HIS A1324 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR A1317 " --> pdb=" O ALA A1322 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ALA A1322 " --> pdb=" O TYR A1317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1225 through 1227 removed outlier: 3.682A pdb=" N TYR A1225 " --> pdb=" O LYS A1219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1377 through 1384 removed outlier: 4.046A pdb=" N LYS A1380 " --> pdb=" O CYS A1405 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1461 through 1463 Processing sheet with id=AB4, first strand: chain 'A' and resid 1461 through 1463 Processing sheet with id=AB5, first strand: chain 'A' and resid 1625 through 1628 removed outlier: 8.850A pdb=" N GLU A1597 " --> pdb=" O PHE A1633 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR A1635 " --> pdb=" O GLU A1597 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A1599 " --> pdb=" O TYR A1635 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR A1580 " --> pdb=" O ILE A1565 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE A1565 " --> pdb=" O THR A1580 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU A1582 " --> pdb=" O VAL A1563 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL A1563 " --> pdb=" O LEU A1582 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE A1584 " --> pdb=" O TYR A1561 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TYR A1561 " --> pdb=" O ILE A1584 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS A1586 " --> pdb=" O TYR A1559 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TYR A1559 " --> pdb=" O LYS A1586 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A1559 " --> pdb=" O GLY A1621 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A1621 " --> pdb=" O TYR A1559 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A1619 " --> pdb=" O TYR A1561 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 48 removed outlier: 5.359A pdb=" N LEU C 57 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 11.371A pdb=" N ARG C 47 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N ASP C 55 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 55 " --> pdb=" O LYS C 77 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU C 57 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR C 75 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLY C 59 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N MET C 73 " --> pdb=" O GLY C 59 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL C 109 " --> pdb=" O LYS C 122 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LYS C 122 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR C 111 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR C 130 " --> pdb=" O SER C 48 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER C 48 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET C 132 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.555A pdb=" N ALA D 51 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 38 through 41 Processing sheet with id=AB9, first strand: chain 'B' and resid 80 through 86 removed outlier: 8.159A pdb=" N ASN B 38 " --> pdb=" O PRO B 28 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 27 " --> pdb=" O THR B 652 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 31 through 32 removed outlier: 6.450A pdb=" N PHE B 31 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 113 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 67 " --> pdb=" O ILE B 56 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 31 through 32 removed outlier: 6.450A pdb=" N PHE B 31 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 113 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 52 " --> pdb=" O VAL B 71 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 125 through 130 Processing sheet with id=AC4, first strand: chain 'B' and resid 134 through 135 removed outlier: 3.520A pdb=" N PHE B 217 " --> pdb=" O TRP B 199 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 159 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 174 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AC6, first strand: chain 'B' and resid 228 through 233 Processing sheet with id=AC7, first strand: chain 'B' and resid 280 through 282 Processing sheet with id=AC8, first strand: chain 'B' and resid 280 through 282 Processing sheet with id=AC9, first strand: chain 'B' and resid 353 through 356 Processing sheet with id=AD1, first strand: chain 'B' and resid 362 through 363 removed outlier: 7.426A pdb=" N THR B 429 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA B 392 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASP B 405 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N THR B 394 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ASP B 403 " --> pdb=" O THR B 394 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 362 through 363 removed outlier: 7.426A pdb=" N THR B 429 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 464 through 468 Processing sheet with id=AD4, first strand: chain 'B' and resid 508 through 509 removed outlier: 3.549A pdb=" N ARG B 539 " --> pdb=" O LEU B 504 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR B 544 " --> pdb=" O VAL B 555 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 8 through 12 removed outlier: 3.535A pdb=" N SER E 54 " --> pdb=" O TYR E 9 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR E 11 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL E 52 " --> pdb=" O THR E 11 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 16 through 17 Processing sheet with id=AD7, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.541A pdb=" N GLU E 69 " --> pdb=" O LYS E 82 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1578 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2521 1.32 - 1.45: 4071 1.45 - 1.58: 8585 1.58 - 1.71: 0 1.71 - 1.85: 109 Bond restraints: 15286 Sorted by residual: bond pdb=" C7 NAG F 2 " pdb=" N2 NAG F 2 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" C7 NAG F 1 " pdb=" N2 NAG F 1 " ideal model delta sigma weight residual 1.346 1.458 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.503 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C5 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.413 1.472 -0.059 2.00e-02 2.50e+03 8.69e+00 ... (remaining 15281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 19996 1.73 - 3.46: 668 3.46 - 5.19: 63 5.19 - 6.91: 11 6.91 - 8.64: 4 Bond angle restraints: 20742 Sorted by residual: angle pdb=" N VAL A 984 " pdb=" CA VAL A 984 " pdb=" C VAL A 984 " ideal model delta sigma weight residual 111.91 106.69 5.22 8.90e-01 1.26e+00 3.44e+01 angle pdb=" N GLY A1522 " pdb=" CA GLY A1522 " pdb=" C GLY A1522 " ideal model delta sigma weight residual 111.35 117.61 -6.26 1.20e+00 6.94e-01 2.72e+01 angle pdb=" N ILE A 683 " pdb=" CA ILE A 683 " pdb=" C ILE A 683 " ideal model delta sigma weight residual 111.81 108.64 3.17 8.60e-01 1.35e+00 1.36e+01 angle pdb=" N ILE A 997 " pdb=" CA ILE A 997 " pdb=" C ILE A 997 " ideal model delta sigma weight residual 113.20 109.77 3.43 9.60e-01 1.09e+00 1.27e+01 angle pdb=" CA TYR B 256 " pdb=" CB TYR B 256 " pdb=" CG TYR B 256 " ideal model delta sigma weight residual 113.90 120.21 -6.31 1.80e+00 3.09e-01 1.23e+01 ... (remaining 20737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 8210 17.59 - 35.17: 864 35.17 - 52.76: 152 52.76 - 70.35: 26 70.35 - 87.93: 14 Dihedral angle restraints: 9266 sinusoidal: 3705 harmonic: 5561 Sorted by residual: dihedral pdb=" CB CYS D 14 " pdb=" SG CYS D 14 " pdb=" SG CYS D 38 " pdb=" CB CYS D 38 " ideal model delta sinusoidal sigma weight residual -86.00 -162.42 76.42 1 1.00e+01 1.00e-02 7.35e+01 dihedral pdb=" CB CYS B 634 " pdb=" SG CYS B 634 " pdb=" SG CYS B 669 " pdb=" CB CYS B 669 " ideal model delta sinusoidal sigma weight residual -86.00 -16.02 -69.98 1 1.00e+01 1.00e-02 6.31e+01 dihedral pdb=" CB CYS A 699 " pdb=" SG CYS A 699 " pdb=" SG CYS A 731 " pdb=" CB CYS A 731 " ideal model delta sinusoidal sigma weight residual 93.00 26.57 66.43 1 1.00e+01 1.00e-02 5.76e+01 ... (remaining 9263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.990: 2366 0.990 - 1.980: 0 1.980 - 2.970: 0 2.970 - 3.960: 0 3.960 - 4.949: 1 Chirality restraints: 2367 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 2.55 -4.95 2.00e-02 2.50e+03 6.12e+04 chirality pdb=" CA TYR B 256 " pdb=" N TYR B 256 " pdb=" C TYR B 256 " pdb=" CB TYR B 256 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB VAL A1015 " pdb=" CA VAL A1015 " pdb=" CG1 VAL A1015 " pdb=" CG2 VAL A1015 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 2364 not shown) Planarity restraints: 2649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS D 34 " -0.056 5.00e-02 4.00e+02 8.51e-02 1.16e+01 pdb=" N PRO D 35 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO D 35 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 35 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1268 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO A1269 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A1269 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1269 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1037 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO A1038 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A1038 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1038 " 0.024 5.00e-02 4.00e+02 ... (remaining 2646 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 186 2.61 - 3.18: 13333 3.18 - 3.76: 21573 3.76 - 4.33: 30818 4.33 - 4.90: 51882 Nonbonded interactions: 117792 Sorted by model distance: nonbonded pdb=" OH TYR B 44 " pdb=" OD1 ASN B 500 " model vdw 2.041 3.040 nonbonded pdb=" NZ LYS B 566 " pdb=" O CYS B 567 " model vdw 2.153 3.120 nonbonded pdb=" O ARG A1060 " pdb=" NH2 ARG B 195 " model vdw 2.164 3.120 nonbonded pdb=" OG1 THR C 49 " pdb=" OD1 ASP C 129 " model vdw 2.167 3.040 nonbonded pdb=" O GLU B 232 " pdb=" OG1 THR B 249 " model vdw 2.203 3.040 ... (remaining 117787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.620 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 : 0.006 0.116 15312 Z= 0.291 Angle : 0.806 44.089 20796 Z= 0.445 Chirality : 0.112 4.949 2367 Planarity : 0.004 0.085 2648 Dihedral : 14.353 87.932 5612 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.85 % Favored : 92.94 % Rotamer: Outliers : 0.06 % Allowed : 6.32 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.28 (0.16), residues: 1883 helix: -2.84 (0.20), residues: 335 sheet: -2.42 (0.18), residues: 626 loop : -3.12 (0.16), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1214 TYR 0.026 0.002 TYR B 256 PHE 0.023 0.002 PHE B 255 TRP 0.012 0.001 TRP A1077 HIS 0.005 0.001 HIS A 692 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.29 (15286) covalent geometry : angle 0.74039 / 0.43 (20742) SS BOND : bond 0.00463 / 0.24 ( 24) SS BOND : angle 1.57686 / 0.82 ( 48) hydrogen bonds : bond 0.24140 / 16.15 ( 565) hydrogen bonds : angle 9.76738 / 7.07 ( 1578) link_BETA1-4 : bond 0.06442 / 3.39 ( 1) link_BETA1-4 : angle 25.98231 / 13.65 ( 3) link_NAG-ASN : bond 0.00234 / 0.12 ( 1) link_NAG-ASN : angle 1.21744 / 0.69 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 53 ASN cc_start: 0.7679 (m-40) cc_final: 0.7015 (p0) outliers start: 1 outliers final: 1 residues processed: 114 average time/residue: 0.1325 time to fit residues: 22.7509 Evaluate side-chains 81 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.0870 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.0170 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 9.9990 overall best weight: 2.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 680 GLN A 692 HIS A 787 GLN A1035 HIS A1088 GLN A1278 GLN A1319 HIS A1343 ASN A1360 HIS ** A1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN B 446 ASN B 500 ASN B 562 ASN E 59 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.080903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.059967 restraints weight = 58927.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.062147 restraints weight = 29984.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.062013 restraints weight = 18696.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.062457 restraints weight = 17692.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.062525 restraints weight = 15499.494| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15312 Z= 0.166 Angle : 0.620 7.707 20796 Z= 0.324 Chirality : 0.045 0.260 2367 Planarity : 0.004 0.076 2648 Dihedral : 5.102 35.495 2043 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.78 % Allowed : 11.69 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.17), residues: 1883 helix: -0.94 (0.27), residues: 345 sheet: -1.84 (0.19), residues: 619 loop : -2.39 (0.17), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1279 TYR 0.017 0.001 TYR B 312 PHE 0.015 0.001 PHE A1019 TRP 0.011 0.001 TRP A1273 HIS 0.005 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (15286) covalent geometry : angle 0.61773 / 0.32 (20742) SS BOND : bond 0.00365 / 0.19 ( 24) SS BOND : angle 1.17273 / 0.73 ( 48) hydrogen bonds : bond 0.03892 / 2.58 ( 565) hydrogen bonds : angle 6.22753 / 4.45 ( 1578) link_BETA1-4 : bond 0.01581 / 0.83 ( 1) link_BETA1-4 : angle 1.66482 / 0.92 ( 3) link_NAG-ASN : bond 0.00319 / 0.17 ( 1) link_NAG-ASN : angle 1.85374 / 1.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1507 MET cc_start: 0.8348 (ttm) cc_final: 0.8110 (ttp) REVERT: A 1635 TYR cc_start: 0.7945 (m-80) cc_final: 0.7715 (m-10) REVERT: D 20 GLU cc_start: 0.8630 (pm20) cc_final: 0.8268 (pm20) REVERT: B 208 ASP cc_start: 0.7447 (t0) cc_final: 0.7063 (t0) REVERT: E 9 TYR cc_start: 0.8270 (p90) cc_final: 0.7767 (p90) REVERT: E 53 ASN cc_start: 0.8732 (m-40) cc_final: 0.8143 (p0) REVERT: E 69 GLU cc_start: 0.7698 (mp0) cc_final: 0.7451 (mp0) outliers start: 13 outliers final: 6 residues processed: 105 average time/residue: 0.1114 time to fit residues: 18.3523 Evaluate side-chains 89 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 134 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 155 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 28 optimal weight: 0.0770 chunk 184 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 753 HIS A1110 ASN ** A1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.073809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.051935 restraints weight = 62294.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.053862 restraints weight = 30245.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.055049 restraints weight = 19895.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.055869 restraints weight = 15534.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.056353 restraints weight = 13346.299| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15312 Z= 0.181 Angle : 0.581 6.949 20796 Z= 0.302 Chirality : 0.043 0.241 2367 Planarity : 0.004 0.074 2648 Dihedral : 4.866 29.840 2043 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.67 % Allowed : 13.19 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.18), residues: 1883 helix: -0.12 (0.28), residues: 344 sheet: -1.48 (0.19), residues: 632 loop : -1.97 (0.18), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 50 TYR 0.017 0.001 TYR B 312 PHE 0.014 0.001 PHE A1019 TRP 0.010 0.001 TRP A1644 HIS 0.004 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (15286) covalent geometry : angle 0.57843 / 0.30 (20742) SS BOND : bond 0.00372 / 0.19 ( 24) SS BOND : angle 1.18055 / 0.67 ( 48) hydrogen bonds : bond 0.03542 / 2.33 ( 565) hydrogen bonds : angle 5.58265 / 3.95 ( 1578) link_BETA1-4 : bond 0.00230 / 0.12 ( 1) link_BETA1-4 : angle 1.02751 / 0.57 ( 3) link_NAG-ASN : bond 0.00348 / 0.18 ( 1) link_NAG-ASN : angle 1.03607 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 747 MET cc_start: 0.8576 (ptm) cc_final: 0.8273 (ptt) REVERT: A 1635 TYR cc_start: 0.8123 (m-80) cc_final: 0.7867 (m-10) REVERT: D 20 GLU cc_start: 0.8679 (pm20) cc_final: 0.8329 (pm20) REVERT: B 208 ASP cc_start: 0.7468 (t0) cc_final: 0.7006 (t0) REVERT: B 364 LYS cc_start: 0.9264 (mmtt) cc_final: 0.8979 (mmmt) REVERT: E 42 LEU cc_start: 0.9223 (tp) cc_final: 0.8602 (mt) REVERT: E 43 SER cc_start: 0.9358 (t) cc_final: 0.9070 (t) REVERT: E 53 ASN cc_start: 0.8842 (m-40) cc_final: 0.8060 (p0) REVERT: E 69 GLU cc_start: 0.8057 (mp0) cc_final: 0.7851 (mp0) outliers start: 28 outliers final: 11 residues processed: 113 average time/residue: 0.1150 time to fit residues: 20.3634 Evaluate side-chains 94 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1247 MET Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 67 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 26 optimal weight: 0.5980 chunk 89 optimal weight: 30.0000 chunk 18 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 828 ASN ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 ASN E 26 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.072905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.051541 restraints weight = 60497.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.053461 restraints weight = 29453.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.054725 restraints weight = 19418.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.055407 restraints weight = 15096.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.055892 restraints weight = 13110.737| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15312 Z= 0.131 Angle : 0.545 6.687 20796 Z= 0.283 Chirality : 0.043 0.238 2367 Planarity : 0.004 0.068 2648 Dihedral : 4.608 27.361 2042 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.79 % Allowed : 14.08 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.18), residues: 1883 helix: 0.44 (0.29), residues: 343 sheet: -1.23 (0.20), residues: 632 loop : -1.61 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 622 TYR 0.015 0.001 TYR B 312 PHE 0.012 0.001 PHE A1019 TRP 0.008 0.001 TRP A1644 HIS 0.004 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (15286) covalent geometry : angle 0.54270 / 0.28 (20742) SS BOND : bond 0.00343 / 0.18 ( 24) SS BOND : angle 1.11213 / 0.63 ( 48) hydrogen bonds : bond 0.03065 / 2.01 ( 565) hydrogen bonds : angle 5.06779 / 3.59 ( 1578) link_BETA1-4 : bond 0.00454 / 0.24 ( 1) link_BETA1-4 : angle 1.04503 / 0.57 ( 3) link_NAG-ASN : bond 0.00196 / 0.10 ( 1) link_NAG-ASN : angle 0.98976 / 0.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 747 MET cc_start: 0.8593 (ptm) cc_final: 0.8277 (ptt) REVERT: A 1507 MET cc_start: 0.8268 (ttp) cc_final: 0.7994 (ttp) REVERT: A 1620 MET cc_start: 0.9026 (mtp) cc_final: 0.8682 (mtm) REVERT: A 1635 TYR cc_start: 0.8147 (m-80) cc_final: 0.7860 (m-10) REVERT: D 20 GLU cc_start: 0.8713 (pm20) cc_final: 0.8305 (pm20) REVERT: B 411 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.9096 (t) REVERT: E 34 LYS cc_start: 0.8755 (ttmt) cc_final: 0.8519 (ttmt) REVERT: E 42 LEU cc_start: 0.9217 (tp) cc_final: 0.8658 (mt) REVERT: E 43 SER cc_start: 0.9409 (t) cc_final: 0.9144 (t) REVERT: E 53 ASN cc_start: 0.8854 (m-40) cc_final: 0.8047 (p0) outliers start: 30 outliers final: 11 residues processed: 113 average time/residue: 0.1121 time to fit residues: 20.2544 Evaluate side-chains 92 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 67 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 90 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 19 optimal weight: 30.0000 chunk 149 optimal weight: 6.9990 chunk 82 optimal weight: 0.2980 chunk 134 optimal weight: 8.9990 chunk 171 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 ASN E 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.071958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.052033 restraints weight = 59742.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.052486 restraints weight = 29440.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.052932 restraints weight = 21766.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.053081 restraints weight = 19288.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.053266 restraints weight = 18269.298| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15312 Z= 0.200 Angle : 0.583 8.932 20796 Z= 0.298 Chirality : 0.043 0.224 2367 Planarity : 0.004 0.067 2648 Dihedral : 4.616 25.764 2042 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.73 % Allowed : 14.92 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.19), residues: 1883 helix: 0.55 (0.29), residues: 343 sheet: -0.92 (0.20), residues: 640 loop : -1.50 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 50 TYR 0.016 0.001 TYR B 312 PHE 0.013 0.001 PHE A1019 TRP 0.008 0.001 TRP A1644 HIS 0.004 0.001 HIS A1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (15286) covalent geometry : angle 0.58127 / 0.30 (20742) SS BOND : bond 0.00358 / 0.20 ( 24) SS BOND : angle 1.14919 / 0.67 ( 48) hydrogen bonds : bond 0.03164 / 2.06 ( 565) hydrogen bonds : angle 5.02038 / 3.52 ( 1578) link_BETA1-4 : bond 0.00421 / 0.22 ( 1) link_BETA1-4 : angle 1.08050 / 0.57 ( 3) link_NAG-ASN : bond 0.00324 / 0.17 ( 1) link_NAG-ASN : angle 1.12283 / 0.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 747 MET cc_start: 0.8622 (ptm) cc_final: 0.8360 (ptp) REVERT: A 1620 MET cc_start: 0.9007 (mtp) cc_final: 0.8624 (mtm) REVERT: A 1635 TYR cc_start: 0.8058 (m-80) cc_final: 0.7798 (m-10) REVERT: C 132 MET cc_start: 0.8054 (ttt) cc_final: 0.7836 (ttt) REVERT: D 20 GLU cc_start: 0.8804 (pm20) cc_final: 0.8370 (pm20) REVERT: B 114 SER cc_start: 0.9231 (OUTLIER) cc_final: 0.9002 (t) REVERT: B 256 TYR cc_start: 0.8230 (p90) cc_final: 0.8006 (p90) REVERT: B 411 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.9057 (t) REVERT: E 53 ASN cc_start: 0.8892 (m-40) cc_final: 0.8081 (p0) outliers start: 29 outliers final: 16 residues processed: 111 average time/residue: 0.1060 time to fit residues: 19.1250 Evaluate side-chains 98 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 67 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 48 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1616 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 = 0.3576 r_free = 0.3576 target = 0.072422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.051099 restraints weight = 60500.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.052984 restraints weight = 29653.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.054191 restraints weight = 19674.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.054989 restraints weight = 15334.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.055504 restraints weight = 13129.471| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15312 Z= 0.151 Angle : 0.565 7.998 20796 Z= 0.289 Chirality : 0.043 0.219 2367 Planarity : 0.004 0.063 2648 Dihedral : 4.519 25.753 2042 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.79 % Allowed : 16.23 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.19), residues: 1883 helix: 0.73 (0.29), residues: 345 sheet: -0.84 (0.20), residues: 625 loop : -1.39 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 50 TYR 0.014 0.001 TYR B 312 PHE 0.012 0.001 PHE A1019 TRP 0.007 0.001 TRP A1644 HIS 0.005 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (15286) covalent geometry : angle 0.56237 / 0.29 (20742) SS BOND : bond 0.00367 / 0.19 ( 24) SS BOND : angle 1.26408 / 0.71 ( 48) hydrogen bonds : bond 0.02996 / 1.96 ( 565) hydrogen bonds : angle 4.82268 / 3.37 ( 1578) link_BETA1-4 : bond 0.00477 / 0.25 ( 1) link_BETA1-4 : angle 1.15268 / 0.61 ( 3) link_NAG-ASN : bond 0.00248 / 0.13 ( 1) link_NAG-ASN : angle 1.07384 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 747 MET cc_start: 0.8648 (ptm) cc_final: 0.8367 (ptp) REVERT: A 1635 TYR cc_start: 0.8174 (m-80) cc_final: 0.7875 (m-10) REVERT: D 20 GLU cc_start: 0.8744 (pm20) cc_final: 0.8297 (pm20) REVERT: B 114 SER cc_start: 0.9254 (OUTLIER) cc_final: 0.9048 (t) REVERT: B 411 THR cc_start: 0.9322 (OUTLIER) cc_final: 0.9089 (t) REVERT: E 50 ARG cc_start: 0.8649 (mtp-110) cc_final: 0.8435 (mtp-110) REVERT: E 53 ASN cc_start: 0.8858 (m-40) cc_final: 0.8067 (p0) outliers start: 30 outliers final: 18 residues processed: 112 average time/residue: 0.1067 time to fit residues: 19.3686 Evaluate side-chains 101 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 884 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 67 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 56 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 129 optimal weight: 0.0970 chunk 51 optimal weight: 0.0270 chunk 166 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 154 optimal weight: 20.0000 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1608 ASN ** A1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.073721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.054496 restraints weight = 60406.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.055086 restraints weight = 30965.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.055409 restraints weight = 22156.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.055843 restraints weight = 19102.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.055893 restraints weight = 17509.054| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15312 Z= 0.113 Angle : 0.556 8.826 20796 Z= 0.284 Chirality : 0.043 0.213 2367 Planarity : 0.004 0.060 2648 Dihedral : 4.357 24.869 2042 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.73 % Allowed : 17.12 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.19), residues: 1883 helix: 0.84 (0.29), residues: 346 sheet: -0.70 (0.20), residues: 637 loop : -1.21 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 50 TYR 0.016 0.001 TYR E 76 PHE 0.012 0.001 PHE A 728 TRP 0.007 0.001 TRP A1031 HIS 0.007 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (15286) covalent geometry : angle 0.55286 / 0.28 (20742) SS BOND : bond 0.00323 / 0.17 ( 24) SS BOND : angle 1.27434 / 0.79 ( 48) hydrogen bonds : bond 0.02838 / 1.85 ( 565) hydrogen bonds : angle 4.64455 / 3.25 ( 1578) link_BETA1-4 : bond 0.00588 / 0.31 ( 1) link_BETA1-4 : angle 1.21712 / 0.64 ( 3) link_NAG-ASN : bond 0.00142 / 0.07 ( 1) link_NAG-ASN : angle 1.00044 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 747 MET cc_start: 0.8633 (ptm) cc_final: 0.8375 (ptp) REVERT: A 1603 LYS cc_start: 0.8781 (mmtm) cc_final: 0.8577 (mmtm) REVERT: A 1635 TYR cc_start: 0.8186 (m-80) cc_final: 0.7884 (m-10) REVERT: D 20 GLU cc_start: 0.8832 (pm20) cc_final: 0.8350 (pm20) REVERT: B 114 SER cc_start: 0.9252 (OUTLIER) cc_final: 0.9037 (t) REVERT: B 411 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.9058 (t) REVERT: B 592 MET cc_start: 0.8516 (mtm) cc_final: 0.7796 (mtm) REVERT: E 53 ASN cc_start: 0.8878 (m-40) cc_final: 0.8110 (p0) REVERT: E 60 ILE cc_start: 0.8932 (mm) cc_final: 0.8619 (mp) outliers start: 29 outliers final: 22 residues processed: 111 average time/residue: 0.1135 time to fit residues: 20.3736 Evaluate side-chains 106 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1247 MET Chi-restraints excluded: chain A residue 1561 TYR Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 67 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 90 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 chunk 113 optimal weight: 0.3980 chunk 172 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 111 optimal weight: 0.2980 chunk 7 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 ASN ** 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 = 0.3604 r_free = 0.3604 target = 0.073996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.052644 restraints weight = 60814.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.054569 restraints weight = 29467.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.055805 restraints weight = 19304.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.056578 restraints weight = 14910.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.057056 restraints weight = 12736.560| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15312 Z= 0.106 Angle : 0.554 9.374 20796 Z= 0.282 Chirality : 0.043 0.210 2367 Planarity : 0.004 0.059 2648 Dihedral : 4.256 25.204 2042 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.67 % Allowed : 17.42 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.19), residues: 1883 helix: 0.98 (0.29), residues: 346 sheet: -0.56 (0.20), residues: 636 loop : -1.11 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 50 TYR 0.012 0.001 TYR B 312 PHE 0.013 0.001 PHE A 728 TRP 0.008 0.001 TRP C 133 HIS 0.005 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (15286) covalent geometry : angle 0.55150 / 0.28 (20742) SS BOND : bond 0.00291 / 0.16 ( 24) SS BOND : angle 1.17623 / 0.72 ( 48) hydrogen bonds : bond 0.02756 / 1.81 ( 565) hydrogen bonds : angle 4.51089 / 3.16 ( 1578) link_BETA1-4 : bond 0.00526 / 0.28 ( 1) link_BETA1-4 : angle 1.20402 / 0.62 ( 3) link_NAG-ASN : bond 0.00108 / 0.06 ( 1) link_NAG-ASN : angle 1.00577 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 747 MET cc_start: 0.8651 (ptm) cc_final: 0.8380 (ptp) REVERT: A 1635 TYR cc_start: 0.8153 (m-80) cc_final: 0.7835 (m-10) REVERT: C 91 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8859 (pt) REVERT: D 20 GLU cc_start: 0.8788 (pm20) cc_final: 0.8307 (pm20) REVERT: B 114 SER cc_start: 0.9252 (OUTLIER) cc_final: 0.9022 (t) REVERT: B 411 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.9082 (t) REVERT: E 50 ARG cc_start: 0.8676 (mtp-110) cc_final: 0.8287 (mtp-110) REVERT: E 53 ASN cc_start: 0.8883 (m-40) cc_final: 0.8097 (p0) REVERT: E 60 ILE cc_start: 0.8965 (mm) cc_final: 0.8653 (mp) outliers start: 28 outliers final: 21 residues processed: 116 average time/residue: 0.1068 time to fit residues: 20.0153 Evaluate side-chains 106 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 884 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 67 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 32 optimal weight: 0.0060 chunk 35 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 62 optimal weight: 0.0870 chunk 59 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.074656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.055184 restraints weight = 60944.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.055400 restraints weight = 29865.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.055687 restraints weight = 25523.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.056046 restraints weight = 20838.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.056326 restraints weight = 18915.419| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15312 Z= 0.095 Angle : 0.564 15.646 20796 Z= 0.284 Chirality : 0.043 0.205 2367 Planarity : 0.004 0.059 2648 Dihedral : 4.185 24.888 2042 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.91 % Allowed : 17.06 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.19), residues: 1883 helix: 1.05 (0.30), residues: 347 sheet: -0.43 (0.20), residues: 638 loop : -1.01 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 50 TYR 0.019 0.001 TYR E 76 PHE 0.013 0.001 PHE A 728 TRP 0.014 0.001 TRP A 917 HIS 0.004 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (15286) covalent geometry : angle 0.56180 / 0.28 (20742) SS BOND : bond 0.00249 / 0.14 ( 24) SS BOND : angle 1.10420 / 0.68 ( 48) hydrogen bonds : bond 0.02726 / 1.79 ( 565) hydrogen bonds : angle 4.39012 / 3.08 ( 1578) link_BETA1-4 : bond 0.00535 / 0.28 ( 1) link_BETA1-4 : angle 1.19961 / 0.62 ( 3) link_NAG-ASN : bond 0.00047 / 0.02 ( 1) link_NAG-ASN : angle 1.00136 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 747 MET cc_start: 0.8663 (ptm) cc_final: 0.8370 (ptt) REVERT: A 1635 TYR cc_start: 0.8223 (m-80) cc_final: 0.7892 (m-10) REVERT: C 91 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8854 (pt) REVERT: D 20 GLU cc_start: 0.8851 (pm20) cc_final: 0.8355 (pm20) REVERT: B 114 SER cc_start: 0.9252 (OUTLIER) cc_final: 0.9038 (t) REVERT: B 411 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9082 (t) REVERT: B 469 TRP cc_start: 0.8878 (p90) cc_final: 0.8636 (p90) REVERT: B 592 MET cc_start: 0.8532 (mtm) cc_final: 0.7784 (mtm) REVERT: E 53 ASN cc_start: 0.8834 (m-40) cc_final: 0.8085 (p0) REVERT: E 60 ILE cc_start: 0.8916 (mm) cc_final: 0.8614 (mp) REVERT: E 78 ASN cc_start: 0.8935 (m110) cc_final: 0.8561 (m-40) outliers start: 32 outliers final: 24 residues processed: 114 average time/residue: 0.1052 time to fit residues: 19.6040 Evaluate side-chains 109 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 884 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1475 VAL Chi-restraints excluded: chain A residue 1568 ILE Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 67 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 79 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 95 optimal weight: 0.0030 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 ASN E 67 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.074502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.052439 restraints weight = 60668.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.054419 restraints weight = 29877.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.055692 restraints weight = 19741.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.056414 restraints weight = 15350.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.056961 restraints weight = 13303.046| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 15312 Z= 0.137 Angle : 0.778 59.193 20796 Z= 0.439 Chirality : 0.043 0.286 2367 Planarity : 0.004 0.058 2648 Dihedral : 4.235 34.172 2042 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.49 % Allowed : 17.66 % Favored : 80.85 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 10.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 1883 helix: 1.05 (0.30), residues: 347 sheet: -0.42 (0.20), residues: 638 loop : -1.00 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 50 TYR 0.025 0.001 TYR E 23 PHE 0.017 0.001 PHE B 227 TRP 0.016 0.001 TRP A 917 HIS 0.004 0.000 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (15286) covalent geometry : angle 0.77757 / 0.44 (20742) SS BOND : bond 0.00258 / 0.14 ( 24) SS BOND : angle 1.04167 / 0.63 ( 48) hydrogen bonds : bond 0.02802 / 1.86 ( 565) hydrogen bonds : angle 4.39444 / 3.08 ( 1578) link_BETA1-4 : bond 0.00024 / 0.01 ( 1) link_BETA1-4 : angle 1.27569 / 0.66 ( 3) link_NAG-ASN : bond 0.00039 / 0.02 ( 1) link_NAG-ASN : angle 0.98199 / 0.56 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 747 MET cc_start: 0.8680 (ptm) cc_final: 0.8370 (ptt) REVERT: A 1635 TYR cc_start: 0.8103 (m-80) cc_final: 0.7784 (m-10) REVERT: C 91 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8843 (pt) REVERT: D 20 GLU cc_start: 0.8807 (pm20) cc_final: 0.8330 (pm20) REVERT: B 114 SER cc_start: 0.9247 (OUTLIER) cc_final: 0.9021 (t) REVERT: B 411 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9094 (t) REVERT: B 469 TRP cc_start: 0.8821 (p90) cc_final: 0.8529 (p90) REVERT: B 592 MET cc_start: 0.8433 (mtm) cc_final: 0.7716 (mtm) REVERT: E 53 ASN cc_start: 0.8883 (m-40) cc_final: 0.8122 (p0) REVERT: E 60 ILE cc_start: 0.8924 (mm) cc_final: 0.8617 (mp) REVERT: E 78 ASN cc_start: 0.8920 (m110) cc_final: 0.8533 (m-40) outliers start: 25 outliers final: 21 residues processed: 105 average time/residue: 0.1071 time to fit residues: 18.4217 Evaluate side-chains 106 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 884 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1475 VAL Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain E residue 66 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 66 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 96 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 187 optimal weight: 0.0470 chunk 161 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.074504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.053565 restraints weight = 60812.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.055731 restraints weight = 29923.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.056030 restraints weight = 18691.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.056227 restraints weight = 15874.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.056361 restraints weight = 15148.540| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 15312 Z= 0.137 Angle : 0.778 59.193 20796 Z= 0.439 Chirality : 0.043 0.286 2367 Planarity : 0.004 0.058 2648 Dihedral : 4.235 34.172 2042 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.43 % Allowed : 17.66 % Favored : 80.91 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 10.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 1883 helix: 1.05 (0.30), residues: 347 sheet: -0.42 (0.20), residues: 638 loop : -1.00 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 50 TYR 0.025 0.001 TYR E 23 PHE 0.017 0.001 PHE B 227 TRP 0.016 0.001 TRP A 917 HIS 0.004 0.000 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (15286) covalent geometry : angle 0.77757 / 0.44 (20742) SS BOND : bond 0.00258 / 0.14 ( 24) SS BOND : angle 1.04167 / 0.63 ( 48) hydrogen bonds : bond 0.02802 / 1.86 ( 565) hydrogen bonds : angle 4.39444 / 3.08 ( 1578) link_BETA1-4 : bond 0.00024 / 0.01 ( 1) link_BETA1-4 : angle 1.27569 / 0.66 ( 3) link_NAG-ASN : bond 0.00039 / 0.02 ( 1) link_NAG-ASN : angle 0.98199 / 0.56 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2535.78 seconds wall clock time: 44 minutes 53.36 seconds (2693.36 seconds total)