Starting phenix.real_space_refine on Sat Aug 23 17:41:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cml_16730/08_2025/8cml_16730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cml_16730/08_2025/8cml_16730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cml_16730/08_2025/8cml_16730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cml_16730/08_2025/8cml_16730.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cml_16730/08_2025/8cml_16730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cml_16730/08_2025/8cml_16730.map" } resolution = 3.6 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= 0.032 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 53 5.16 5 C 8662 2.51 5 N 2258 2.21 5 O 2621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13594 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 909 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "E" Number of atoms: 5141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5141 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 34, 'TRANS': 616} Chain: "B" Number of atoms: 6560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 829, 6560 Classifications: {'peptide': 829} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 796} Chain breaks: 3 Chain: "C" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 956 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "D" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.59, per 1000 atoms: 0.19 Number of scatterers: 13594 At special positions: 0 Unit cell: (100.88, 154.96, 140.4, 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 53 16.00 O 2621 8.00 N 2258 7.00 C 8662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 567 " - pdb=" SG CYS B 810 " distance=2.03 Simple disulfide: pdb=" SG CYS E 634 " - pdb=" SG CYS E 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 698 " - pdb=" SG CYS B 724 " distance=2.04 Simple disulfide: pdb=" SG CYS B 699 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 711 " - pdb=" SG CYS B 732 " distance=2.03 Simple disulfide: pdb=" SG CYS B 856 " - pdb=" SG CYS B 883 " distance=2.03 Simple disulfide: pdb=" SG CYS B 866 " - pdb=" SG CYS B1527 " distance=2.03 Simple disulfide: pdb=" SG CYS B1101 " - pdb=" SG CYS B1159 " distance=2.03 Simple disulfide: pdb=" SG CYS B1375 " - pdb=" SG CYS B1505 " distance=2.03 Simple disulfide: pdb=" SG CYS B1405 " - pdb=" SG CYS B1474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " 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 D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN B 911 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 500.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 32 sheets defined 19.8% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.804A pdb=" N LEU E 92 " --> pdb=" O PRO E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 309 removed outlier: 4.049A pdb=" N GLU E 309 " --> pdb=" O THR E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 447 Processing helix chain 'E' and resid 531 through 535 removed outlier: 3.907A pdb=" N VAL E 535 " --> pdb=" O GLN E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 611 Processing helix chain 'E' and resid 618 through 628 removed outlier: 5.030A pdb=" N PHE E 624 " --> pdb=" O LEU E 620 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLN E 625 " --> pdb=" O GLU E 621 " (cutoff:3.500A) Processing helix chain 'E' and resid 629 through 631 No H-bonds generated for 'chain 'E' and resid 629 through 631' Processing helix chain 'E' and resid 641 through 649 Processing helix chain 'B' and resid 680 through 691 removed outlier: 3.789A pdb=" N ILE B 686 " --> pdb=" O LYS B 682 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS B 691 " --> pdb=" O ALA B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 703 removed outlier: 3.855A pdb=" N LYS B 697 " --> pdb=" O SER B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 717 removed outlier: 4.035A pdb=" N ARG B 717 " --> pdb=" O GLN B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 739 removed outlier: 3.553A pdb=" N ILE B 725 " --> pdb=" O GLY B 721 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA B 727 " --> pdb=" O ARG B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 755 removed outlier: 3.542A pdb=" N LEU B 749 " --> pdb=" O LYS B 745 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG B 751 " --> pdb=" O MET B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 992 Processing helix chain 'B' and resid 1007 through 1014 removed outlier: 3.668A pdb=" N SER B1014 " --> pdb=" O ALA B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1029 Processing helix chain 'B' and resid 1030 through 1034 removed outlier: 3.768A pdb=" N PHE B1034 " --> pdb=" O TRP B1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 1037 through 1056 removed outlier: 3.675A pdb=" N GLU B1041 " --> pdb=" O ASP B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1060 Processing helix chain 'B' and resid 1075 through 1090 Processing helix chain 'B' and resid 1096 through 1110 Processing helix chain 'B' and resid 1132 through 1155 Processing helix chain 'B' and resid 1161 through 1180 removed outlier: 3.567A pdb=" N ASP B1165 " --> pdb=" O LEU B1161 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU B1180 " --> pdb=" O LEU B1176 " (cutoff:3.500A) Processing helix chain 'B' and resid 1184 through 1197 Processing helix chain 'B' and resid 1202 through 1215 removed outlier: 3.634A pdb=" N GLU B1215 " --> pdb=" O ALA B1211 " (cutoff:3.500A) Processing helix chain 'B' and resid 1244 through 1261 Processing helix chain 'B' and resid 1267 through 1278 Processing helix chain 'B' and resid 1286 through 1304 removed outlier: 3.631A pdb=" N ASN B1292 " --> pdb=" O GLN B1288 " (cutoff:3.500A) Processing helix chain 'B' and resid 1435 through 1444 removed outlier: 3.981A pdb=" N LEU B1439 " --> pdb=" O ASN B1435 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 31 Processing helix chain 'C' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.555A pdb=" N THR A 113 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A 115 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 92 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE A 95 " --> pdb=" O PHE A 37 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ARG A 38 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N PHE A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 23 Processing sheet with id=AA3, first strand: chain 'E' and resid 80 through 85 removed outlier: 8.322A pdb=" N ASN E 38 " --> pdb=" O PRO E 28 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 31 through 32 removed outlier: 6.286A pdb=" N PHE E 31 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER E 67 " --> pdb=" O ILE E 56 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 125 through 130 Processing sheet with id=AA6, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.232A pdb=" N ASP E 172 " --> pdb=" O PHE E 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AA8, first strand: chain 'E' and resid 221 through 222 removed outlier: 5.773A pdb=" N GLU E 221 " --> pdb=" O ILE B 765 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 228 through 233 Processing sheet with id=AB1, first strand: chain 'E' and resid 237 through 238 Processing sheet with id=AB2, first strand: chain 'E' and resid 281 through 282 Processing sheet with id=AB3, first strand: chain 'E' and resid 281 through 282 Processing sheet with id=AB4, first strand: chain 'E' and resid 353 through 356 removed outlier: 3.912A pdb=" N VAL E 373 " --> pdb=" O ALA E 418 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 401 through 403 Processing sheet with id=AB6, first strand: chain 'E' and resid 401 through 403 Processing sheet with id=AB7, first strand: chain 'E' and resid 466 through 469 Processing sheet with id=AB8, first strand: chain 'E' and resid 508 through 516 removed outlier: 5.508A pdb=" N ILE E 509 " --> pdb=" O SER E 505 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER E 505 " --> pdb=" O ILE E 509 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS E 498 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ILE E 545 " --> pdb=" O HIS E 498 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 572 through 575 Processing sheet with id=AC1, first strand: chain 'E' and resid 581 through 582 Processing sheet with id=AC2, first strand: chain 'E' and resid 581 through 582 Processing sheet with id=AC3, first strand: chain 'B' and resid 823 through 827 removed outlier: 3.652A pdb=" N LEU B 901 " --> pdb=" O CYS B 866 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 823 through 827 Processing sheet with id=AC5, first strand: chain 'B' and resid 832 through 834 removed outlier: 6.045A pdb=" N VAL B 833 " --> pdb=" O VAL B 930 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 886 through 888 Processing sheet with id=AC7, first strand: chain 'B' and resid 934 through 944 removed outlier: 4.509A pdb=" N ARG B 975 " --> pdb=" O VAL B1340 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B1338 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 956 through 959 removed outlier: 3.994A pdb=" N VAL B1315 " --> pdb=" O HIS B1324 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N HIS B1324 " --> pdb=" O VAL B1315 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N TYR B1317 " --> pdb=" O ALA B1322 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ALA B1322 " --> pdb=" O TYR B1317 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1217 through 1219 Processing sheet with id=AD1, first strand: chain 'B' and resid 1377 through 1385 removed outlier: 4.106A pdb=" N LYS B1400 " --> pdb=" O ILE B1479 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1452 through 1456 removed outlier: 4.482A pdb=" N THR B1492 " --> pdb=" O SER B1427 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.915A pdb=" N GLY C 16 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU C 18 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN C 84 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU C 20 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLN C 82 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N CYS C 22 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TYR C 80 " --> pdb=" O CYS C 22 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA C 24 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N THR C 78 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 10 through 13 removed outlier: 5.920A pdb=" N GLY C 10 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER C 126 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C 12 " --> pdb=" O SER C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.613A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N CYS C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE C 34 " --> pdb=" O CYS C 50 " (cutoff:3.500A) 562 hydrogen bonds defined for protein. 1512 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: 3.10 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4356 1.34 - 1.46: 3094 1.46 - 1.58: 6354 1.58 - 1.70: 0 1.70 - 1.83: 79 Bond restraints: 13883 Sorted by residual: bond pdb=" N ASP E 61 " pdb=" CA ASP E 61 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 7.78e+00 bond pdb=" N ILE B1127 " pdb=" CA ILE B1127 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.35e+00 bond pdb=" N ASP E 187 " pdb=" CA ASP E 187 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.27e-02 6.20e+03 7.15e+00 bond pdb=" N PHE E 185 " pdb=" CA PHE E 185 " ideal model delta sigma weight residual 1.453 1.486 -0.034 1.51e-02 4.39e+03 4.97e+00 bond pdb=" N TYR E 59 " pdb=" CA TYR E 59 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.41e-02 5.03e+03 4.94e+00 ... (remaining 13878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 18506 2.15 - 4.30: 280 4.30 - 6.46: 31 6.46 - 8.61: 6 8.61 - 10.76: 4 Bond angle restraints: 18827 Sorted by residual: angle pdb=" CB MET C 83 " pdb=" CG MET C 83 " pdb=" SD MET C 83 " ideal model delta sigma weight residual 112.70 122.68 -9.98 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CA ASP E 187 " pdb=" C ASP E 187 " pdb=" O ASP E 187 " ideal model delta sigma weight residual 121.88 118.37 3.51 1.13e+00 7.83e-01 9.66e+00 angle pdb=" C VAL B1015 " pdb=" N VAL B1016 " pdb=" CA VAL B1016 " ideal model delta sigma weight residual 120.33 122.69 -2.36 8.00e-01 1.56e+00 8.70e+00 angle pdb=" C THR B 756 " pdb=" N LEU B 757 " pdb=" CA LEU B 757 " ideal model delta sigma weight residual 121.54 126.86 -5.32 1.91e+00 2.74e-01 7.76e+00 angle pdb=" CA GLU A 44 " pdb=" CB GLU A 44 " pdb=" CG GLU A 44 " ideal model delta sigma weight residual 114.10 119.62 -5.52 2.00e+00 2.50e-01 7.61e+00 ... (remaining 18822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.34: 7527 21.34 - 42.68: 724 42.68 - 64.02: 104 64.02 - 85.36: 16 85.36 - 106.70: 13 Dihedral angle restraints: 8384 sinusoidal: 3352 harmonic: 5032 Sorted by residual: dihedral pdb=" CB CYS E 634 " pdb=" SG CYS E 634 " pdb=" SG CYS E 669 " pdb=" CB CYS E 669 " ideal model delta sinusoidal sigma weight residual -86.00 -3.53 -82.47 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS B 698 " pdb=" SG CYS B 698 " pdb=" SG CYS B 724 " pdb=" CB CYS B 724 " ideal model delta sinusoidal sigma weight residual -86.00 -15.91 -70.09 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CA GLU A 99 " pdb=" C GLU A 99 " pdb=" N PHE A 100 " pdb=" CA PHE A 100 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 8381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1606 0.045 - 0.090: 353 0.090 - 0.135: 167 0.135 - 0.180: 6 0.180 - 0.225: 1 Chirality restraints: 2133 Sorted by residual: chirality pdb=" CB ILE B 725 " pdb=" CA ILE B 725 " pdb=" CG1 ILE B 725 " pdb=" CG2 ILE B 725 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" N2 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CB VAL C 93 " pdb=" CA VAL C 93 " pdb=" CG1 VAL C 93 " pdb=" CG2 VAL C 93 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.25e-01 ... (remaining 2130 not shown) Planarity restraints: 2406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 237 " 0.013 2.00e-02 2.50e+03 1.58e-02 4.38e+00 pdb=" CG PHE E 237 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE E 237 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE E 237 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE E 237 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 237 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE E 237 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 490 " -0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO E 491 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO E 491 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 491 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 930 " 0.031 5.00e-02 4.00e+02 4.61e-02 3.41e+00 pdb=" N PRO B 931 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 931 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 931 " 0.025 5.00e-02 4.00e+02 ... (remaining 2403 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 207 2.67 - 3.23: 12314 3.23 - 3.79: 19669 3.79 - 4.34: 26256 4.34 - 4.90: 44764 Nonbonded interactions: 103210 Sorted by model distance: nonbonded pdb=" OE2 GLU B1009 " pdb=" OG1 THR B1287 " model vdw 2.115 3.040 nonbonded pdb=" OG SER C 7 " pdb=" OG SER C 21 " model vdw 2.159 3.040 nonbonded pdb=" NH1 ARG A 101 " pdb=" O LEU B1197 " model vdw 2.190 3.120 nonbonded pdb=" OE1 GLU B 937 " pdb=" OH TYR B 939 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR E 196 " pdb=" OE2 GLU E 221 " model vdw 2.222 3.040 ... (remaining 103205 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.920 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 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 : 0.003 0.057 13897 Z= 0.148 Angle : 0.659 10.760 18857 Z= 0.349 Chirality : 0.045 0.225 2133 Planarity : 0.004 0.052 2405 Dihedral : 16.467 106.701 5120 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.25 % Favored : 94.52 % Rotamer: Outliers : 0.60 % Allowed : 23.61 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.48 (0.20), residues: 1714 helix: 0.92 (0.32), residues: 287 sheet: 0.53 (0.22), residues: 586 loop : -1.41 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 928 TYR 0.015 0.001 TYR B1326 PHE 0.037 0.002 PHE E 237 TRP 0.019 0.001 TRP C 36 HIS 0.005 0.001 HIS E 498 Details of bonding type rmsd covalent geometry : bond 0.00299 (13883) covalent geometry : angle 0.65853 (18827) SS BOND : bond 0.00328 ( 12) SS BOND : angle 0.84020 ( 24) hydrogen bonds : bond 0.12491 ( 549) hydrogen bonds : angle 5.93841 ( 1512) link_BETA1-4 : bond 0.00161 ( 1) link_BETA1-4 : angle 0.79484 ( 3) link_NAG-ASN : bond 0.00103 ( 1) link_NAG-ASN : angle 1.58778 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 171 time to evaluate : 0.482 Fit side-chains REVERT: B 1326 TYR cc_start: 0.6372 (m-80) cc_final: 0.6143 (m-80) outliers start: 9 outliers final: 5 residues processed: 173 average time/residue: 0.0899 time to fit residues: 23.4444 Evaluate side-chains 162 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 157 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain B residue 1311 MET Chi-restraints excluded: chain C residue 20 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN E 42 GLN E 242 ASN E 656 ASN B 706 ASN B 753 HIS B1360 HIS ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.202638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.174364 restraints weight = 16826.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.172036 restraints weight = 25083.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.172964 restraints weight = 24089.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.173932 restraints weight = 17719.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.174145 restraints weight = 15833.021| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13897 Z= 0.181 Angle : 0.640 10.364 18857 Z= 0.325 Chirality : 0.047 0.218 2133 Planarity : 0.004 0.050 2405 Dihedral : 7.560 85.698 1919 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.83 % Favored : 93.99 % Rotamer: Outliers : 3.90 % Allowed : 23.48 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.54 (0.20), residues: 1714 helix: 0.79 (0.31), residues: 290 sheet: 0.46 (0.22), residues: 584 loop : -1.40 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1153 TYR 0.016 0.002 TYR E 543 PHE 0.017 0.002 PHE B1483 TRP 0.012 0.001 TRP E 469 HIS 0.004 0.001 HIS E 498 Details of bonding type rmsd covalent geometry : bond 0.00440 (13883) covalent geometry : angle 0.63733 (18827) SS BOND : bond 0.00317 ( 12) SS BOND : angle 1.22546 ( 24) hydrogen bonds : bond 0.04050 ( 549) hydrogen bonds : angle 5.26451 ( 1512) link_BETA1-4 : bond 0.00437 ( 1) link_BETA1-4 : angle 2.57038 ( 3) link_NAG-ASN : bond 0.00381 ( 1) link_NAG-ASN : angle 2.38854 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 165 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6616 (m-10) REVERT: E 282 MET cc_start: 0.6319 (mmt) cc_final: 0.6113 (mmm) REVERT: B 955 ARG cc_start: 0.4002 (ptm160) cc_final: 0.3418 (mtp85) REVERT: B 1104 LEU cc_start: 0.7367 (tt) cc_final: 0.7128 (tt) outliers start: 59 outliers final: 36 residues processed: 207 average time/residue: 0.0881 time to fit residues: 27.9596 Evaluate side-chains 191 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 747 MET Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 987 ILE Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain B residue 1212 LEU Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1267 VAL Chi-restraints excluded: chain B residue 1298 THR Chi-restraints excluded: chain B residue 1328 MET Chi-restraints excluded: chain B residue 1457 ASP Chi-restraints excluded: chain B residue 1492 THR Chi-restraints excluded: chain B residue 1506 THR Chi-restraints excluded: chain B residue 1507 MET Chi-restraints excluded: chain C residue 20 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 72 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 19 optimal weight: 0.0570 chunk 37 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 0.0030 chunk 136 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 124 optimal weight: 0.4980 overall best weight: 0.3108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 706 ASN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.208224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.180582 restraints weight = 17012.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.178175 restraints weight = 24179.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.179113 restraints weight = 22827.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.179809 restraints weight = 17561.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.179874 restraints weight = 17085.103| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13897 Z= 0.104 Angle : 0.568 9.771 18857 Z= 0.285 Chirality : 0.044 0.249 2133 Planarity : 0.004 0.044 2405 Dihedral : 6.905 77.671 1913 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.73 % Favored : 95.10 % Rotamer: Outliers : 3.64 % Allowed : 24.47 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.29 (0.21), residues: 1714 helix: 1.13 (0.31), residues: 290 sheet: 0.61 (0.22), residues: 588 loop : -1.29 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1153 TYR 0.020 0.001 TYR E 196 PHE 0.019 0.001 PHE B1019 TRP 0.015 0.001 TRP C 36 HIS 0.003 0.000 HIS E 498 Details of bonding type rmsd covalent geometry : bond 0.00238 (13883) covalent geometry : angle 0.56640 (18827) SS BOND : bond 0.00213 ( 12) SS BOND : angle 0.81716 ( 24) hydrogen bonds : bond 0.03367 ( 549) hydrogen bonds : angle 4.91211 ( 1512) link_BETA1-4 : bond 0.00080 ( 1) link_BETA1-4 : angle 2.04924 ( 3) link_NAG-ASN : bond 0.00052 ( 1) link_NAG-ASN : angle 1.85304 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 171 time to evaluate : 0.546 Fit side-chains REVERT: B 923 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.7032 (tm) REVERT: B 955 ARG cc_start: 0.4012 (ptm160) cc_final: 0.3474 (mtp85) REVERT: B 1259 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8383 (mt) REVERT: C 68 PHE cc_start: 0.7651 (m-80) cc_final: 0.7340 (m-10) REVERT: C 104 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.7046 (mm) outliers start: 55 outliers final: 28 residues processed: 210 average time/residue: 0.0948 time to fit residues: 30.3726 Evaluate side-chains 186 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain B residue 1271 ILE Chi-restraints excluded: chain B residue 1328 MET Chi-restraints excluded: chain B residue 1506 THR Chi-restraints excluded: chain B residue 1507 MET Chi-restraints excluded: chain B residue 1527 CYS Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 125 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 112 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 57 optimal weight: 0.0070 chunk 156 optimal weight: 0.0770 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 119 optimal weight: 0.3980 chunk 145 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN E 80 GLN E 446 ASN ** E 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.208087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.177785 restraints weight = 16775.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.175466 restraints weight = 22925.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.177258 restraints weight = 21943.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.177824 restraints weight = 15599.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.177989 restraints weight = 16355.418| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13897 Z= 0.105 Angle : 0.563 9.462 18857 Z= 0.281 Chirality : 0.044 0.259 2133 Planarity : 0.004 0.042 2405 Dihedral : 6.162 65.994 1909 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.25 % Favored : 94.57 % Rotamer: Outliers : 3.84 % Allowed : 24.87 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.17 (0.21), residues: 1714 helix: 1.22 (0.31), residues: 291 sheet: 0.72 (0.22), residues: 577 loop : -1.23 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 19 TYR 0.022 0.001 TYR B1300 PHE 0.018 0.001 PHE B1019 TRP 0.016 0.001 TRP C 36 HIS 0.006 0.001 HIS B 753 Details of bonding type rmsd covalent geometry : bond 0.00245 (13883) covalent geometry : angle 0.56146 (18827) SS BOND : bond 0.00213 ( 12) SS BOND : angle 0.81515 ( 24) hydrogen bonds : bond 0.03168 ( 549) hydrogen bonds : angle 4.72043 ( 1512) link_BETA1-4 : bond 0.00060 ( 1) link_BETA1-4 : angle 2.06700 ( 3) link_NAG-ASN : bond 0.00067 ( 1) link_NAG-ASN : angle 1.96615 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 169 time to evaluate : 0.316 Fit side-chains REVERT: A 76 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7076 (tttt) REVERT: B 923 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6899 (tm) REVERT: B 955 ARG cc_start: 0.4233 (ptm160) cc_final: 0.3796 (mtp-110) REVERT: C 19 ARG cc_start: 0.7277 (tpp80) cc_final: 0.6999 (tpp80) REVERT: C 82 GLN cc_start: 0.5713 (tp40) cc_final: 0.5375 (tm-30) REVERT: C 104 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.7092 (mm) outliers start: 58 outliers final: 37 residues processed: 213 average time/residue: 0.0930 time to fit residues: 30.3098 Evaluate side-chains 198 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1184 SER Chi-restraints excluded: chain B residue 1212 LEU Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1267 VAL Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1506 THR Chi-restraints excluded: chain B residue 1507 MET Chi-restraints excluded: chain B residue 1527 CYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 125 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 102 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 165 optimal weight: 0.0870 chunk 80 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 34 optimal weight: 0.0570 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1465 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.207400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.180024 restraints weight = 17063.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.177874 restraints weight = 25155.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.179869 restraints weight = 24319.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.180111 restraints weight = 16177.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.180228 restraints weight = 16634.195| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13897 Z= 0.121 Angle : 0.580 10.572 18857 Z= 0.290 Chirality : 0.045 0.256 2133 Planarity : 0.004 0.042 2405 Dihedral : 5.735 55.760 1909 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.31 % Favored : 94.52 % Rotamer: Outliers : 4.23 % Allowed : 24.60 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.15 (0.21), residues: 1714 helix: 1.29 (0.31), residues: 291 sheet: 0.67 (0.22), residues: 585 loop : -1.20 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 19 TYR 0.028 0.001 TYR E 196 PHE 0.019 0.001 PHE B1019 TRP 0.018 0.001 TRP C 36 HIS 0.005 0.001 HIS B 908 Details of bonding type rmsd covalent geometry : bond 0.00289 (13883) covalent geometry : angle 0.57823 (18827) SS BOND : bond 0.00238 ( 12) SS BOND : angle 0.81968 ( 24) hydrogen bonds : bond 0.03229 ( 549) hydrogen bonds : angle 4.66366 ( 1512) link_BETA1-4 : bond 0.00280 ( 1) link_BETA1-4 : angle 2.07332 ( 3) link_NAG-ASN : bond 0.00160 ( 1) link_NAG-ASN : angle 2.05823 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 172 time to evaluate : 0.354 Fit side-chains REVERT: A 103 ARG cc_start: 0.6356 (OUTLIER) cc_final: 0.5948 (ttm110) REVERT: E 282 MET cc_start: 0.6341 (mmt) cc_final: 0.6131 (mmm) REVERT: B 820 PHE cc_start: 0.6784 (OUTLIER) cc_final: 0.6074 (t80) REVERT: B 923 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6902 (tm) REVERT: B 955 ARG cc_start: 0.4255 (ptm160) cc_final: 0.3888 (mtp-110) REVERT: B 1259 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8440 (mt) REVERT: C 104 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7047 (mm) outliers start: 64 outliers final: 43 residues processed: 221 average time/residue: 0.0836 time to fit residues: 28.7002 Evaluate side-chains 201 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 809 ILE Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1184 SER Chi-restraints excluded: chain B residue 1212 LEU Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1267 VAL Chi-restraints excluded: chain B residue 1328 MET Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1506 THR Chi-restraints excluded: chain B residue 1507 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 125 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 84 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 76 optimal weight: 0.0870 chunk 117 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 85 optimal weight: 0.0060 chunk 90 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 overall best weight: 0.4574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.207918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.178590 restraints weight = 17014.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.175130 restraints weight = 23744.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.177462 restraints weight = 23076.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.177529 restraints weight = 17277.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.178256 restraints weight = 14796.750| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13897 Z= 0.110 Angle : 0.568 9.453 18857 Z= 0.283 Chirality : 0.044 0.272 2133 Planarity : 0.004 0.041 2405 Dihedral : 5.324 55.879 1909 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.25 % Favored : 94.57 % Rotamer: Outliers : 3.90 % Allowed : 25.07 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.10 (0.20), residues: 1714 helix: 1.43 (0.31), residues: 290 sheet: 0.71 (0.22), residues: 585 loop : -1.21 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1153 TYR 0.024 0.001 TYR C 32 PHE 0.026 0.001 PHE E 237 TRP 0.010 0.001 TRP C 36 HIS 0.002 0.000 HIS E 498 Details of bonding type rmsd covalent geometry : bond 0.00256 (13883) covalent geometry : angle 0.56607 (18827) SS BOND : bond 0.00224 ( 12) SS BOND : angle 0.74824 ( 24) hydrogen bonds : bond 0.03073 ( 549) hydrogen bonds : angle 4.59367 ( 1512) link_BETA1-4 : bond 0.00085 ( 1) link_BETA1-4 : angle 2.11966 ( 3) link_NAG-ASN : bond 0.00119 ( 1) link_NAG-ASN : angle 2.18643 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 162 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 282 MET cc_start: 0.6471 (mmt) cc_final: 0.6221 (mmm) REVERT: E 618 LYS cc_start: 0.5469 (mptt) cc_final: 0.5204 (mttt) REVERT: B 820 PHE cc_start: 0.6858 (OUTLIER) cc_final: 0.6147 (t80) REVERT: B 923 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6847 (tm) REVERT: B 955 ARG cc_start: 0.4345 (ptm160) cc_final: 0.4009 (ttm-80) REVERT: B 1212 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7829 (tp) REVERT: B 1259 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8408 (mt) REVERT: B 1311 MET cc_start: 0.6156 (ttt) cc_final: 0.5939 (ttt) REVERT: C 19 ARG cc_start: 0.7261 (tpp80) cc_final: 0.7044 (tpp80) REVERT: C 104 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.7032 (mm) outliers start: 59 outliers final: 44 residues processed: 204 average time/residue: 0.0807 time to fit residues: 25.4368 Evaluate side-chains 204 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 571 LEU Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1161 LEU Chi-restraints excluded: chain B residue 1184 SER Chi-restraints excluded: chain B residue 1212 LEU Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain B residue 1328 MET Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1506 THR Chi-restraints excluded: chain B residue 1507 MET Chi-restraints excluded: chain B residue 1527 CYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 125 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 17 optimal weight: 4.9990 chunk 76 optimal weight: 0.0060 chunk 156 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN E 446 ASN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.202154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175109 restraints weight = 16952.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.172508 restraints weight = 26456.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.174242 restraints weight = 25021.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.174409 restraints weight = 17697.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.174695 restraints weight = 15949.047| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13897 Z= 0.187 Angle : 0.635 9.507 18857 Z= 0.320 Chirality : 0.046 0.277 2133 Planarity : 0.004 0.044 2405 Dihedral : 5.263 56.235 1909 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.72 % Favored : 94.11 % Rotamer: Outliers : 4.56 % Allowed : 24.74 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.34 (0.20), residues: 1714 helix: 1.20 (0.31), residues: 290 sheet: 0.51 (0.22), residues: 583 loop : -1.30 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 885 TYR 0.031 0.002 TYR C 32 PHE 0.017 0.002 PHE B1019 TRP 0.010 0.001 TRP E 469 HIS 0.003 0.001 HIS E 498 Details of bonding type rmsd covalent geometry : bond 0.00452 (13883) covalent geometry : angle 0.63338 (18827) SS BOND : bond 0.00281 ( 12) SS BOND : angle 0.80470 ( 24) hydrogen bonds : bond 0.03753 ( 549) hydrogen bonds : angle 4.81249 ( 1512) link_BETA1-4 : bond 0.00053 ( 1) link_BETA1-4 : angle 2.19314 ( 3) link_NAG-ASN : bond 0.00414 ( 1) link_NAG-ASN : angle 2.44713 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 165 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.6965 (m-10) REVERT: E 282 MET cc_start: 0.6317 (mmt) cc_final: 0.6116 (mmm) REVERT: E 592 MET cc_start: 0.7370 (mtt) cc_final: 0.7159 (mtt) REVERT: E 618 LYS cc_start: 0.5612 (mptt) cc_final: 0.5381 (mttt) REVERT: B 820 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.6231 (t80) REVERT: B 923 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6989 (tm) REVERT: B 955 ARG cc_start: 0.4509 (ptm160) cc_final: 0.4210 (mtp-110) REVERT: B 986 GLU cc_start: 0.5796 (OUTLIER) cc_final: 0.5042 (mp0) REVERT: C 32 TYR cc_start: 0.6872 (t80) cc_final: 0.6411 (t80) REVERT: C 104 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7087 (mm) outliers start: 69 outliers final: 51 residues processed: 218 average time/residue: 0.1034 time to fit residues: 33.2169 Evaluate side-chains 216 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 160 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 571 LEU Chi-restraints excluded: chain B residue 747 MET Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 809 ILE Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 986 GLU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1056 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1161 LEU Chi-restraints excluded: chain B residue 1184 SER Chi-restraints excluded: chain B residue 1212 LEU Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1267 VAL Chi-restraints excluded: chain B residue 1446 VAL Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1457 ASP Chi-restraints excluded: chain B residue 1506 THR Chi-restraints excluded: chain B residue 1527 CYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 125 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 104 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 159 optimal weight: 20.0000 chunk 123 optimal weight: 0.8980 chunk 46 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 706 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 = 0.4547 r_free = 0.4547 target = 0.216764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.184996 restraints weight = 17726.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.184539 restraints weight = 20674.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.186497 restraints weight = 17742.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.187158 restraints weight = 12081.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.187336 restraints weight = 11818.106| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13897 Z= 0.129 Angle : 0.592 10.154 18857 Z= 0.296 Chirality : 0.045 0.258 2133 Planarity : 0.004 0.042 2405 Dihedral : 4.995 56.150 1909 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.48 % Favored : 94.34 % Rotamer: Outliers : 4.76 % Allowed : 24.54 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.27 (0.20), residues: 1714 helix: 1.32 (0.31), residues: 291 sheet: 0.52 (0.21), residues: 593 loop : -1.28 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1153 TYR 0.020 0.001 TYR C 32 PHE 0.022 0.001 PHE B1019 TRP 0.008 0.001 TRP C 36 HIS 0.002 0.001 HIS B1459 Details of bonding type rmsd covalent geometry : bond 0.00310 (13883) covalent geometry : angle 0.59066 (18827) SS BOND : bond 0.00249 ( 12) SS BOND : angle 0.71716 ( 24) hydrogen bonds : bond 0.03353 ( 549) hydrogen bonds : angle 4.67501 ( 1512) link_BETA1-4 : bond 0.00271 ( 1) link_BETA1-4 : angle 1.92014 ( 3) link_NAG-ASN : bond 0.00200 ( 1) link_NAG-ASN : angle 2.10914 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 170 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7215 (OUTLIER) cc_final: 0.6930 (m-10) REVERT: E 282 MET cc_start: 0.6608 (mmt) cc_final: 0.6392 (mmm) REVERT: E 618 LYS cc_start: 0.5747 (mptt) cc_final: 0.5500 (mttt) REVERT: B 753 HIS cc_start: 0.5033 (t-90) cc_final: 0.4774 (t-170) REVERT: B 820 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.6335 (t80) REVERT: B 923 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6730 (tm) REVERT: B 955 ARG cc_start: 0.4495 (ptm160) cc_final: 0.4111 (mtp-110) REVERT: B 986 GLU cc_start: 0.5790 (OUTLIER) cc_final: 0.4977 (mp0) REVERT: C 32 TYR cc_start: 0.6988 (OUTLIER) cc_final: 0.6442 (t80) REVERT: C 104 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.7071 (mm) outliers start: 72 outliers final: 56 residues processed: 229 average time/residue: 0.0925 time to fit residues: 32.5328 Evaluate side-chains 224 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 162 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 534 MET Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 571 LEU Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 809 ILE Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 986 GLU Chi-restraints excluded: chain B residue 987 ILE Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1161 LEU Chi-restraints excluded: chain B residue 1184 SER Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain B residue 1212 LEU Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1267 VAL Chi-restraints excluded: chain B residue 1315 VAL Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1492 THR Chi-restraints excluded: chain B residue 1506 THR Chi-restraints excluded: chain B residue 1527 CYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 125 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 150 optimal weight: 0.0370 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 158 optimal weight: 0.2980 chunk 138 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 446 ASN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.218084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.187176 restraints weight = 17734.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.186918 restraints weight = 21952.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.188857 restraints weight = 17322.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.189382 restraints weight = 11903.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.189533 restraints weight = 12094.603| |-----------------------------------------------------------------------------| r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13897 Z= 0.111 Angle : 0.576 9.669 18857 Z= 0.288 Chirality : 0.045 0.255 2133 Planarity : 0.004 0.042 2405 Dihedral : 4.783 56.407 1909 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.37 % Favored : 94.46 % Rotamer: Outliers : 3.97 % Allowed : 25.40 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.23 (0.21), residues: 1714 helix: 1.37 (0.32), residues: 291 sheet: 0.52 (0.21), residues: 612 loop : -1.28 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 962 TYR 0.018 0.001 TYR C 32 PHE 0.023 0.001 PHE B1019 TRP 0.009 0.001 TRP C 36 HIS 0.002 0.000 HIS B1421 Details of bonding type rmsd covalent geometry : bond 0.00259 (13883) covalent geometry : angle 0.57540 (18827) SS BOND : bond 0.00223 ( 12) SS BOND : angle 0.73282 ( 24) hydrogen bonds : bond 0.03168 ( 549) hydrogen bonds : angle 4.56953 ( 1512) link_BETA1-4 : bond 0.00323 ( 1) link_BETA1-4 : angle 1.70523 ( 3) link_NAG-ASN : bond 0.00097 ( 1) link_NAG-ASN : angle 1.87043 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 170 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 282 MET cc_start: 0.6631 (mmt) cc_final: 0.6406 (mmm) REVERT: E 618 LYS cc_start: 0.5726 (mptt) cc_final: 0.5498 (mttt) REVERT: B 753 HIS cc_start: 0.4984 (t-90) cc_final: 0.4692 (t-170) REVERT: B 820 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.6306 (t80) REVERT: B 923 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6809 (tm) REVERT: B 955 ARG cc_start: 0.4556 (ptm160) cc_final: 0.4319 (ttm-80) REVERT: B 1044 LYS cc_start: 0.6776 (ptmm) cc_final: 0.6362 (pttt) REVERT: C 104 ILE cc_start: 0.7363 (OUTLIER) cc_final: 0.7043 (mm) outliers start: 60 outliers final: 50 residues processed: 217 average time/residue: 0.0995 time to fit residues: 33.0737 Evaluate side-chains 210 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 157 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 534 MET Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 571 LEU Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 809 ILE Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 987 ILE Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1161 LEU Chi-restraints excluded: chain B residue 1184 SER Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain B residue 1267 VAL Chi-restraints excluded: chain B residue 1315 VAL Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1492 THR Chi-restraints excluded: chain B residue 1506 THR Chi-restraints excluded: chain B residue 1527 CYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 125 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 167 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 69 optimal weight: 0.0370 chunk 152 optimal weight: 0.5980 chunk 157 optimal weight: 0.0870 chunk 160 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN E 446 ASN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.218567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.188031 restraints weight = 17773.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.187665 restraints weight = 21402.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.189492 restraints weight = 17355.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.190029 restraints weight = 12236.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.190404 restraints weight = 11412.657| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13897 Z= 0.112 Angle : 0.593 9.885 18857 Z= 0.295 Chirality : 0.045 0.254 2133 Planarity : 0.004 0.041 2405 Dihedral : 4.688 56.555 1909 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.25 % Favored : 94.57 % Rotamer: Outliers : 3.51 % Allowed : 25.86 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.21 (0.20), residues: 1714 helix: 1.35 (0.31), residues: 292 sheet: 0.55 (0.21), residues: 613 loop : -1.26 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1153 TYR 0.018 0.001 TYR C 32 PHE 0.023 0.001 PHE B1019 TRP 0.019 0.001 TRP C 36 HIS 0.002 0.000 HIS E 498 Details of bonding type rmsd covalent geometry : bond 0.00263 (13883) covalent geometry : angle 0.59227 (18827) SS BOND : bond 0.00216 ( 12) SS BOND : angle 0.73050 ( 24) hydrogen bonds : bond 0.03131 ( 549) hydrogen bonds : angle 4.49249 ( 1512) link_BETA1-4 : bond 0.00295 ( 1) link_BETA1-4 : angle 1.52347 ( 3) link_NAG-ASN : bond 0.00062 ( 1) link_NAG-ASN : angle 1.67307 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 161 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 282 MET cc_start: 0.6610 (mmt) cc_final: 0.6373 (mmm) REVERT: E 618 LYS cc_start: 0.5732 (mptt) cc_final: 0.5529 (mttt) REVERT: B 753 HIS cc_start: 0.4857 (t-90) cc_final: 0.4647 (t-170) REVERT: B 765 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.6861 (tp) REVERT: B 820 PHE cc_start: 0.7074 (OUTLIER) cc_final: 0.6343 (t80) REVERT: B 923 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6867 (tm) REVERT: B 1044 LYS cc_start: 0.6758 (ptmm) cc_final: 0.6342 (pttt) REVERT: C 104 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.7063 (mm) outliers start: 53 outliers final: 48 residues processed: 202 average time/residue: 0.0944 time to fit residues: 29.0734 Evaluate side-chains 211 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 159 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 534 MET Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 571 LEU Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 809 ILE Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1161 LEU Chi-restraints excluded: chain B residue 1184 SER Chi-restraints excluded: chain B residue 1267 VAL Chi-restraints excluded: chain B residue 1315 VAL Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1492 THR Chi-restraints excluded: chain B residue 1506 THR Chi-restraints excluded: chain B residue 1527 CYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 125 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 23 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 91 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.212544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.180857 restraints weight = 17829.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.180554 restraints weight = 21581.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.182869 restraints weight = 17807.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.182679 restraints weight = 12059.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.183139 restraints weight = 12429.415| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13897 Z= 0.190 Angle : 0.653 10.592 18857 Z= 0.331 Chirality : 0.047 0.256 2133 Planarity : 0.004 0.047 2405 Dihedral : 4.990 56.937 1909 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.18 % Favored : 93.70 % Rotamer: Outliers : 3.97 % Allowed : 25.46 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.39 (0.20), residues: 1714 helix: 1.10 (0.31), residues: 291 sheet: 0.42 (0.21), residues: 593 loop : -1.29 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 955 TYR 0.021 0.002 TYR C 32 PHE 0.025 0.002 PHE C 68 TRP 0.024 0.002 TRP C 36 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00463 (13883) covalent geometry : angle 0.65093 (18827) SS BOND : bond 0.00234 ( 12) SS BOND : angle 1.30877 ( 24) hydrogen bonds : bond 0.03840 ( 549) hydrogen bonds : angle 4.75988 ( 1512) link_BETA1-4 : bond 0.00219 ( 1) link_BETA1-4 : angle 1.43367 ( 3) link_NAG-ASN : bond 0.00373 ( 1) link_NAG-ASN : angle 1.77400 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1869.32 seconds wall clock time: 33 minutes 12.58 seconds (1992.58 seconds total)