Starting phenix.real_space_refine on Thu May 15 22:40:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cml_16730/05_2025/8cml_16730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cml_16730/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cml_16730/05_2025/8cml_16730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cml_16730/05_2025/8cml_16730.map" model { file = "/net/cci-nas-00/data/ceres_data/8cml_16730/05_2025/8cml_16730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cml_16730/05_2025/8cml_16730.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.40, per 1000 atoms: 0.62 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: 3.42 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.95 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: 6.03 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 0.010 Normalize map: mean=0, sd=1: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 34.630 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.550 ------------------------------------------------------------------------------- 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 : 9.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.20), 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 TRP 0.019 0.001 TRP C 36 HIS 0.005 0.001 HIS E 498 PHE 0.037 0.002 PHE E 237 TYR 0.015 0.001 TYR B1326 ARG 0.006 0.000 ARG B 928 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 1) link_NAG-ASN : angle 1.58778 ( 3) link_BETA1-4 : bond 0.00161 ( 1) link_BETA1-4 : angle 0.79484 ( 3) hydrogen bonds : bond 0.12491 ( 549) hydrogen bonds : angle 5.93841 ( 1512) SS BOND : bond 0.00328 ( 12) SS BOND : angle 0.84020 ( 24) covalent geometry : bond 0.00299 (13883) covalent geometry : angle 0.65853 (18827) *********************** 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 : 1.442 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: 0.2416 time to fit residues: 62.6935 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 : 1.542 ------------------------------------------------------------------------------- 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 144 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 0.0670 chunk 134 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- 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 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4311 r_free = 0.4311 target = 0.203108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.174661 restraints weight = 16840.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.171866 restraints weight = 25128.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.173833 restraints weight = 24980.249| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13897 Z= 0.176 Angle : 0.633 10.280 18857 Z= 0.322 Chirality : 0.046 0.266 2133 Planarity : 0.004 0.050 2405 Dihedral : 7.577 86.517 1919 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.83 % Favored : 93.99 % Rotamer: Outliers : 3.64 % Allowed : 23.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.20), residues: 1714 helix: 0.81 (0.31), residues: 291 sheet: 0.47 (0.22), residues: 584 loop : -1.39 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 469 HIS 0.004 0.001 HIS E 498 PHE 0.017 0.002 PHE E 237 TYR 0.016 0.001 TYR E 543 ARG 0.004 0.000 ARG B1153 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 1) link_NAG-ASN : angle 2.38748 ( 3) link_BETA1-4 : bond 0.00666 ( 1) link_BETA1-4 : angle 2.48595 ( 3) hydrogen bonds : bond 0.03976 ( 549) hydrogen bonds : angle 5.24769 ( 1512) SS BOND : bond 0.00316 ( 12) SS BOND : angle 1.18938 ( 24) covalent geometry : bond 0.00428 (13883) covalent geometry : angle 0.63101 (18827) *********************** 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 218 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 1.597 Fit side-chains revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6594 (m-10) REVERT: B 955 ARG cc_start: 0.3983 (ptm160) cc_final: 0.3415 (mtp85) outliers start: 55 outliers final: 34 residues processed: 202 average time/residue: 0.2325 time to fit residues: 72.0387 Evaluate side-chains 188 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 1.396 ------------------------------------------------------------------------------- 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 143 VAL Chi-restraints excluded: chain E residue 192 SER 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 135 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 147 optimal weight: 0.0050 chunk 52 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 104 optimal weight: 0.0980 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.4346 r_free = 0.4346 target = 0.206657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.177761 restraints weight = 16966.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.175919 restraints weight = 23758.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.177835 restraints weight = 22411.226| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13897 Z= 0.115 Angle : 0.577 9.826 18857 Z= 0.290 Chirality : 0.044 0.252 2133 Planarity : 0.004 0.045 2405 Dihedral : 7.062 79.809 1913 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.02 % Favored : 94.81 % Rotamer: Outliers : 3.77 % Allowed : 24.47 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.20), residues: 1714 helix: 1.09 (0.31), residues: 290 sheet: 0.56 (0.22), residues: 592 loop : -1.33 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 36 HIS 0.003 0.001 HIS E 498 PHE 0.018 0.001 PHE B1019 TYR 0.019 0.001 TYR E 196 ARG 0.003 0.000 ARG B1153 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 1) link_NAG-ASN : angle 1.97594 ( 3) link_BETA1-4 : bond 0.00034 ( 1) link_BETA1-4 : angle 2.08257 ( 3) hydrogen bonds : bond 0.03514 ( 549) hydrogen bonds : angle 4.99251 ( 1512) SS BOND : bond 0.00237 ( 12) SS BOND : angle 0.77269 ( 24) covalent geometry : bond 0.00270 (13883) covalent geometry : angle 0.57564 (18827) *********************** 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 227 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 170 time to evaluate : 1.502 Fit side-chains revert: symmetry clash REVERT: E 282 MET cc_start: 0.6361 (mmt) cc_final: 0.6116 (mmm) REVERT: B 923 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6856 (tm) REVERT: B 955 ARG cc_start: 0.4038 (ptm160) cc_final: 0.3471 (mtp85) REVERT: B 1259 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8376 (mt) REVERT: C 68 PHE cc_start: 0.7757 (m-80) cc_final: 0.7460 (m-10) REVERT: C 104 ILE cc_start: 0.7414 (OUTLIER) cc_final: 0.7096 (mm) outliers start: 57 outliers final: 33 residues processed: 211 average time/residue: 0.2254 time to fit residues: 74.0876 Evaluate side-chains 190 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 143 VAL Chi-restraints excluded: chain E residue 162 THR 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 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 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 952 THR Chi-restraints excluded: chain B residue 987 ILE Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1107 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 11 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** B 753 HIS B1030 HIS B1306 GLN B1465 ASN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.215234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.182935 restraints weight = 17612.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.182654 restraints weight = 20956.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.184684 restraints weight = 17830.281| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13897 Z= 0.170 Angle : 0.622 9.906 18857 Z= 0.313 Chirality : 0.046 0.280 2133 Planarity : 0.004 0.046 2405 Dihedral : 6.531 66.547 1911 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.07 % Favored : 93.76 % Rotamer: Outliers : 5.36 % Allowed : 23.88 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1714 helix: 1.00 (0.31), residues: 290 sheet: 0.50 (0.22), residues: 585 loop : -1.34 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 36 HIS 0.006 0.001 HIS B 753 PHE 0.022 0.002 PHE E 237 TYR 0.022 0.002 TYR B1300 ARG 0.005 0.000 ARG C 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 1) link_NAG-ASN : angle 2.34115 ( 3) link_BETA1-4 : bond 0.00240 ( 1) link_BETA1-4 : angle 2.25342 ( 3) hydrogen bonds : bond 0.03819 ( 549) hydrogen bonds : angle 5.00445 ( 1512) SS BOND : bond 0.00314 ( 12) SS BOND : angle 0.88037 ( 24) covalent geometry : bond 0.00413 (13883) covalent geometry : angle 0.62004 (18827) *********************** 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 253 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 172 time to evaluate : 1.471 Fit side-chains revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6804 (m-10) REVERT: E 282 MET cc_start: 0.6480 (mmt) cc_final: 0.6254 (mmm) REVERT: B 923 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6765 (tm) REVERT: B 955 ARG cc_start: 0.4287 (ptm160) cc_final: 0.3906 (mtp-110) REVERT: C 19 ARG cc_start: 0.7448 (tpp80) cc_final: 0.7080 (tpp80) REVERT: C 82 GLN cc_start: 0.5984 (tp40) cc_final: 0.5562 (tm-30) REVERT: C 104 ILE cc_start: 0.7346 (OUTLIER) cc_final: 0.7046 (mm) outliers start: 81 outliers final: 56 residues processed: 235 average time/residue: 0.2276 time to fit residues: 81.7709 Evaluate side-chains 222 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 163 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 115 VAL Chi-restraints excluded: chain E residue 41 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 145 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 257 ASN 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 410 VAL Chi-restraints excluded: chain E residue 417 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 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 795 THR Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 841 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 1076 THR Chi-restraints excluded: chain B residue 1148 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 1328 MET Chi-restraints excluded: chain B residue 1448 GLN 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 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 73 optimal weight: 0.4980 chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 159 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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** ** B1306 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 = 0.4289 r_free = 0.4289 target = 0.200700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.173535 restraints weight = 17016.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.170393 restraints weight = 27259.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.172171 restraints weight = 25675.713| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13897 Z= 0.180 Angle : 0.644 9.950 18857 Z= 0.323 Chirality : 0.046 0.278 2133 Planarity : 0.004 0.046 2405 Dihedral : 6.049 55.990 1909 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.07 % Favored : 93.76 % Rotamer: Outliers : 5.62 % Allowed : 23.94 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.20), residues: 1714 helix: 0.94 (0.31), residues: 290 sheet: 0.45 (0.22), residues: 577 loop : -1.40 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 199 HIS 0.006 0.001 HIS B 908 PHE 0.019 0.002 PHE B1019 TYR 0.023 0.002 TYR E 196 ARG 0.003 0.000 ARG C 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 1) link_NAG-ASN : angle 2.28641 ( 3) link_BETA1-4 : bond 0.00453 ( 1) link_BETA1-4 : angle 2.37114 ( 3) hydrogen bonds : bond 0.03853 ( 549) hydrogen bonds : angle 5.00461 ( 1512) SS BOND : bond 0.00269 ( 12) SS BOND : angle 0.89583 ( 24) covalent geometry : bond 0.00437 (13883) covalent geometry : angle 0.64267 (18827) *********************** 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 258 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 173 time to evaluate : 1.606 Fit side-chains revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6799 (m-10) REVERT: E 618 LYS cc_start: 0.5501 (mptt) cc_final: 0.5238 (mttt) REVERT: B 820 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.6234 (t80) REVERT: B 923 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.7006 (tm) REVERT: B 955 ARG cc_start: 0.4466 (ptm160) cc_final: 0.4120 (mtp-110) REVERT: B 1104 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7168 (tt) REVERT: C 104 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.7065 (mm) outliers start: 85 outliers final: 64 residues processed: 237 average time/residue: 0.2412 time to fit residues: 86.0645 Evaluate side-chains 233 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 164 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 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 145 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 257 ASN 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 410 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 441 ASP 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 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 804 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 895 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 1056 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1104 LEU 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 1249 GLU Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1267 VAL Chi-restraints excluded: chain B residue 1311 MET Chi-restraints excluded: chain B residue 1328 MET Chi-restraints excluded: chain B residue 1448 GLN 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 B residue 1527 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 55 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 0.0060 chunk 115 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 76 optimal weight: 0.0070 chunk 110 optimal weight: 0.8980 overall best weight: 0.4414 ------------------------------------------------------------------------------- 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** ** B1306 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 = 0.4327 r_free = 0.4327 target = 0.204596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175004 restraints weight = 17031.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.171860 restraints weight = 24540.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.173935 restraints weight = 23797.417| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1995 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 : 0.586 9.567 18857 Z= 0.291 Chirality : 0.045 0.255 2133 Planarity : 0.004 0.042 2405 Dihedral : 5.520 55.594 1909 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.13 % Favored : 94.69 % Rotamer: Outliers : 4.37 % Allowed : 25.20 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.20), residues: 1714 helix: 1.19 (0.32), residues: 291 sheet: 0.56 (0.22), residues: 584 loop : -1.30 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 36 HIS 0.003 0.000 HIS B1421 PHE 0.021 0.001 PHE B1019 TYR 0.032 0.001 TYR E 196 ARG 0.003 0.000 ARG B1153 Details of bonding type rmsd link_NAG-ASN : bond 0.00080 ( 1) link_NAG-ASN : angle 2.17079 ( 3) link_BETA1-4 : bond 0.00317 ( 1) link_BETA1-4 : angle 2.01301 ( 3) hydrogen bonds : bond 0.03270 ( 549) hydrogen bonds : angle 4.76694 ( 1512) SS BOND : bond 0.00212 ( 12) SS BOND : angle 0.71332 ( 24) covalent geometry : bond 0.00259 (13883) covalent geometry : angle 0.58428 (18827) *********************** 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 243 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 177 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.5254 (OUTLIER) cc_final: 0.5038 (p) REVERT: A 100 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6841 (m-10) REVERT: E 618 LYS cc_start: 0.5687 (mptt) cc_final: 0.5416 (mttt) REVERT: B 820 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6222 (t80) REVERT: B 923 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6964 (tm) REVERT: B 955 ARG cc_start: 0.4487 (ptm160) cc_final: 0.4202 (ttm-80) REVERT: B 986 GLU cc_start: 0.5923 (OUTLIER) cc_final: 0.5620 (mm-30) REVERT: B 1104 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7043 (tt) REVERT: C 19 ARG cc_start: 0.6930 (tpp80) cc_final: 0.6657 (tpp80) REVERT: C 32 TYR cc_start: 0.6777 (t80) cc_final: 0.6237 (t80) REVERT: C 82 GLN cc_start: 0.5837 (tp40) cc_final: 0.5482 (tm-30) REVERT: C 104 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.6989 (mm) outliers start: 66 outliers final: 47 residues processed: 225 average time/residue: 0.2215 time to fit residues: 76.5368 Evaluate side-chains 216 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 100 PHE 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 126 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 THR 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 430 VAL Chi-restraints excluded: chain E residue 441 ASP 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 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 986 GLU 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 1104 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 1271 ILE Chi-restraints excluded: chain B residue 1311 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 50 CYS Chi-restraints excluded: chain C residue 70 ILE 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 101 optimal weight: 0.1980 chunk 145 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 140 optimal weight: 8.9990 chunk 23 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 chunk 86 optimal weight: 0.3980 chunk 113 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** B 753 HIS B1306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.204761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.177255 restraints weight = 17058.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.175777 restraints weight = 28047.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.177564 restraints weight = 24713.772| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13897 Z= 0.118 Angle : 0.581 9.551 18857 Z= 0.290 Chirality : 0.044 0.255 2133 Planarity : 0.004 0.043 2405 Dihedral : 5.184 55.803 1909 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.60 % Favored : 94.22 % Rotamer: Outliers : 4.37 % Allowed : 25.79 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.20), residues: 1714 helix: 1.27 (0.32), residues: 290 sheet: 0.54 (0.21), residues: 587 loop : -1.26 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 36 HIS 0.002 0.001 HIS E 498 PHE 0.026 0.001 PHE E 237 TYR 0.025 0.001 TYR B1024 ARG 0.003 0.000 ARG B1153 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 1) link_NAG-ASN : angle 2.20550 ( 3) link_BETA1-4 : bond 0.00350 ( 1) link_BETA1-4 : angle 1.99791 ( 3) hydrogen bonds : bond 0.03287 ( 549) hydrogen bonds : angle 4.69190 ( 1512) SS BOND : bond 0.00230 ( 12) SS BOND : angle 0.72357 ( 24) covalent geometry : bond 0.00281 (13883) covalent geometry : angle 0.58002 (18827) *********************** 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 237 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 171 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6820 (m-10) REVERT: E 618 LYS cc_start: 0.5622 (mptt) cc_final: 0.5386 (mttt) REVERT: E 627 LEU cc_start: 0.9073 (tp) cc_final: 0.8858 (tt) REVERT: B 820 PHE cc_start: 0.6966 (OUTLIER) cc_final: 0.6268 (t80) REVERT: B 923 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6873 (tm) REVERT: B 986 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.5598 (mm-30) REVERT: B 1104 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7034 (tt) REVERT: C 19 ARG cc_start: 0.7015 (tpp80) cc_final: 0.6781 (tpp80) REVERT: C 32 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.6375 (t80) REVERT: C 82 GLN cc_start: 0.5610 (tp40) cc_final: 0.5306 (tm-30) REVERT: C 104 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.6976 (mm) outliers start: 66 outliers final: 53 residues processed: 224 average time/residue: 0.2394 time to fit residues: 80.3733 Evaluate side-chains 225 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 165 time to evaluate : 1.539 ------------------------------------------------------------------------------- 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 76 LYS 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 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 192 SER 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 413 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 441 ASP 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 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 1016 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1104 LEU 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 1311 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 133 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4286 r_free = 0.4286 target = 0.200243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.173094 restraints weight = 17151.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.169512 restraints weight = 26301.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.171515 restraints weight = 26813.895| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13897 Z= 0.183 Angle : 0.632 9.585 18857 Z= 0.319 Chirality : 0.046 0.263 2133 Planarity : 0.004 0.046 2405 Dihedral : 5.206 56.375 1909 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.42 % Favored : 93.41 % Rotamer: Outliers : 4.96 % Allowed : 24.80 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.20), residues: 1714 helix: 1.14 (0.32), residues: 291 sheet: 0.43 (0.21), residues: 597 loop : -1.34 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 36 HIS 0.003 0.001 HIS E 72 PHE 0.020 0.002 PHE B1019 TYR 0.025 0.002 TYR B1024 ARG 0.003 0.000 ARG B 849 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 1) link_NAG-ASN : angle 2.34541 ( 3) link_BETA1-4 : bond 0.00168 ( 1) link_BETA1-4 : angle 2.03511 ( 3) hydrogen bonds : bond 0.03822 ( 549) hydrogen bonds : angle 4.86533 ( 1512) SS BOND : bond 0.00290 ( 12) SS BOND : angle 0.85640 ( 24) covalent geometry : bond 0.00444 (13883) covalent geometry : angle 0.63084 (18827) *********************** 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 243 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 168 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.6809 (m-10) REVERT: E 618 LYS cc_start: 0.5702 (mptt) cc_final: 0.5494 (mttt) REVERT: B 820 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6294 (t80) REVERT: B 915 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7101 (tt0) REVERT: B 923 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7017 (tm) REVERT: B 1104 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7430 (tt) REVERT: C 19 ARG cc_start: 0.7016 (tpp80) cc_final: 0.6742 (tpp80) REVERT: C 32 TYR cc_start: 0.6987 (OUTLIER) cc_final: 0.6537 (t80) REVERT: C 82 GLN cc_start: 0.5644 (tp40) cc_final: 0.5318 (tm-30) REVERT: C 104 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7161 (mm) outliers start: 75 outliers final: 55 residues processed: 231 average time/residue: 0.2317 time to fit residues: 81.6028 Evaluate side-chains 220 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 158 time to evaluate : 1.388 ------------------------------------------------------------------------------- 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 76 LYS Chi-restraints excluded: chain A residue 100 PHE 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 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 292 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 441 ASP 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 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 844 THR Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 915 GLU 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 1016 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1104 LEU 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 1311 MET Chi-restraints excluded: chain B residue 1315 VAL Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1506 THR Chi-restraints excluded: chain B residue 1527 CYS 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 153 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 109 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.0000 chunk 139 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.201957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.175596 restraints weight = 16944.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.172951 restraints weight = 26215.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.174036 restraints weight = 26268.864| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13897 Z= 0.141 Angle : 0.607 10.499 18857 Z= 0.304 Chirality : 0.045 0.260 2133 Planarity : 0.004 0.044 2405 Dihedral : 5.028 56.415 1909 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.66 % Favored : 94.17 % Rotamer: Outliers : 4.43 % Allowed : 25.73 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.20), residues: 1714 helix: 1.22 (0.32), residues: 291 sheet: 0.46 (0.21), residues: 585 loop : -1.29 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 36 HIS 0.002 0.001 HIS B1459 PHE 0.022 0.001 PHE B1019 TYR 0.024 0.001 TYR B1024 ARG 0.004 0.000 ARG B 955 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 1) link_NAG-ASN : angle 2.02665 ( 3) link_BETA1-4 : bond 0.00212 ( 1) link_BETA1-4 : angle 1.79881 ( 3) hydrogen bonds : bond 0.03516 ( 549) hydrogen bonds : angle 4.75896 ( 1512) SS BOND : bond 0.00253 ( 12) SS BOND : angle 0.74808 ( 24) covalent geometry : bond 0.00337 (13883) covalent geometry : angle 0.60589 (18827) *********************** 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 241 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 174 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.7076 (tttt) REVERT: A 100 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.6809 (m-10) REVERT: E 359 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8175 (p) REVERT: B 820 PHE cc_start: 0.6985 (OUTLIER) cc_final: 0.6308 (t80) REVERT: B 915 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.7087 (tt0) REVERT: B 923 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6993 (tm) REVERT: B 986 GLU cc_start: 0.5998 (OUTLIER) cc_final: 0.5676 (mm-30) REVERT: B 1044 LYS cc_start: 0.6564 (ptmm) cc_final: 0.6121 (pttt) REVERT: B 1104 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7146 (tt) REVERT: C 32 TYR cc_start: 0.6940 (OUTLIER) cc_final: 0.6519 (t80) REVERT: C 82 GLN cc_start: 0.5503 (tp40) cc_final: 0.5244 (tm-30) REVERT: C 104 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.7107 (mm) outliers start: 67 outliers final: 54 residues processed: 228 average time/residue: 0.2339 time to fit residues: 81.7459 Evaluate side-chains 227 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 163 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 76 LYS Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain E residue 41 ILE 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 292 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 441 ASP 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 844 THR Chi-restraints excluded: chain B residue 915 GLU 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 1089 VAL Chi-restraints excluded: chain B residue 1104 LEU 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 1311 MET Chi-restraints excluded: chain B residue 1315 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 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 8 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 96 optimal weight: 0.0020 chunk 113 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 114 GLN E 647 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.201676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.176005 restraints weight = 16895.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.173523 restraints weight = 25009.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.175228 restraints weight = 23817.123| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13897 Z= 0.145 Angle : 0.611 10.089 18857 Z= 0.307 Chirality : 0.046 0.257 2133 Planarity : 0.004 0.045 2405 Dihedral : 5.006 56.618 1909 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.83 % Favored : 93.99 % Rotamer: Outliers : 4.50 % Allowed : 25.33 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.20), residues: 1714 helix: 1.19 (0.31), residues: 291 sheet: 0.45 (0.21), residues: 587 loop : -1.28 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 36 HIS 0.003 0.001 HIS E 72 PHE 0.022 0.002 PHE B1019 TYR 0.033 0.001 TYR B1300 ARG 0.004 0.000 ARG B 955 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 1) link_NAG-ASN : angle 1.89437 ( 3) link_BETA1-4 : bond 0.00250 ( 1) link_BETA1-4 : angle 1.60993 ( 3) hydrogen bonds : bond 0.03579 ( 549) hydrogen bonds : angle 4.76231 ( 1512) SS BOND : bond 0.00301 ( 12) SS BOND : angle 0.84504 ( 24) covalent geometry : bond 0.00349 (13883) covalent geometry : angle 0.60958 (18827) ********************** 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 231 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 163 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.7139 (ttm110) cc_final: 0.6939 (ttm-80) REVERT: A 100 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.6900 (m-10) REVERT: E 359 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8199 (p) REVERT: B 820 PHE cc_start: 0.6889 (OUTLIER) cc_final: 0.6267 (t80) REVERT: B 923 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6991 (tm) REVERT: B 986 GLU cc_start: 0.5997 (OUTLIER) cc_final: 0.5712 (mm-30) REVERT: B 1044 LYS cc_start: 0.6558 (ptmm) cc_final: 0.6110 (pttt) REVERT: B 1104 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7206 (tt) REVERT: C 104 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7127 (mm) outliers start: 68 outliers final: 55 residues processed: 216 average time/residue: 0.2264 time to fit residues: 75.4788 Evaluate side-chains 222 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 160 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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 100 PHE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain E residue 41 ILE 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 292 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 441 ASP 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 799 ILE Chi-restraints excluded: chain B residue 809 ILE Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 844 THR 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 1016 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1104 LEU 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 1311 MET Chi-restraints excluded: chain B residue 1315 VAL Chi-restraints excluded: chain B residue 1446 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 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 145 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4597 r_free = 0.4597 target = 0.240352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.4368 r_free = 0.4368 target = 0.198655 restraints weight = 19264.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.198924 restraints weight = 19777.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.200338 restraints weight = 17390.558| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13897 Z= 0.144 Angle : 0.621 12.216 18857 Z= 0.313 Chirality : 0.046 0.253 2133 Planarity : 0.004 0.044 2405 Dihedral : 4.991 56.684 1909 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.78 % Favored : 94.11 % Rotamer: Outliers : 4.50 % Allowed : 25.53 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1714 helix: 1.18 (0.31), residues: 292 sheet: 0.45 (0.21), residues: 603 loop : -1.28 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 36 HIS 0.002 0.001 HIS E 72 PHE 0.031 0.002 PHE C 68 TYR 0.027 0.001 TYR B1300 ARG 0.004 0.000 ARG C 107 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 1) link_NAG-ASN : angle 1.66074 ( 3) link_BETA1-4 : bond 0.00283 ( 1) link_BETA1-4 : angle 1.44240 ( 3) hydrogen bonds : bond 0.03543 ( 549) hydrogen bonds : angle 4.72387 ( 1512) SS BOND : bond 0.00388 ( 12) SS BOND : angle 1.25445 ( 24) covalent geometry : bond 0.00348 (13883) covalent geometry : angle 0.61938 (18827) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4181.04 seconds wall clock time: 74 minutes 16.31 seconds (4456.31 seconds total)