Starting phenix.real_space_refine on Thu Feb 15 22:30:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cml_16730/02_2024/8cml_16730.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cml_16730/02_2024/8cml_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cml_16730/02_2024/8cml_16730.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cml_16730/02_2024/8cml_16730.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cml_16730/02_2024/8cml_16730.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cml_16730/02_2024/8cml_16730.pdb" } 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 Residue "A GLU 44": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E GLU 444": "OE1" <-> "OE2" Residue "E GLU 445": "OE1" <-> "OE2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "E GLU 564": "OE1" <-> "OE2" Residue "E GLU 628": "OE1" <-> "OE2" Residue "B GLU 709": "OE1" <-> "OE2" Residue "B GLU 932": "OE1" <-> "OE2" Residue "B GLU 1094": "OE1" <-> "OE2" Residue "B GLU 1295": "OE1" <-> "OE2" Residue "B GLU 1339": "OE1" <-> "OE2" Residue "B GLU 1437": "OE1" <-> "OE2" Residue "B GLU 1484": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.32, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN B 911 " Time building additional restraints: 5.05 Conformation dependent library (CDL) restraints added in 2.4 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: 1.68 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: 5.70 Time building geometry restraints manager: 5.49 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: 98.85 - 105.88: 281 105.88 - 112.90: 7493 112.90 - 119.93: 4498 119.93 - 126.96: 6408 126.96 - 133.98: 147 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 2.440 nonbonded pdb=" OG SER C 7 " pdb=" OG SER C 21 " model vdw 2.159 2.440 nonbonded pdb=" NH1 ARG A 101 " pdb=" O LEU B1197 " model vdw 2.190 2.520 nonbonded pdb=" OE1 GLU B 937 " pdb=" OH TYR B 939 " model vdw 2.200 2.440 nonbonded pdb=" OH TYR E 196 " pdb=" OE2 GLU E 221 " model vdw 2.222 2.440 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 7.590 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 37.970 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.470 ------------------------------------------------------------------------------- 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 13883 Z= 0.193 Angle : 0.659 10.760 18827 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 *********************** 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 fitting. rotamer outliers: 9 poor density : 171 time to evaluate : 1.603 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: 0.2544 time to fit residues: 65.8548 Evaluate side-chains 162 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 157 time to evaluate : 1.651 ------------------------------------------------------------------------------- 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: 5.9990 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: 3.9990 chunk 134 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 20.0000 chunk 99 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 ASN E 656 ASN B 706 ASN B 753 HIS B1360 HIS B1465 ASN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 13883 Z= 0.388 Angle : 0.694 12.171 18827 Z= 0.353 Chirality : 0.049 0.259 2133 Planarity : 0.005 0.052 2405 Dihedral : 7.653 84.262 1919 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.53 % Favored : 93.23 % Rotamer: Outliers : 4.96 % Allowed : 23.68 % Favored : 71.36 % 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: -0.74 (0.20), residues: 1714 helix: 0.56 (0.31), residues: 290 sheet: 0.35 (0.21), residues: 611 loop : -1.58 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 469 HIS 0.005 0.001 HIS E 72 PHE 0.020 0.002 PHE E 237 TYR 0.020 0.002 TYR E 543 ARG 0.004 0.001 ARG A 67 *********************** 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 239 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 164 time to evaluate : 1.594 Fit side-chains revert: symmetry clash REVERT: B 1078 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7376 (tt) outliers start: 75 outliers final: 50 residues processed: 222 average time/residue: 0.2408 time to fit residues: 81.6298 Evaluate side-chains 206 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 155 time to evaluate : 1.589 ------------------------------------------------------------------------------- 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 45 ARG Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 138 ASP 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 330 ILE Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 431 LEU 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 B residue 725 ILE Chi-restraints excluded: chain B residue 747 MET Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 909 ASN Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 987 ILE Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain B residue 1148 THR 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 86 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 105 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 124 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 446 ASN B 706 ASN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13883 Z= 0.187 Angle : 0.581 11.872 18827 Z= 0.292 Chirality : 0.045 0.238 2133 Planarity : 0.004 0.047 2405 Dihedral : 7.069 77.601 1914 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.19 % Favored : 94.57 % 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: -0.47 (0.21), residues: 1714 helix: 1.00 (0.31), residues: 290 sheet: 0.50 (0.21), residues: 605 loop : -1.46 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 469 HIS 0.003 0.001 HIS E 498 PHE 0.021 0.001 PHE E 237 TYR 0.016 0.001 TYR B1024 ARG 0.003 0.000 ARG B1153 *********************** 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 242 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 174 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.6961 (OUTLIER) cc_final: 0.6611 (m-10) REVERT: E 618 LYS cc_start: 0.5273 (mptt) cc_final: 0.4886 (mttt) REVERT: B 923 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6891 (tm) REVERT: B 1259 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8574 (mt) REVERT: C 68 PHE cc_start: 0.7612 (m-80) cc_final: 0.7286 (m-10) REVERT: C 104 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7184 (mm) outliers start: 68 outliers final: 40 residues processed: 219 average time/residue: 0.2643 time to fit residues: 85.8968 Evaluate side-chains 208 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 164 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 77 ASN 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 56 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 145 VAL 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 296 ILE 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 792 ASP Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 936 ARG Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1056 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1161 LEU Chi-restraints excluded: chain B residue 1259 LEU 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 48 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 104 optimal weight: 0.0470 chunk 156 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 147 optimal weight: 0.0870 chunk 44 optimal weight: 3.9990 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13883 Z= 0.211 Angle : 0.590 11.591 18827 Z= 0.294 Chirality : 0.045 0.258 2133 Planarity : 0.004 0.043 2405 Dihedral : 6.473 66.492 1911 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.07 % Favored : 93.70 % Rotamer: Outliers : 5.75 % Allowed : 24.60 % Favored : 69.64 % 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: -0.44 (0.21), residues: 1714 helix: 1.07 (0.31), residues: 290 sheet: 0.56 (0.22), residues: 590 loop : -1.46 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 36 HIS 0.008 0.001 HIS B 908 PHE 0.020 0.001 PHE B1019 TYR 0.018 0.001 TYR B1024 ARG 0.002 0.000 ARG B1153 *********************** 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 259 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 172 time to evaluate : 1.590 Fit side-chains revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6762 (m-10) REVERT: E 618 LYS cc_start: 0.5469 (mptt) cc_final: 0.5160 (mttt) REVERT: B 820 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.6188 (t80) REVERT: B 923 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.7011 (tm) REVERT: B 1104 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7091 (tt) REVERT: C 32 TYR cc_start: 0.7023 (t80) cc_final: 0.6772 (t80) REVERT: C 104 ILE cc_start: 0.7348 (OUTLIER) cc_final: 0.7004 (mm) outliers start: 87 outliers final: 58 residues processed: 232 average time/residue: 0.2802 time to fit residues: 100.3370 Evaluate side-chains 228 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 165 time to evaluate : 1.696 ------------------------------------------------------------------------------- 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 77 ASN 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 102 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 320 ASN Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 520 ASP 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 B residue 725 ILE Chi-restraints excluded: chain B residue 747 MET Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 795 THR 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 909 ASN Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 936 ARG Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1104 LEU 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 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 1328 MET Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1506 THR Chi-restraints excluded: chain B residue 1507 MET Chi-restraints excluded: chain B residue 1527 CYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 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 137 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 141 optimal weight: 0.4980 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN E 446 ASN E 647 HIS B 840 GLN B1260 ASN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13883 Z= 0.350 Angle : 0.667 11.829 18827 Z= 0.337 Chirality : 0.048 0.279 2133 Planarity : 0.004 0.045 2405 Dihedral : 6.099 56.023 1909 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.77 % Favored : 93.00 % Rotamer: Outliers : 6.68 % Allowed : 24.60 % Favored : 68.72 % 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: -0.66 (0.20), residues: 1714 helix: 0.89 (0.31), residues: 290 sheet: 0.34 (0.21), residues: 599 loop : -1.57 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B1069 HIS 0.006 0.001 HIS B 908 PHE 0.020 0.002 PHE B1483 TYR 0.021 0.002 TYR B1024 ARG 0.003 0.000 ARG B 885 *********************** 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 272 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 171 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6638 (m-10) REVERT: E 618 LYS cc_start: 0.5651 (mptt) cc_final: 0.5346 (mttt) REVERT: B 820 PHE cc_start: 0.7110 (OUTLIER) cc_final: 0.6418 (t80) REVERT: B 859 MET cc_start: 0.6346 (OUTLIER) cc_final: 0.6001 (mtp) REVERT: B 923 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7184 (tm) REVERT: B 955 ARG cc_start: 0.4446 (ptm160) cc_final: 0.4075 (ttm-80) REVERT: B 986 GLU cc_start: 0.5944 (OUTLIER) cc_final: 0.5049 (mp0) REVERT: B 1401 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7291 (ttm170) REVERT: C 104 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7119 (mm) outliers start: 101 outliers final: 72 residues processed: 252 average time/residue: 0.2310 time to fit residues: 88.5229 Evaluate side-chains 237 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 158 time to evaluate : 1.531 ------------------------------------------------------------------------------- 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 77 ASN 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 102 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 138 ASP 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 242 ASN 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 320 ASN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 520 ASP 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 B residue 765 ILE Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 792 ASP 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 840 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 844 THR Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 909 ASN Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 936 ARG 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 1161 LEU 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 1315 VAL Chi-restraints excluded: chain B residue 1401 ARG Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1492 THR Chi-restraints excluded: chain B residue 1506 THR Chi-restraints excluded: chain B residue 1507 MET Chi-restraints excluded: chain B residue 1527 CYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 53 THR 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: 0.7980 chunk 148 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN E 446 ASN ** B1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13883 Z= 0.229 Angle : 0.607 11.884 18827 Z= 0.304 Chirality : 0.045 0.261 2133 Planarity : 0.004 0.045 2405 Dihedral : 5.677 55.733 1909 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.95 % Favored : 93.82 % Rotamer: Outliers : 5.29 % Allowed : 26.39 % Favored : 68.32 % 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: -0.57 (0.21), residues: 1714 helix: 0.97 (0.32), residues: 291 sheet: 0.39 (0.21), residues: 613 loop : -1.53 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 36 HIS 0.003 0.001 HIS B 908 PHE 0.020 0.002 PHE B1019 TYR 0.018 0.001 TYR B1024 ARG 0.003 0.000 ARG B1153 *********************** 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 250 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 170 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6872 (m-10) REVERT: E 618 LYS cc_start: 0.5671 (mptt) cc_final: 0.5415 (mttt) REVERT: B 820 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.6439 (t80) REVERT: B 859 MET cc_start: 0.6394 (OUTLIER) cc_final: 0.6059 (mtp) REVERT: B 923 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7141 (tm) REVERT: B 955 ARG cc_start: 0.4501 (ptm160) cc_final: 0.4134 (ttm-80) REVERT: B 1104 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7205 (tt) REVERT: B 1401 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7247 (ttm170) REVERT: C 104 ILE cc_start: 0.7380 (OUTLIER) cc_final: 0.7066 (mm) outliers start: 80 outliers final: 63 residues processed: 226 average time/residue: 0.2457 time to fit residues: 84.7696 Evaluate side-chains 235 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 165 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 77 ASN 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 102 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 138 ASP 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 267 ILE Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 320 ASN Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 520 ASP 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 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 792 ASP Chi-restraints excluded: chain B residue 795 THR 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 850 THR Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 909 ASN Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 936 ARG Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1104 LEU 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 1271 ILE Chi-restraints excluded: chain B residue 1401 ARG Chi-restraints excluded: chain B residue 1446 VAL Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1457 ASP Chi-restraints excluded: chain B residue 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN E 446 ASN B 840 GLN B1306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13883 Z= 0.338 Angle : 0.665 12.240 18827 Z= 0.335 Chirality : 0.047 0.264 2133 Planarity : 0.004 0.046 2405 Dihedral : 5.522 56.049 1909 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.47 % Favored : 92.30 % Rotamer: Outliers : 7.01 % Allowed : 25.13 % Favored : 67.86 % 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: -0.81 (0.20), residues: 1714 helix: 0.77 (0.31), residues: 290 sheet: 0.20 (0.21), residues: 623 loop : -1.66 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 36 HIS 0.005 0.001 HIS B 908 PHE 0.020 0.002 PHE B1483 TYR 0.018 0.002 TYR E 544 ARG 0.004 0.000 ARG B1153 *********************** 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 278 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 172 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.6692 (m-10) REVERT: E 618 LYS cc_start: 0.5775 (mptt) cc_final: 0.5549 (mttt) REVERT: B 820 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.6515 (t80) REVERT: B 859 MET cc_start: 0.6491 (OUTLIER) cc_final: 0.6192 (mtp) REVERT: B 923 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7208 (tm) REVERT: B 944 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6047 (mt) REVERT: B 1401 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7316 (ttm170) REVERT: C 104 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7121 (mm) outliers start: 106 outliers final: 78 residues processed: 252 average time/residue: 0.2383 time to fit residues: 90.7547 Evaluate side-chains 248 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 163 time to evaluate : 1.928 ------------------------------------------------------------------------------- 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 77 ASN 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 102 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 138 ASP 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 242 ASN Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 320 ASN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 520 ASP 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 630 SER 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 792 ASP 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 833 VAL Chi-restraints excluded: chain B residue 840 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 844 THR Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 909 ASN Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 936 ARG Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 986 GLU Chi-restraints excluded: chain B residue 987 ILE Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1089 VAL 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 1306 GLN Chi-restraints excluded: chain B residue 1315 VAL Chi-restraints excluded: chain B residue 1401 ARG Chi-restraints excluded: chain B residue 1446 VAL Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1457 ASP Chi-restraints excluded: chain B residue 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 50 CYS Chi-restraints excluded: chain C residue 53 THR 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 101 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13883 Z= 0.251 Angle : 0.627 12.278 18827 Z= 0.315 Chirality : 0.046 0.256 2133 Planarity : 0.004 0.046 2405 Dihedral : 5.308 56.073 1909 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.24 % Favored : 93.52 % Rotamer: Outliers : 6.08 % Allowed : 26.06 % Favored : 67.86 % 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: -0.74 (0.21), residues: 1714 helix: 0.92 (0.31), residues: 291 sheet: 0.24 (0.21), residues: 620 loop : -1.64 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 36 HIS 0.003 0.001 HIS B 753 PHE 0.021 0.002 PHE C 68 TYR 0.036 0.001 TYR C 32 ARG 0.003 0.000 ARG B1153 *********************** 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 260 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 168 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.6846 (m-10) REVERT: E 359 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8305 (p) REVERT: E 618 LYS cc_start: 0.5861 (mptt) cc_final: 0.5643 (mttt) REVERT: B 820 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6499 (t80) REVERT: B 859 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.6172 (mtp) REVERT: B 923 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7148 (tm) REVERT: B 986 GLU cc_start: 0.6136 (OUTLIER) cc_final: 0.5701 (mm-30) REVERT: B 1044 LYS cc_start: 0.6707 (ptmm) cc_final: 0.6217 (pttt) REVERT: B 1401 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7331 (ttm170) REVERT: C 32 TYR cc_start: 0.6896 (t80) cc_final: 0.6612 (t80) REVERT: C 104 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7082 (mm) outliers start: 92 outliers final: 73 residues processed: 237 average time/residue: 0.2438 time to fit residues: 86.8718 Evaluate side-chains 248 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 167 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 77 ASN 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 102 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 242 ASN 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 320 ASN 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 417 VAL Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 520 ASP 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 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 792 ASP 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 844 THR Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 909 ASN Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 936 ARG Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 986 GLU Chi-restraints excluded: chain B residue 987 ILE Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1161 LEU Chi-restraints excluded: chain B residue 1162 VAL 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 1271 ILE Chi-restraints excluded: chain B residue 1401 ARG Chi-restraints excluded: chain B residue 1446 VAL Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1457 ASP Chi-restraints excluded: chain B residue 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 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 149 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 138 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN E 446 ASN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13883 Z= 0.203 Angle : 0.604 11.729 18827 Z= 0.300 Chirality : 0.045 0.255 2133 Planarity : 0.004 0.045 2405 Dihedral : 5.043 56.209 1909 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.36 % Favored : 93.41 % Rotamer: Outliers : 5.69 % Allowed : 26.19 % Favored : 68.12 % 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: -0.60 (0.21), residues: 1714 helix: 1.06 (0.31), residues: 291 sheet: 0.24 (0.21), residues: 633 loop : -1.53 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 36 HIS 0.003 0.001 HIS B1421 PHE 0.020 0.001 PHE B1019 TYR 0.023 0.001 TYR C 32 ARG 0.003 0.000 ARG B1153 *********************** 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 258 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 172 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6898 (m-10) REVERT: E 359 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8231 (p) REVERT: B 820 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6547 (t80) REVERT: B 859 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.6330 (mtp) REVERT: B 923 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7073 (tm) REVERT: B 986 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5827 (mm-30) REVERT: B 1044 LYS cc_start: 0.6728 (ptmm) cc_final: 0.6245 (pttt) REVERT: B 1401 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7251 (ttm170) REVERT: C 104 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.7070 (mm) outliers start: 86 outliers final: 66 residues processed: 238 average time/residue: 0.2403 time to fit residues: 86.0037 Evaluate side-chains 237 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 163 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 77 ASN 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 102 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 242 ASN 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 359 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 516 GLU Chi-restraints excluded: chain E residue 520 ASP 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 B residue 748 GLN 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 792 ASP 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 844 THR Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 909 ASN Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 936 ARG Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 986 GLU Chi-restraints excluded: chain B residue 987 ILE Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1089 VAL 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 1267 VAL Chi-restraints excluded: chain B residue 1315 VAL Chi-restraints excluded: chain B residue 1401 ARG Chi-restraints excluded: chain B residue 1446 VAL Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1457 ASP Chi-restraints excluded: chain B residue 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 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 162 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 170 optimal weight: 0.4980 chunk 156 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 104 optimal weight: 0.0570 chunk 83 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN E 446 ASN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13883 Z= 0.259 Angle : 0.634 12.209 18827 Z= 0.317 Chirality : 0.046 0.258 2133 Planarity : 0.004 0.044 2405 Dihedral : 5.074 56.660 1909 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.42 % Favored : 93.35 % Rotamer: Outliers : 5.42 % Allowed : 26.26 % Favored : 68.32 % 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: -0.69 (0.21), residues: 1714 helix: 1.02 (0.31), residues: 291 sheet: 0.20 (0.21), residues: 633 loop : -1.60 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 36 HIS 0.003 0.001 HIS B 908 PHE 0.025 0.002 PHE B1019 TYR 0.031 0.002 TYR C 32 ARG 0.004 0.000 ARG B1153 ********************** 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 246 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 164 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6988 (m-10) REVERT: E 359 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8279 (p) REVERT: B 820 PHE cc_start: 0.7014 (OUTLIER) cc_final: 0.6577 (t80) REVERT: B 859 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6337 (mtp) REVERT: B 923 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7082 (tm) REVERT: B 986 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5842 (mm-30) REVERT: B 1401 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7351 (ttm170) REVERT: C 104 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7079 (mm) outliers start: 82 outliers final: 69 residues processed: 226 average time/residue: 0.2399 time to fit residues: 82.2573 Evaluate side-chains 240 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 163 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 77 ASN 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 102 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 242 ASN 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 359 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 516 GLU Chi-restraints excluded: chain E residue 520 ASP 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 630 SER Chi-restraints excluded: chain B residue 748 GLN Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 792 ASP 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 844 THR Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 909 ASN Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 936 ARG Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 986 GLU Chi-restraints excluded: chain B residue 987 ILE Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1161 LEU Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1212 LEU Chi-restraints excluded: chain B residue 1267 VAL Chi-restraints excluded: chain B residue 1271 ILE Chi-restraints excluded: chain B residue 1315 VAL Chi-restraints excluded: chain B residue 1401 ARG Chi-restraints excluded: chain B residue 1446 VAL Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1457 ASP Chi-restraints excluded: chain B residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 10.0000 chunk 41 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 446 ASN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.212229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.181054 restraints weight = 17745.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.180233 restraints weight = 21558.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.182032 restraints weight = 18571.847| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13883 Z= 0.212 Angle : 0.604 11.248 18827 Z= 0.300 Chirality : 0.045 0.246 2133 Planarity : 0.004 0.043 2405 Dihedral : 4.926 56.383 1909 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.13 % Favored : 93.64 % Rotamer: Outliers : 5.69 % Allowed : 26.06 % Favored : 68.25 % 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: -0.57 (0.21), residues: 1714 helix: 1.12 (0.31), residues: 292 sheet: 0.26 (0.21), residues: 631 loop : -1.51 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 36 HIS 0.003 0.001 HIS B1459 PHE 0.024 0.002 PHE B1019 TYR 0.016 0.001 TYR C 32 ARG 0.003 0.000 ARG B1153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2869.79 seconds wall clock time: 53 minutes 11.20 seconds (3191.20 seconds total)