Starting phenix.real_space_refine on Wed Feb 4 09:24:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qee_53058/02_2026/9qee_53058.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qee_53058/02_2026/9qee_53058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qee_53058/02_2026/9qee_53058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qee_53058/02_2026/9qee_53058.map" model { file = "/net/cci-nas-00/data/ceres_data/9qee_53058/02_2026/9qee_53058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qee_53058/02_2026/9qee_53058.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 40 5.49 5 S 39 5.16 5 C 6135 2.51 5 N 1685 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9789 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1568 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 11, 'TRANS': 185} Chain: "C" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 976 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "U" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 409 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "V" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 546 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 5, 'TRANS': 64} Chain breaks: 1 Chain: "A" Number of atoms: 5877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5877 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 36, 'TRANS': 695} Chain breaks: 4 Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.92, per 1000 atoms: 0.20 Number of scatterers: 9789 At special positions: 0 Unit cell: (107.433, 108.575, 126.862, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 39 16.00 P 40 15.00 O 1888 8.00 N 1685 7.00 C 6135 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 458.3 milliseconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 55.5% alpha, 12.9% beta 19 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'B' and resid 105 through 108 removed outlier: 4.055A pdb=" N ARG B 108 " --> pdb=" O PRO B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 105 through 108' Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.793A pdb=" N VAL B 116 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 149 Processing helix chain 'B' and resid 151 through 161 removed outlier: 4.285A pdb=" N GLY B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 219 through 223 removed outlier: 4.317A pdb=" N LEU B 222 " --> pdb=" O PRO B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 239 Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'B' and resid 259 through 266 removed outlier: 3.765A pdb=" N LEU B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 274 removed outlier: 4.183A pdb=" N CYS B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 290 Processing helix chain 'C' and resid 34 through 37 Processing helix chain 'C' and resid 38 through 45 removed outlier: 3.970A pdb=" N CYS C 42 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 removed outlier: 3.691A pdb=" N ILE C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU C 57 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 474 removed outlier: 3.689A pdb=" N VAL D 473 " --> pdb=" O PRO D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 491 Processing helix chain 'D' and resid 506 through 511 removed outlier: 3.606A pdb=" N LYS D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'A' and resid 18 through 29 removed outlier: 3.995A pdb=" N LEU A 22 " --> pdb=" O TYR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 52 removed outlier: 3.879A pdb=" N LEU A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 80 Processing helix chain 'A' and resid 93 through 104 removed outlier: 4.000A pdb=" N TYR A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLU A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.673A pdb=" N LEU A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.642A pdb=" N PHE A 171 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 185 Processing helix chain 'A' and resid 197 through 205 Processing helix chain 'A' and resid 219 through 244 removed outlier: 3.543A pdb=" N ASN A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 261 through 271 removed outlier: 3.681A pdb=" N THR A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 271 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 4.255A pdb=" N HIS A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN A 276 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 276' Processing helix chain 'A' and resid 279 through 282 Processing helix chain 'A' and resid 283 through 301 Processing helix chain 'A' and resid 302 through 320 removed outlier: 3.666A pdb=" N PHE A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 343 Processing helix chain 'A' and resid 378 through 398 removed outlier: 4.200A pdb=" N GLU A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 427 through 440 removed outlier: 3.511A pdb=" N PHE A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 565 through 573 Processing helix chain 'A' and resid 584 through 597 Processing helix chain 'A' and resid 613 through 642 removed outlier: 3.585A pdb=" N GLN A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 691 No H-bonds generated for 'chain 'A' and resid 689 through 691' Processing helix chain 'A' and resid 694 through 703 removed outlier: 3.751A pdb=" N ARG A 702 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A 703 " --> pdb=" O ILE A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 739 Processing helix chain 'A' and resid 739 through 752 removed outlier: 3.981A pdb=" N SER A 743 " --> pdb=" O GLY A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 795 Processing helix chain 'A' and resid 805 through 816 removed outlier: 3.669A pdb=" N GLU A 811 " --> pdb=" O HIS A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 855 removed outlier: 3.733A pdb=" N LYS A 854 " --> pdb=" O ASP A 850 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A 855 " --> pdb=" O PHE A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 870 removed outlier: 3.548A pdb=" N LEU A 866 " --> pdb=" O ASN A 862 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 879 removed outlier: 3.527A pdb=" N LEU A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 889 Processing helix chain 'A' and resid 890 through 903 Processing sheet with id=AA1, first strand: chain 'B' and resid 121 through 123 removed outlier: 5.587A pdb=" N ILE B 101 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 102 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 131 " --> pdb=" O ILE B 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 136 through 137 Processing sheet with id=AA3, first strand: chain 'B' and resid 140 through 142 removed outlier: 6.797A pdb=" N LEU B 141 " --> pdb=" O GLN B 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.638A pdb=" N ALA C 87 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 119 " --> pdb=" O GLN C 84 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP C 112 " --> pdb=" O ALA C 14 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU C 16 " --> pdb=" O ASP C 112 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE C 114 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS C 98 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 407 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N HIS A 555 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A 409 " --> pdb=" O HIS A 555 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLN A 406 " --> pdb=" O TYR A 577 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL A 579 " --> pdb=" O GLN A 406 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU A 408 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 90 through 91 removed outlier: 7.548A pdb=" N ASP C 112 " --> pdb=" O ALA C 14 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU C 16 " --> pdb=" O ASP C 112 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE C 114 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY A 545 " --> pdb=" O LYS C 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 88 removed outlier: 6.929A pdb=" N ARG A 86 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 59 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA A 109 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL A 61 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU A 58 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N LEU A 132 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU A 60 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY A 31 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU A 32 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N TRP A 193 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL A 34 " --> pdb=" O TRP A 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 344 through 345 removed outlier: 3.770A pdb=" N GLU A 372 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 705 through 709 removed outlier: 6.893A pdb=" N ILE A 684 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL A 709 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL A 686 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 9.972A pdb=" N SER A 683 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N THR A 719 " --> pdb=" O SER A 683 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 685 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 718 " --> pdb=" O MET A 722 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N CYS A 723 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU A 758 " --> pdb=" O CYS A 723 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A 725 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N GLU A 760 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS A 727 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 799 " --> pdb=" O PRO A 755 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2200 1.33 - 1.45: 2163 1.45 - 1.57: 5570 1.57 - 1.69: 79 1.69 - 1.81: 53 Bond restraints: 10065 Sorted by residual: bond pdb=" CA GLU A 721 " pdb=" CB GLU A 721 " ideal model delta sigma weight residual 1.531 1.603 -0.072 3.12e-02 1.03e+03 5.37e+00 bond pdb=" C ARG B 167 " pdb=" N VAL B 168 " ideal model delta sigma weight residual 1.335 1.308 0.027 1.41e-02 5.03e+03 3.73e+00 bond pdb=" CG1 ILE A 290 " pdb=" CD1 ILE A 290 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.15e+00 bond pdb=" CB VAL A 200 " pdb=" CG1 VAL A 200 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.97e+00 bond pdb=" C HIS B 149 " pdb=" O HIS B 149 " ideal model delta sigma weight residual 1.249 1.237 0.012 8.50e-03 1.38e+04 1.84e+00 ... (remaining 10060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 13290 1.57 - 3.14: 438 3.14 - 4.71: 55 4.71 - 6.28: 12 6.28 - 7.85: 6 Bond angle restraints: 13801 Sorted by residual: angle pdb=" C ARG A 342 " pdb=" N VAL A 343 " pdb=" CA VAL A 343 " ideal model delta sigma weight residual 122.97 119.09 3.88 9.80e-01 1.04e+00 1.57e+01 angle pdb=" CA GLN C 62 " pdb=" CB GLN C 62 " pdb=" CG GLN C 62 " ideal model delta sigma weight residual 114.10 121.95 -7.85 2.00e+00 2.50e-01 1.54e+01 angle pdb=" N GLU A 399 " pdb=" CA GLU A 399 " pdb=" C GLU A 399 " ideal model delta sigma weight residual 114.56 110.28 4.28 1.27e+00 6.20e-01 1.14e+01 angle pdb=" C GLN C 103 " pdb=" N ASN C 104 " pdb=" CA ASN C 104 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" N LEU A 62 " pdb=" CA LEU A 62 " pdb=" C LEU A 62 " ideal model delta sigma weight residual 111.96 116.37 -4.41 1.41e+00 5.03e-01 9.78e+00 ... (remaining 13796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.74: 5380 28.74 - 57.48: 600 57.48 - 86.21: 46 86.21 - 114.95: 6 114.95 - 143.69: 1 Dihedral angle restraints: 6033 sinusoidal: 2738 harmonic: 3295 Sorted by residual: dihedral pdb=" CA THR A 165 " pdb=" C THR A 165 " pdb=" N ASP A 166 " pdb=" CA ASP A 166 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ASP A 166 " pdb=" C ASP A 166 " pdb=" N ASN A 167 " pdb=" CA ASN A 167 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" C4' DT U 22 " pdb=" C3' DT U 22 " pdb=" O3' DT U 22 " pdb=" P DA U 23 " ideal model delta sinusoidal sigma weight residual 220.00 76.31 143.69 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 6030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 881 0.031 - 0.061: 496 0.061 - 0.092: 125 0.092 - 0.122: 68 0.122 - 0.153: 17 Chirality restraints: 1587 Sorted by residual: chirality pdb=" CA ASN C 104 " pdb=" N ASN C 104 " pdb=" C ASN C 104 " pdb=" CB ASN C 104 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE C 85 " pdb=" N ILE C 85 " pdb=" C ILE C 85 " pdb=" CB ILE C 85 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA LEU A 62 " pdb=" N LEU A 62 " pdb=" C LEU A 62 " pdb=" CB LEU A 62 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.34e-01 ... (remaining 1584 not shown) Planarity restraints: 1619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 129 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.52e+00 pdb=" CG ASP B 129 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP B 129 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 129 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 110 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO C 111 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 111 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 111 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 719 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO A 720 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 720 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 720 " 0.025 5.00e-02 4.00e+02 ... (remaining 1616 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 85 2.58 - 3.16: 7976 3.16 - 3.74: 14780 3.74 - 4.32: 19945 4.32 - 4.90: 33065 Nonbonded interactions: 75851 Sorted by model distance: nonbonded pdb=" OP1 DA U 27 " pdb="MN MN U 101 " model vdw 2.000 2.320 nonbonded pdb=" OG1 THR A 165 " pdb=" O ASP A 166 " model vdw 2.180 3.040 nonbonded pdb=" O ARG C 100 " pdb=" N ASN C 104 " model vdw 2.225 3.120 nonbonded pdb=" O PRO D 504 " pdb=" NH2 ARG A 604 " model vdw 2.237 3.120 nonbonded pdb=" OD1 ASP A 413 " pdb=" N ASP A 414 " model vdw 2.243 3.120 ... (remaining 75846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.670 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 10065 Z= 0.259 Angle : 0.680 7.847 13801 Z= 0.367 Chirality : 0.043 0.153 1587 Planarity : 0.005 0.053 1619 Dihedral : 20.907 143.690 3885 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.50 % Allowed : 28.49 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.25), residues: 1102 helix: 0.42 (0.22), residues: 564 sheet: -1.27 (0.41), residues: 155 loop : -1.64 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 234 TYR 0.021 0.002 TYR C 88 PHE 0.021 0.002 PHE A 186 TRP 0.012 0.002 TRP A 274 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00624 (10065) covalent geometry : angle 0.67999 (13801) hydrogen bonds : bond 0.15408 ( 469) hydrogen bonds : angle 5.94738 ( 1301) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.263 Fit side-chains REVERT: B 224 MET cc_start: 0.8166 (mmm) cc_final: 0.7795 (mmm) REVERT: C 84 GLN cc_start: 0.7901 (tp40) cc_final: 0.7547 (tp40) outliers start: 5 outliers final: 2 residues processed: 114 average time/residue: 0.1048 time to fit residues: 16.4363 Evaluate side-chains 104 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 246 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN C 67 ASN D 474 GLN A 197 HIS A 201 ASN A 286 GLN A 700 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.145735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.109475 restraints weight = 15277.812| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.26 r_work: 0.3206 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10065 Z= 0.139 Angle : 0.557 6.856 13801 Z= 0.295 Chirality : 0.039 0.156 1587 Planarity : 0.004 0.045 1619 Dihedral : 17.993 146.087 1663 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.11 % Allowed : 25.38 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.27), residues: 1102 helix: 1.09 (0.23), residues: 566 sheet: -1.04 (0.43), residues: 152 loop : -1.30 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 702 TYR 0.010 0.001 TYR B 130 PHE 0.011 0.001 PHE A 186 TRP 0.006 0.001 TRP A 326 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00319 (10065) covalent geometry : angle 0.55710 (13801) hydrogen bonds : bond 0.04496 ( 469) hydrogen bonds : angle 4.22311 ( 1301) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.417 Fit side-chains REVERT: B 224 MET cc_start: 0.8181 (mmm) cc_final: 0.7904 (mmm) REVERT: C 71 THR cc_start: 0.8072 (t) cc_final: 0.7856 (m) REVERT: C 84 GLN cc_start: 0.8156 (tp40) cc_final: 0.7738 (tp40) REVERT: D 542 MET cc_start: 0.7544 (tpt) cc_final: 0.7317 (tpt) REVERT: A 392 GLU cc_start: 0.8286 (tp30) cc_final: 0.8044 (tm-30) REVERT: A 850 ASP cc_start: 0.8585 (t0) cc_final: 0.8339 (t70) outliers start: 31 outliers final: 18 residues processed: 137 average time/residue: 0.1145 time to fit residues: 21.7103 Evaluate side-chains 119 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 904 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 93 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 474 GLN A 890 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.145236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.108635 restraints weight = 15456.979| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.32 r_work: 0.3173 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10065 Z= 0.170 Angle : 0.581 8.035 13801 Z= 0.304 Chirality : 0.040 0.161 1587 Planarity : 0.004 0.057 1619 Dihedral : 17.950 144.870 1659 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.71 % Allowed : 25.78 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.26), residues: 1102 helix: 1.17 (0.23), residues: 566 sheet: -0.98 (0.43), residues: 152 loop : -1.33 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 52 TYR 0.013 0.001 TYR C 88 PHE 0.014 0.001 PHE A 186 TRP 0.006 0.001 TRP A 274 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00406 (10065) covalent geometry : angle 0.58095 (13801) hydrogen bonds : bond 0.04651 ( 469) hydrogen bonds : angle 4.08771 ( 1301) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 0.383 Fit side-chains REVERT: B 224 MET cc_start: 0.8259 (mmm) cc_final: 0.8048 (mmm) REVERT: C 5 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8090 (mttt) REVERT: C 50 ASP cc_start: 0.7422 (m-30) cc_final: 0.7132 (m-30) REVERT: C 84 GLN cc_start: 0.8119 (tp40) cc_final: 0.7711 (tp40) REVERT: A 392 GLU cc_start: 0.8330 (tp30) cc_final: 0.8101 (tm-30) REVERT: A 850 ASP cc_start: 0.8712 (t0) cc_final: 0.8476 (t70) REVERT: A 875 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7270 (mm-30) REVERT: A 897 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6454 (tt) outliers start: 37 outliers final: 31 residues processed: 137 average time/residue: 0.1044 time to fit residues: 20.1237 Evaluate side-chains 137 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 474 GLN Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 17 optimal weight: 0.0270 chunk 95 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN ** D 474 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 = 0.3894 r_free = 0.3894 target = 0.148341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112285 restraints weight = 15332.278| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.29 r_work: 0.3256 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10065 Z= 0.112 Angle : 0.529 7.613 13801 Z= 0.278 Chirality : 0.038 0.153 1587 Planarity : 0.004 0.047 1619 Dihedral : 17.576 145.869 1659 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.41 % Allowed : 26.18 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.26), residues: 1102 helix: 1.38 (0.23), residues: 566 sheet: -0.82 (0.43), residues: 154 loop : -1.24 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 234 TYR 0.017 0.001 TYR B 130 PHE 0.012 0.001 PHE A 607 TRP 0.007 0.001 TRP A 326 HIS 0.002 0.000 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00253 (10065) covalent geometry : angle 0.52924 (13801) hydrogen bonds : bond 0.03652 ( 469) hydrogen bonds : angle 3.88721 ( 1301) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.368 Fit side-chains REVERT: B 224 MET cc_start: 0.8207 (mmm) cc_final: 0.7960 (mmm) REVERT: C 47 GLU cc_start: 0.8071 (tp30) cc_final: 0.7860 (tp30) REVERT: C 50 ASP cc_start: 0.7403 (m-30) cc_final: 0.7120 (m-30) REVERT: C 55 GLU cc_start: 0.7128 (pt0) cc_final: 0.6229 (tm-30) REVERT: C 84 GLN cc_start: 0.8107 (tp40) cc_final: 0.7641 (tp40) REVERT: A 392 GLU cc_start: 0.8239 (tp30) cc_final: 0.8006 (tt0) REVERT: A 722 MET cc_start: 0.8703 (tpp) cc_final: 0.8205 (ttm) REVERT: A 850 ASP cc_start: 0.8651 (t0) cc_final: 0.8384 (t70) REVERT: A 867 MET cc_start: 0.8022 (mtm) cc_final: 0.7702 (mtm) REVERT: A 875 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7144 (mm-30) REVERT: A 897 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6322 (tt) outliers start: 34 outliers final: 25 residues processed: 132 average time/residue: 0.1018 time to fit residues: 19.1513 Evaluate side-chains 129 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 73 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 58 optimal weight: 0.0770 chunk 85 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 overall best weight: 2.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN D 482 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.145109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.108018 restraints weight = 15367.659| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.28 r_work: 0.3176 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10065 Z= 0.187 Angle : 0.583 7.818 13801 Z= 0.306 Chirality : 0.040 0.159 1587 Planarity : 0.004 0.061 1619 Dihedral : 17.679 147.366 1659 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.51 % Allowed : 25.48 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.26), residues: 1102 helix: 1.32 (0.23), residues: 565 sheet: -0.85 (0.43), residues: 152 loop : -1.35 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 234 TYR 0.017 0.002 TYR B 130 PHE 0.016 0.002 PHE A 160 TRP 0.007 0.001 TRP C 32 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00449 (10065) covalent geometry : angle 0.58319 (13801) hydrogen bonds : bond 0.04562 ( 469) hydrogen bonds : angle 3.93126 ( 1301) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 110 time to evaluate : 0.393 Fit side-chains REVERT: B 224 MET cc_start: 0.8240 (mmm) cc_final: 0.8035 (mmm) REVERT: C 5 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8109 (mttt) REVERT: C 50 ASP cc_start: 0.7420 (m-30) cc_final: 0.7080 (m-30) REVERT: C 84 GLN cc_start: 0.8172 (tp40) cc_final: 0.7684 (tp40) REVERT: A 121 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8431 (t0) REVERT: A 392 GLU cc_start: 0.8323 (tp30) cc_final: 0.8093 (tm-30) REVERT: A 722 MET cc_start: 0.8761 (tpp) cc_final: 0.8421 (ttm) REVERT: A 850 ASP cc_start: 0.8671 (t0) cc_final: 0.8410 (t70) REVERT: A 867 MET cc_start: 0.8062 (mtm) cc_final: 0.7733 (mtm) REVERT: A 897 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6411 (tt) outliers start: 45 outliers final: 37 residues processed: 148 average time/residue: 0.1029 time to fit residues: 21.4903 Evaluate side-chains 145 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 105 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 90 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 79 optimal weight: 0.0670 chunk 19 optimal weight: 0.0670 chunk 54 optimal weight: 0.9990 overall best weight: 0.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.148180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.112406 restraints weight = 15331.445| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.33 r_work: 0.3228 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10065 Z= 0.113 Angle : 0.529 7.901 13801 Z= 0.278 Chirality : 0.038 0.149 1587 Planarity : 0.004 0.051 1619 Dihedral : 17.366 146.707 1659 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.11 % Allowed : 25.88 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.26), residues: 1102 helix: 1.54 (0.23), residues: 561 sheet: -0.70 (0.43), residues: 154 loop : -1.18 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 234 TYR 0.027 0.001 TYR B 152 PHE 0.011 0.001 PHE A 607 TRP 0.010 0.001 TRP C 32 HIS 0.002 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00258 (10065) covalent geometry : angle 0.52870 (13801) hydrogen bonds : bond 0.03547 ( 469) hydrogen bonds : angle 3.79546 ( 1301) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 0.306 Fit side-chains REVERT: B 213 LYS cc_start: 0.7400 (tptt) cc_final: 0.7144 (tppt) REVERT: B 224 MET cc_start: 0.8218 (mmm) cc_final: 0.7777 (mmm) REVERT: C 5 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8023 (mttt) REVERT: C 50 ASP cc_start: 0.7448 (m-30) cc_final: 0.7102 (m-30) REVERT: C 55 GLU cc_start: 0.7061 (pt0) cc_final: 0.6168 (tm-30) REVERT: C 84 GLN cc_start: 0.8159 (tp40) cc_final: 0.7725 (tp40) REVERT: D 532 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7261 (mt-10) REVERT: A 392 GLU cc_start: 0.8324 (tp30) cc_final: 0.8089 (tm-30) REVERT: A 722 MET cc_start: 0.8714 (tpp) cc_final: 0.8272 (ttm) REVERT: A 850 ASP cc_start: 0.8642 (t0) cc_final: 0.8384 (t70) REVERT: A 867 MET cc_start: 0.8036 (mtm) cc_final: 0.7739 (mtm) REVERT: A 875 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7206 (mm-30) REVERT: A 897 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6387 (tt) outliers start: 41 outliers final: 28 residues processed: 138 average time/residue: 0.1055 time to fit residues: 20.4411 Evaluate side-chains 139 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.146853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.110477 restraints weight = 15254.162| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.20 r_work: 0.3245 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10065 Z= 0.128 Angle : 0.537 8.025 13801 Z= 0.282 Chirality : 0.038 0.155 1587 Planarity : 0.004 0.060 1619 Dihedral : 17.345 146.886 1659 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.81 % Allowed : 26.08 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.26), residues: 1102 helix: 1.59 (0.23), residues: 560 sheet: -0.68 (0.43), residues: 154 loop : -1.18 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 52 TYR 0.023 0.001 TYR B 152 PHE 0.011 0.001 PHE A 607 TRP 0.010 0.001 TRP C 32 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00300 (10065) covalent geometry : angle 0.53696 (13801) hydrogen bonds : bond 0.03715 ( 469) hydrogen bonds : angle 3.76427 ( 1301) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.254 Fit side-chains REVERT: B 213 LYS cc_start: 0.7457 (tptt) cc_final: 0.7202 (tppt) REVERT: B 224 MET cc_start: 0.8223 (mmm) cc_final: 0.7778 (mmm) REVERT: C 5 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8198 (mttt) REVERT: C 50 ASP cc_start: 0.7536 (m-30) cc_final: 0.7233 (m-30) REVERT: C 55 GLU cc_start: 0.7117 (pt0) cc_final: 0.6187 (tm-30) REVERT: C 84 GLN cc_start: 0.8268 (tp40) cc_final: 0.7806 (tp40) REVERT: D 532 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: A 392 GLU cc_start: 0.8525 (tp30) cc_final: 0.8210 (tm-30) REVERT: A 722 MET cc_start: 0.8872 (tpp) cc_final: 0.8445 (ttm) REVERT: A 850 ASP cc_start: 0.8749 (t0) cc_final: 0.8480 (t70) REVERT: A 867 MET cc_start: 0.8190 (mtm) cc_final: 0.7919 (mtm) REVERT: A 875 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7252 (mm-30) REVERT: A 897 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6441 (tt) outliers start: 38 outliers final: 32 residues processed: 139 average time/residue: 0.1034 time to fit residues: 20.0690 Evaluate side-chains 141 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 21 optimal weight: 0.0050 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.148993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.113243 restraints weight = 15176.178| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.26 r_work: 0.3258 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10065 Z= 0.109 Angle : 0.526 8.178 13801 Z= 0.276 Chirality : 0.038 0.154 1587 Planarity : 0.004 0.060 1619 Dihedral : 17.195 147.076 1659 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.81 % Allowed : 26.18 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.27), residues: 1102 helix: 1.68 (0.23), residues: 560 sheet: -0.57 (0.43), residues: 154 loop : -1.10 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 234 TYR 0.016 0.001 TYR B 145 PHE 0.011 0.001 PHE A 607 TRP 0.030 0.001 TRP C 32 HIS 0.002 0.000 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00251 (10065) covalent geometry : angle 0.52607 (13801) hydrogen bonds : bond 0.03253 ( 469) hydrogen bonds : angle 3.71507 ( 1301) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: B 213 LYS cc_start: 0.7284 (tptt) cc_final: 0.7040 (tppt) REVERT: B 224 MET cc_start: 0.8143 (mmm) cc_final: 0.7677 (mmm) REVERT: C 5 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8041 (mttt) REVERT: C 47 GLU cc_start: 0.8106 (tp30) cc_final: 0.7840 (tp30) REVERT: C 50 ASP cc_start: 0.7491 (m-30) cc_final: 0.7166 (m-30) REVERT: C 55 GLU cc_start: 0.7021 (pt0) cc_final: 0.6154 (tm-30) REVERT: C 84 GLN cc_start: 0.8013 (tp40) cc_final: 0.7582 (tp40) REVERT: D 532 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: A 328 PHE cc_start: 0.8144 (m-80) cc_final: 0.7927 (m-80) REVERT: A 392 GLU cc_start: 0.8339 (tp30) cc_final: 0.8037 (tm-30) REVERT: A 722 MET cc_start: 0.8695 (tpp) cc_final: 0.8196 (ttm) REVERT: A 850 ASP cc_start: 0.8643 (t0) cc_final: 0.8360 (t70) REVERT: A 867 MET cc_start: 0.8098 (mtm) cc_final: 0.7849 (mtm) REVERT: A 875 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: A 897 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6386 (tt) outliers start: 38 outliers final: 29 residues processed: 142 average time/residue: 0.0947 time to fit residues: 19.1330 Evaluate side-chains 140 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 22 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.148561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112465 restraints weight = 15313.886| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.24 r_work: 0.3251 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10065 Z= 0.114 Angle : 0.530 8.118 13801 Z= 0.278 Chirality : 0.038 0.157 1587 Planarity : 0.004 0.059 1619 Dihedral : 17.206 147.144 1659 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.81 % Allowed : 26.38 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.26), residues: 1102 helix: 1.66 (0.23), residues: 561 sheet: -0.55 (0.43), residues: 154 loop : -1.10 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 234 TYR 0.017 0.001 TYR B 152 PHE 0.011 0.001 PHE A 607 TRP 0.031 0.001 TRP C 32 HIS 0.002 0.000 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00265 (10065) covalent geometry : angle 0.53048 (13801) hydrogen bonds : bond 0.03337 ( 469) hydrogen bonds : angle 3.67833 ( 1301) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: B 213 LYS cc_start: 0.7291 (tptt) cc_final: 0.7047 (tppt) REVERT: B 224 MET cc_start: 0.8138 (mmm) cc_final: 0.7671 (mmm) REVERT: C 5 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8017 (mttt) REVERT: C 47 GLU cc_start: 0.8158 (tp30) cc_final: 0.7852 (tp30) REVERT: C 50 ASP cc_start: 0.7437 (m-30) cc_final: 0.7110 (m-30) REVERT: C 55 GLU cc_start: 0.7082 (pt0) cc_final: 0.6177 (tm-30) REVERT: C 84 GLN cc_start: 0.7998 (tp40) cc_final: 0.7682 (tp40) REVERT: D 532 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: A 121 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8299 (t0) REVERT: A 328 PHE cc_start: 0.7983 (m-80) cc_final: 0.7761 (m-80) REVERT: A 392 GLU cc_start: 0.8317 (tp30) cc_final: 0.8032 (tm-30) REVERT: A 722 MET cc_start: 0.8728 (tpp) cc_final: 0.8252 (ttm) REVERT: A 850 ASP cc_start: 0.8620 (t0) cc_final: 0.8334 (t70) REVERT: A 867 MET cc_start: 0.8058 (mtm) cc_final: 0.7810 (mtm) REVERT: A 875 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7137 (mm-30) REVERT: A 897 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6240 (tt) outliers start: 38 outliers final: 31 residues processed: 138 average time/residue: 0.1035 time to fit residues: 20.1955 Evaluate side-chains 142 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 897 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 114 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.146171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.110420 restraints weight = 15124.527| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.23 r_work: 0.3235 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10065 Z= 0.154 Angle : 0.574 8.072 13801 Z= 0.299 Chirality : 0.040 0.169 1587 Planarity : 0.004 0.062 1619 Dihedral : 17.424 147.764 1659 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.71 % Allowed : 26.68 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.26), residues: 1102 helix: 1.57 (0.23), residues: 561 sheet: -0.65 (0.43), residues: 154 loop : -1.13 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 234 TYR 0.017 0.001 TYR B 152 PHE 0.013 0.001 PHE A 186 TRP 0.027 0.002 TRP C 32 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00370 (10065) covalent geometry : angle 0.57354 (13801) hydrogen bonds : bond 0.04007 ( 469) hydrogen bonds : angle 3.75645 ( 1301) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 0.343 Fit side-chains REVERT: B 213 LYS cc_start: 0.7330 (tptt) cc_final: 0.7066 (tppt) REVERT: B 224 MET cc_start: 0.8224 (mmm) cc_final: 0.7823 (mmm) REVERT: C 5 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8090 (mttt) REVERT: C 47 GLU cc_start: 0.8170 (tp30) cc_final: 0.7880 (tp30) REVERT: C 50 ASP cc_start: 0.7411 (m-30) cc_final: 0.7025 (m-30) REVERT: C 84 GLN cc_start: 0.7985 (tp40) cc_final: 0.7536 (tp40) REVERT: D 532 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7158 (mt-10) REVERT: A 121 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8350 (t0) REVERT: A 392 GLU cc_start: 0.8365 (tp30) cc_final: 0.8107 (tm-30) REVERT: A 722 MET cc_start: 0.8677 (tpp) cc_final: 0.8328 (ttm) REVERT: A 850 ASP cc_start: 0.8648 (t0) cc_final: 0.8367 (t70) REVERT: A 867 MET cc_start: 0.8045 (mtm) cc_final: 0.7779 (mtm) REVERT: A 875 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7134 (mm-30) REVERT: A 897 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.6094 (tt) outliers start: 37 outliers final: 30 residues processed: 138 average time/residue: 0.0954 time to fit residues: 18.7527 Evaluate side-chains 142 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 22 optimal weight: 2.9990 chunk 94 optimal weight: 0.0670 chunk 86 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.147510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.111443 restraints weight = 15395.906| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.19 r_work: 0.3245 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10065 Z= 0.133 Angle : 0.554 8.058 13801 Z= 0.289 Chirality : 0.039 0.165 1587 Planarity : 0.004 0.061 1619 Dihedral : 17.371 147.248 1659 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.81 % Allowed : 26.58 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.26), residues: 1102 helix: 1.57 (0.23), residues: 561 sheet: -0.64 (0.43), residues: 154 loop : -1.09 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 234 TYR 0.010 0.001 TYR C 88 PHE 0.011 0.001 PHE A 160 TRP 0.027 0.001 TRP C 32 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00317 (10065) covalent geometry : angle 0.55355 (13801) hydrogen bonds : bond 0.03710 ( 469) hydrogen bonds : angle 3.73794 ( 1301) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2080.51 seconds wall clock time: 36 minutes 29.03 seconds (2189.03 seconds total)