Starting phenix.real_space_refine on Wed Sep 17 16:42:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o38_70072/09_2025/9o38_70072.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o38_70072/09_2025/9o38_70072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o38_70072/09_2025/9o38_70072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o38_70072/09_2025/9o38_70072.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o38_70072/09_2025/9o38_70072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o38_70072/09_2025/9o38_70072.map" } resolution = 3.0 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6294 2.51 5 N 1674 2.21 5 O 1784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9824 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1954 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Chain: "C" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 400 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "E" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "A" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2031 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 1 Chain: "F" Number of atoms: 1859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1859 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 17, 'TRANS': 225} Chain breaks: 1 Time building chain proxies: 2.43, per 1000 atoms: 0.25 Number of scatterers: 9824 At special positions: 0 Unit cell: (92.176, 97.937, 130.857, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1784 8.00 N 1674 7.00 C 6294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 365.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2354 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 53.1% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 7 through 35 removed outlier: 3.610A pdb=" N VAL B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 61 removed outlier: 3.695A pdb=" N ILE B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 106 removed outlier: 3.605A pdb=" N GLN B 102 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 105 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP B 106 " --> pdb=" O CYS B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 Processing helix chain 'B' and resid 149 through 160 Processing helix chain 'B' and resid 163 through 168 removed outlier: 4.276A pdb=" N TYR B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 172 removed outlier: 3.712A pdb=" N ALA B 172 " --> pdb=" O PRO B 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 169 through 172' Processing helix chain 'B' and resid 187 through 209 removed outlier: 4.124A pdb=" N ILE B 204 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 247 Processing helix chain 'C' and resid 3 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.594A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.739A pdb=" N ASN D 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.663A pdb=" N ASN E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'A' and resid 563 through 590 Processing helix chain 'A' and resid 593 through 600 Processing helix chain 'A' and resid 601 through 617 removed outlier: 3.537A pdb=" N PHE A 605 " --> pdb=" O GLY A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 622 removed outlier: 3.644A pdb=" N TYR A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 622 " --> pdb=" O VAL A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 622' Processing helix chain 'A' and resid 626 through 636 removed outlier: 4.018A pdb=" N GLN A 634 " --> pdb=" O CYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 660 Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 676 through 699 removed outlier: 3.782A pdb=" N MET A 682 " --> pdb=" O PRO A 678 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 683 " --> pdb=" O TYR A 679 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 747 removed outlier: 3.775A pdb=" N PHE A 730 " --> pdb=" O ASN A 726 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN A 731 " --> pdb=" O SER A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 750 No H-bonds generated for 'chain 'A' and resid 748 through 750' Processing helix chain 'A' and resid 758 through 782 removed outlier: 4.095A pdb=" N SER A 781 " --> pdb=" O CYS A 777 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 818 removed outlier: 4.670A pdb=" N TYR A 807 " --> pdb=" O ILE A 803 " (cutoff:3.500A) Proline residue: A 810 - end of helix Processing helix chain 'A' and resid 819 through 822 Processing helix chain 'A' and resid 823 through 836 Processing helix chain 'F' and resid 567 through 593 Processing helix chain 'F' and resid 596 through 602 Processing helix chain 'F' and resid 604 through 621 removed outlier: 3.545A pdb=" N CYS F 608 " --> pdb=" O GLY F 604 " (cutoff:3.500A) Processing helix chain 'F' and resid 622 through 624 No H-bonds generated for 'chain 'F' and resid 622 through 624' Processing helix chain 'F' and resid 629 through 663 removed outlier: 5.270A pdb=" N GLN F 637 " --> pdb=" O CYS F 633 " (cutoff:3.500A) Proline residue: F 638 - end of helix Proline residue: F 643 - end of helix Processing helix chain 'F' and resid 665 through 677 removed outlier: 4.220A pdb=" N ARG F 671 " --> pdb=" O SER F 667 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY F 674 " --> pdb=" O ASP F 670 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS F 675 " --> pdb=" O ARG F 671 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG F 677 " --> pdb=" O SER F 673 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 703 Processing helix chain 'F' and resid 728 through 749 removed outlier: 4.473A pdb=" N THR F 736 " --> pdb=" O LEU F 732 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN F 737 " --> pdb=" O ALA F 733 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 785 Proline residue: F 780 - end of helix Processing helix chain 'F' and resid 786 through 788 No H-bonds generated for 'chain 'F' and resid 786 through 788' Processing helix chain 'F' and resid 789 through 819 removed outlier: 4.828A pdb=" N LEU F 811 " --> pdb=" O ALA F 807 " (cutoff:3.500A) Proline residue: F 812 - end of helix removed outlier: 3.637A pdb=" N LEU F 816 " --> pdb=" O PRO F 812 " (cutoff:3.500A) Processing helix chain 'F' and resid 820 through 824 removed outlier: 3.994A pdb=" N LEU F 823 " --> pdb=" O GLN F 820 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN F 824 " --> pdb=" O PRO F 821 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 820 through 824' Processing helix chain 'F' and resid 825 through 830 Processing sheet with id=AA1, first strand: chain 'B' and resid 76 through 79 removed outlier: 8.952A pdb=" N ALA B 109 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG B 39 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE B 111 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 41 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL B 113 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU B 43 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ASP B 115 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE B 110 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N PHE B 146 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE B 112 " --> pdb=" O PHE B 146 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN B 148 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL B 114 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL B 143 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N HIS B 218 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 145 " --> pdb=" O HIS B 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.176A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.852A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN C 88 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 4.177A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 6.439A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.559A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.663A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.076A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.821A pdb=" N MET E 34 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3166 1.34 - 1.46: 2366 1.46 - 1.58: 4406 1.58 - 1.70: 0 1.70 - 1.81: 102 Bond restraints: 10040 Sorted by residual: bond pdb=" N LEU F 642 " pdb=" CA LEU F 642 " ideal model delta sigma weight residual 1.462 1.494 -0.033 9.50e-03 1.11e+04 1.20e+01 bond pdb=" N ASP B 179 " pdb=" CA ASP B 179 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.77e+00 bond pdb=" N HIS F 641 " pdb=" CA HIS F 641 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.27e+00 bond pdb=" N LEU F 639 " pdb=" CA LEU F 639 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.25e-02 6.40e+03 6.37e+00 bond pdb=" CA LEU F 642 " pdb=" C LEU F 642 " ideal model delta sigma weight residual 1.521 1.548 -0.027 1.17e-02 7.31e+03 5.21e+00 ... (remaining 10035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 13421 1.84 - 3.68: 171 3.68 - 5.53: 25 5.53 - 7.37: 8 7.37 - 9.21: 4 Bond angle restraints: 13629 Sorted by residual: angle pdb=" C LEU F 642 " pdb=" N PRO F 643 " pdb=" CA PRO F 643 " ideal model delta sigma weight residual 118.85 123.13 -4.28 1.09e+00 8.42e-01 1.54e+01 angle pdb=" CB MET C 325 " pdb=" CG MET C 325 " pdb=" SD MET C 325 " ideal model delta sigma weight residual 112.70 121.91 -9.21 3.00e+00 1.11e-01 9.43e+00 angle pdb=" N PRO F 638 " pdb=" CA PRO F 638 " pdb=" C PRO F 638 " ideal model delta sigma weight residual 113.75 109.70 4.05 1.49e+00 4.50e-01 7.39e+00 angle pdb=" CA LEU A 728 " pdb=" CB LEU A 728 " pdb=" CG LEU A 728 " ideal model delta sigma weight residual 116.30 125.23 -8.93 3.50e+00 8.16e-02 6.51e+00 angle pdb=" N LEU F 642 " pdb=" CA LEU F 642 " pdb=" C LEU F 642 " ideal model delta sigma weight residual 113.25 110.05 3.20 1.30e+00 5.92e-01 6.04e+00 ... (remaining 13624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 5010 17.19 - 34.38: 658 34.38 - 51.57: 245 51.57 - 68.77: 35 68.77 - 85.96: 10 Dihedral angle restraints: 5958 sinusoidal: 2312 harmonic: 3646 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual -86.00 -132.99 46.99 1 1.00e+01 1.00e-02 3.05e+01 dihedral pdb=" CA ASP C 76 " pdb=" CB ASP C 76 " pdb=" CG ASP C 76 " pdb=" OD1 ASP C 76 " ideal model delta sinusoidal sigma weight residual -30.00 -89.63 59.63 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CG ARG B 94 " pdb=" CD ARG B 94 " pdb=" NE ARG B 94 " pdb=" CZ ARG B 94 " ideal model delta sinusoidal sigma weight residual 180.00 135.01 44.99 2 1.50e+01 4.44e-03 1.07e+01 ... (remaining 5955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1172 0.043 - 0.086: 285 0.086 - 0.129: 97 0.129 - 0.172: 2 0.172 - 0.215: 2 Chirality restraints: 1558 Sorted by residual: chirality pdb=" CB ILE F 773 " pdb=" CA ILE F 773 " pdb=" CG1 ILE F 773 " pdb=" CG2 ILE F 773 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB VAL A 797 " pdb=" CA VAL A 797 " pdb=" CG1 VAL A 797 " pdb=" CG2 VAL A 797 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE A 695 " pdb=" CA ILE A 695 " pdb=" CG1 ILE A 695 " pdb=" CG2 ILE A 695 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1555 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 775 " 0.012 2.00e-02 2.50e+03 1.35e-02 4.54e+00 pdb=" CG TRP F 775 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP F 775 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP F 775 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 775 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 775 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 775 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 775 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 775 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP F 775 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER F 596 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO F 597 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO F 597 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 597 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 196 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" C THR C 196 " 0.027 2.00e-02 2.50e+03 pdb=" O THR C 196 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG C 197 " -0.009 2.00e-02 2.50e+03 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 14 2.63 - 3.20: 8704 3.20 - 3.76: 15489 3.76 - 4.33: 20813 4.33 - 4.90: 35147 Nonbonded interactions: 80167 Sorted by model distance: nonbonded pdb=" CG1 VAL A 627 " pdb=" CB ALA F 631 " model vdw 2.062 3.880 nonbonded pdb=" O LEU F 574 " pdb=" OG SER F 577 " model vdw 2.401 3.040 nonbonded pdb=" NE2 HIS C 225 " pdb=" OG1 THR C 243 " model vdw 2.428 3.120 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.554 3.040 nonbonded pdb=" C THR F 736 " pdb=" OG1 THR F 736 " model vdw 2.561 2.616 ... (remaining 80162 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: 5.720 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.040 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10042 Z= 0.153 Angle : 0.561 9.212 13633 Z= 0.291 Chirality : 0.041 0.215 1558 Planarity : 0.004 0.041 1728 Dihedral : 17.713 85.957 3598 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.44 % Allowed : 29.64 % Favored : 67.92 % 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 aren not related in a simple way. whole: 1.09 (0.24), residues: 1240 helix: 2.08 (0.22), residues: 584 sheet: -0.59 (0.35), residues: 216 loop : -0.36 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 19 TYR 0.013 0.001 TYR A 621 PHE 0.023 0.001 PHE A 761 TRP 0.037 0.001 TRP F 775 HIS 0.008 0.001 HIS F 734 Details of bonding type rmsd covalent geometry : bond 0.00298 (10040) covalent geometry : angle 0.56063 (13629) SS BOND : bond 0.00194 ( 2) SS BOND : angle 0.55855 ( 4) hydrogen bonds : bond 0.14424 ( 564) hydrogen bonds : angle 5.82996 ( 1635) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7766 (mm-40) outliers start: 26 outliers final: 6 residues processed: 221 average time/residue: 0.6801 time to fit residues: 159.5605 Evaluate side-chains 113 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.0970 chunk 97 optimal weight: 0.2980 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 636 GLN ** F 734 HIS ** 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 = 0.4141 r_free = 0.4141 target = 0.129292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.078517 restraints weight = 22333.664| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.88 r_work: 0.3050 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10042 Z= 0.158 Angle : 0.685 12.307 13633 Z= 0.331 Chirality : 0.043 0.161 1558 Planarity : 0.004 0.038 1728 Dihedral : 5.780 128.473 1375 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 6.47 % Allowed : 26.27 % Favored : 67.26 % 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 aren not related in a simple way. whole: 1.05 (0.24), residues: 1240 helix: 1.95 (0.21), residues: 581 sheet: -0.15 (0.35), residues: 208 loop : -0.50 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 837 TYR 0.024 0.001 TYR F 699 PHE 0.013 0.001 PHE C 199 TRP 0.014 0.001 TRP F 698 HIS 0.008 0.001 HIS F 592 Details of bonding type rmsd covalent geometry : bond 0.00355 (10040) covalent geometry : angle 0.68458 (13629) SS BOND : bond 0.00332 ( 2) SS BOND : angle 0.91116 ( 4) hydrogen bonds : bond 0.03971 ( 564) hydrogen bonds : angle 4.55907 ( 1635) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 127 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 MET cc_start: 0.8620 (ttt) cc_final: 0.8337 (tmm) REVERT: B 242 GLU cc_start: 0.9097 (tt0) cc_final: 0.8774 (tp30) REVERT: B 245 LYS cc_start: 0.9074 (mttp) cc_final: 0.8833 (mtmm) REVERT: C 3 GLU cc_start: 0.8568 (tp30) cc_final: 0.8297 (tp30) REVERT: C 172 GLU cc_start: 0.9207 (tp30) cc_final: 0.8954 (tp30) REVERT: C 215 GLU cc_start: 0.8896 (mp0) cc_final: 0.8611 (mp0) REVERT: C 217 MET cc_start: 0.8518 (pmm) cc_final: 0.8208 (pmt) REVERT: D 21 MET cc_start: 0.8696 (tpp) cc_final: 0.8187 (tmm) REVERT: D 42 GLU cc_start: 0.8879 (pp20) cc_final: 0.8650 (pp20) REVERT: D 47 GLU cc_start: 0.8366 (mp0) cc_final: 0.8102 (mp0) REVERT: E 89 GLU cc_start: 0.8900 (pm20) cc_final: 0.8689 (pm20) REVERT: E 105 ARG cc_start: 0.8185 (ttp-110) cc_final: 0.7586 (ptt180) REVERT: E 117 TYR cc_start: 0.8310 (m-80) cc_final: 0.7936 (m-80) REVERT: A 647 CYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7826 (p) REVERT: A 676 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7319 (mm-40) REVERT: A 682 MET cc_start: 0.7175 (mmp) cc_final: 0.6255 (ppp) REVERT: A 748 MET cc_start: 0.8849 (pmm) cc_final: 0.8424 (pmm) REVERT: F 583 VAL cc_start: 0.5742 (OUTLIER) cc_final: 0.5442 (t) REVERT: F 621 VAL cc_start: 0.7567 (OUTLIER) cc_final: 0.7244 (t) REVERT: F 649 SER cc_start: 0.6896 (OUTLIER) cc_final: 0.6545 (p) REVERT: F 689 MET cc_start: 0.7925 (mmm) cc_final: 0.7632 (mpm) REVERT: F 699 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.6007 (p90) REVERT: F 816 LEU cc_start: 0.3849 (OUTLIER) cc_final: 0.3638 (pt) outliers start: 69 outliers final: 17 residues processed: 183 average time/residue: 0.5662 time to fit residues: 111.6258 Evaluate side-chains 128 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 588 TRP Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 699 TYR Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 816 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 64 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 119 optimal weight: 40.0000 chunk 121 optimal weight: 30.0000 chunk 32 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS D 18 GLN E 1 GLN ** F 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 820 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.126391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.074900 restraints weight = 22343.072| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.86 r_work: 0.2977 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 10042 Z= 0.181 Angle : 0.660 10.565 13633 Z= 0.315 Chirality : 0.043 0.142 1558 Planarity : 0.004 0.033 1728 Dihedral : 4.385 53.934 1368 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.16 % Allowed : 26.92 % Favored : 67.92 % 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 aren not related in a simple way. whole: 1.18 (0.24), residues: 1240 helix: 2.05 (0.22), residues: 577 sheet: -0.08 (0.35), residues: 215 loop : -0.41 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 219 TYR 0.021 0.001 TYR F 699 PHE 0.015 0.001 PHE A 577 TRP 0.015 0.001 TRP F 698 HIS 0.010 0.001 HIS F 592 Details of bonding type rmsd covalent geometry : bond 0.00416 (10040) covalent geometry : angle 0.65944 (13629) SS BOND : bond 0.00442 ( 2) SS BOND : angle 1.15261 ( 4) hydrogen bonds : bond 0.03972 ( 564) hydrogen bonds : angle 4.40210 ( 1635) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 111 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: B 57 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8404 (tmm) REVERT: B 242 GLU cc_start: 0.9119 (tt0) cc_final: 0.8760 (tp30) REVERT: C 172 GLU cc_start: 0.9246 (tp30) cc_final: 0.8977 (tp30) REVERT: C 215 GLU cc_start: 0.8935 (mp0) cc_final: 0.8481 (mp0) REVERT: C 217 MET cc_start: 0.8596 (pmm) cc_final: 0.8291 (pmt) REVERT: D 42 GLU cc_start: 0.8863 (pp20) cc_final: 0.8586 (pp20) REVERT: E 12 VAL cc_start: 0.8611 (t) cc_final: 0.8350 (p) REVERT: E 43 LYS cc_start: 0.8875 (mmmm) cc_final: 0.8673 (mmmm) REVERT: E 89 GLU cc_start: 0.8786 (pm20) cc_final: 0.8491 (pm20) REVERT: E 105 ARG cc_start: 0.8220 (ttp-110) cc_final: 0.7596 (ptt180) REVERT: E 117 TYR cc_start: 0.8651 (m-80) cc_final: 0.8235 (m-80) REVERT: A 606 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6918 (pp) REVERT: A 676 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7399 (mm-40) REVERT: A 748 MET cc_start: 0.8691 (pmm) cc_final: 0.8281 (pmm) REVERT: A 776 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6798 (tm) REVERT: A 792 ASP cc_start: 0.8647 (m-30) cc_final: 0.8392 (t70) REVERT: F 621 VAL cc_start: 0.7939 (OUTLIER) cc_final: 0.7708 (t) REVERT: F 689 MET cc_start: 0.8349 (mmm) cc_final: 0.8077 (mpm) REVERT: F 699 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.6118 (p90) REVERT: F 775 TRP cc_start: 0.5469 (m100) cc_final: 0.5257 (m100) outliers start: 55 outliers final: 23 residues processed: 154 average time/residue: 0.5806 time to fit residues: 96.0031 Evaluate side-chains 131 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 588 TRP Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain F residue 593 HIS Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 699 TYR Chi-restraints excluded: chain F residue 825 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 118 optimal weight: 20.0000 chunk 14 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 734 HIS ** 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 = 0.4075 r_free = 0.4075 target = 0.125596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.074075 restraints weight = 22595.631| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.87 r_work: 0.2990 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10042 Z= 0.143 Angle : 0.643 11.353 13633 Z= 0.306 Chirality : 0.042 0.218 1558 Planarity : 0.004 0.035 1728 Dihedral : 4.324 56.738 1368 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.60 % Allowed : 27.77 % Favored : 67.64 % 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 aren not related in a simple way. whole: 1.28 (0.24), residues: 1240 helix: 2.16 (0.22), residues: 575 sheet: -0.01 (0.36), residues: 207 loop : -0.40 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 219 TYR 0.017 0.001 TYR F 699 PHE 0.014 0.001 PHE F 730 TRP 0.015 0.001 TRP F 698 HIS 0.010 0.001 HIS F 734 Details of bonding type rmsd covalent geometry : bond 0.00320 (10040) covalent geometry : angle 0.64252 (13629) SS BOND : bond 0.00225 ( 2) SS BOND : angle 0.91034 ( 4) hydrogen bonds : bond 0.03579 ( 564) hydrogen bonds : angle 4.24830 ( 1635) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 108 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8471 (tmm) REVERT: B 214 TYR cc_start: 0.8189 (t80) cc_final: 0.7830 (t80) REVERT: B 242 GLU cc_start: 0.9118 (tt0) cc_final: 0.8756 (tp30) REVERT: C 172 GLU cc_start: 0.9261 (tp30) cc_final: 0.8981 (tp30) REVERT: C 215 GLU cc_start: 0.8952 (mp0) cc_final: 0.8457 (mp0) REVERT: C 217 MET cc_start: 0.8643 (pmm) cc_final: 0.8329 (pmt) REVERT: C 339 TRP cc_start: 0.8477 (OUTLIER) cc_final: 0.7835 (m100) REVERT: D 11 GLN cc_start: 0.8942 (pp30) cc_final: 0.8710 (pp30) REVERT: D 21 MET cc_start: 0.8730 (tpp) cc_final: 0.8187 (tmm) REVERT: D 42 GLU cc_start: 0.8879 (pp20) cc_final: 0.8597 (pp20) REVERT: D 47 GLU cc_start: 0.8512 (mp0) cc_final: 0.8203 (mp0) REVERT: E 89 GLU cc_start: 0.8868 (pm20) cc_final: 0.8644 (pm20) REVERT: E 105 ARG cc_start: 0.8231 (ttp-110) cc_final: 0.7613 (ptt180) REVERT: A 676 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7449 (mm-40) REVERT: A 682 MET cc_start: 0.7152 (mmp) cc_final: 0.6197 (ppp) REVERT: A 748 MET cc_start: 0.8646 (pmm) cc_final: 0.8238 (pmm) REVERT: A 765 SER cc_start: 0.8303 (OUTLIER) cc_final: 0.7547 (m) REVERT: A 776 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6979 (tm) REVERT: A 792 ASP cc_start: 0.8789 (m-30) cc_final: 0.8561 (t70) REVERT: F 621 VAL cc_start: 0.8046 (OUTLIER) cc_final: 0.7839 (t) REVERT: F 637 GLN cc_start: 0.8192 (pm20) cc_final: 0.7771 (pm20) REVERT: F 689 MET cc_start: 0.8430 (mmm) cc_final: 0.8161 (mpm) REVERT: F 775 TRP cc_start: 0.5495 (m100) cc_final: 0.5087 (m100) outliers start: 49 outliers final: 24 residues processed: 151 average time/residue: 0.5497 time to fit residues: 89.2269 Evaluate side-chains 134 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 632 ARG Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 825 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 72 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 734 HIS ** 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 = 0.4051 r_free = 0.4051 target = 0.122837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.071495 restraints weight = 22192.556| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.80 r_work: 0.2905 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10042 Z= 0.215 Angle : 0.663 12.833 13633 Z= 0.323 Chirality : 0.043 0.218 1558 Planarity : 0.004 0.057 1728 Dihedral : 4.347 57.111 1367 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 5.25 % Allowed : 26.55 % Favored : 68.20 % 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 aren not related in a simple way. whole: 1.21 (0.24), residues: 1240 helix: 2.11 (0.22), residues: 576 sheet: -0.05 (0.36), residues: 214 loop : -0.44 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 633 TYR 0.018 0.001 TYR F 699 PHE 0.013 0.001 PHE C 235 TRP 0.024 0.001 TRP F 698 HIS 0.014 0.002 HIS F 734 Details of bonding type rmsd covalent geometry : bond 0.00493 (10040) covalent geometry : angle 0.66304 (13629) SS BOND : bond 0.00352 ( 2) SS BOND : angle 1.14666 ( 4) hydrogen bonds : bond 0.03741 ( 564) hydrogen bonds : angle 4.30291 ( 1635) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 113 time to evaluate : 0.368 Fit side-chains REVERT: B 214 TYR cc_start: 0.8240 (t80) cc_final: 0.7878 (t80) REVERT: B 242 GLU cc_start: 0.9143 (tt0) cc_final: 0.8810 (tp30) REVERT: C 10 GLU cc_start: 0.8556 (pt0) cc_final: 0.8330 (pt0) REVERT: C 172 GLU cc_start: 0.9293 (tp30) cc_final: 0.9020 (tp30) REVERT: C 215 GLU cc_start: 0.8880 (mp0) cc_final: 0.8350 (mp0) REVERT: C 217 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8312 (pmt) REVERT: D 21 MET cc_start: 0.8958 (tpp) cc_final: 0.8363 (tmm) REVERT: D 42 GLU cc_start: 0.8917 (pp20) cc_final: 0.8634 (pp20) REVERT: D 47 GLU cc_start: 0.8582 (mp0) cc_final: 0.8182 (mp0) REVERT: E 38 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.7648 (ptp90) REVERT: E 89 GLU cc_start: 0.8877 (pm20) cc_final: 0.8470 (pm20) REVERT: A 676 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7632 (mm-40) REVERT: A 682 MET cc_start: 0.7184 (mmp) cc_final: 0.6357 (ppp) REVERT: A 748 MET cc_start: 0.8696 (pmm) cc_final: 0.8343 (pmm) REVERT: A 776 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7303 (tm) REVERT: F 621 VAL cc_start: 0.8199 (OUTLIER) cc_final: 0.7976 (t) REVERT: F 637 GLN cc_start: 0.8350 (pm20) cc_final: 0.7933 (pm20) REVERT: F 689 MET cc_start: 0.8479 (mmm) cc_final: 0.8170 (mpm) outliers start: 56 outliers final: 28 residues processed: 159 average time/residue: 0.5563 time to fit residues: 95.3086 Evaluate side-chains 136 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 825 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 109 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 101 optimal weight: 40.0000 chunk 105 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 99 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 58 optimal weight: 0.4980 chunk 115 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 734 HIS ** 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 = 0.4027 r_free = 0.4027 target = 0.122181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.071091 restraints weight = 22299.009| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.69 r_work: 0.2930 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10042 Z= 0.182 Angle : 0.660 14.624 13633 Z= 0.318 Chirality : 0.043 0.216 1558 Planarity : 0.004 0.045 1728 Dihedral : 4.382 57.188 1367 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.22 % Allowed : 28.05 % Favored : 67.73 % 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 aren not related in a simple way. whole: 1.13 (0.24), residues: 1240 helix: 1.97 (0.22), residues: 588 sheet: -0.05 (0.36), residues: 204 loop : -0.47 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 105 TYR 0.020 0.001 TYR F 699 PHE 0.040 0.001 PHE A 641 TRP 0.026 0.001 TRP F 698 HIS 0.016 0.002 HIS F 734 Details of bonding type rmsd covalent geometry : bond 0.00422 (10040) covalent geometry : angle 0.65969 (13629) SS BOND : bond 0.00326 ( 2) SS BOND : angle 0.83258 ( 4) hydrogen bonds : bond 0.03637 ( 564) hydrogen bonds : angle 4.26300 ( 1635) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 105 time to evaluate : 0.358 Fit side-chains REVERT: B 214 TYR cc_start: 0.8242 (t80) cc_final: 0.7886 (t80) REVERT: C 10 GLU cc_start: 0.8593 (pt0) cc_final: 0.8369 (pt0) REVERT: C 172 GLU cc_start: 0.9286 (tp30) cc_final: 0.9011 (tp30) REVERT: C 215 GLU cc_start: 0.8933 (mp0) cc_final: 0.8393 (mp0) REVERT: C 217 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8365 (pmt) REVERT: D 21 MET cc_start: 0.9055 (tpp) cc_final: 0.8471 (tmm) REVERT: D 42 GLU cc_start: 0.8899 (pp20) cc_final: 0.8606 (pp20) REVERT: D 47 GLU cc_start: 0.8624 (mp0) cc_final: 0.8376 (mp0) REVERT: E 38 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.7661 (ptp90) REVERT: E 43 LYS cc_start: 0.8937 (mmmm) cc_final: 0.8629 (mmmm) REVERT: E 89 GLU cc_start: 0.9174 (pm20) cc_final: 0.8869 (pm20) REVERT: E 105 ARG cc_start: 0.8290 (ttp-110) cc_final: 0.7559 (ptt180) REVERT: A 646 SER cc_start: 0.8724 (m) cc_final: 0.8253 (p) REVERT: A 676 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7627 (mm-40) REVERT: A 748 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8282 (pmm) REVERT: F 637 GLN cc_start: 0.8494 (pm20) cc_final: 0.8147 (pm20) REVERT: F 689 MET cc_start: 0.8502 (mmm) cc_final: 0.8188 (mpm) outliers start: 45 outliers final: 23 residues processed: 142 average time/residue: 0.5311 time to fit residues: 81.3881 Evaluate side-chains 127 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 825 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 82 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 9 optimal weight: 0.0040 chunk 80 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 734 HIS ** 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 = 0.4033 r_free = 0.4033 target = 0.121545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.070516 restraints weight = 22142.363| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.74 r_work: 0.2892 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10042 Z= 0.192 Angle : 0.663 14.208 13633 Z= 0.319 Chirality : 0.043 0.218 1558 Planarity : 0.004 0.045 1728 Dihedral : 4.377 55.435 1367 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.85 % Allowed : 28.99 % Favored : 67.17 % 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 aren not related in a simple way. whole: 1.15 (0.24), residues: 1240 helix: 1.95 (0.22), residues: 586 sheet: -0.06 (0.34), residues: 223 loop : -0.37 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 105 TYR 0.021 0.001 TYR F 699 PHE 0.027 0.001 PHE A 770 TRP 0.031 0.001 TRP F 698 HIS 0.013 0.002 HIS F 592 Details of bonding type rmsd covalent geometry : bond 0.00445 (10040) covalent geometry : angle 0.66312 (13629) SS BOND : bond 0.00317 ( 2) SS BOND : angle 0.90397 ( 4) hydrogen bonds : bond 0.03626 ( 564) hydrogen bonds : angle 4.30422 ( 1635) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: B 214 TYR cc_start: 0.8231 (t80) cc_final: 0.7886 (t80) REVERT: C 10 GLU cc_start: 0.8537 (pt0) cc_final: 0.8333 (pm20) REVERT: C 172 GLU cc_start: 0.9297 (tp30) cc_final: 0.9030 (tp30) REVERT: C 215 GLU cc_start: 0.8927 (mp0) cc_final: 0.8380 (mp0) REVERT: C 217 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8383 (pmt) REVERT: D 21 MET cc_start: 0.9128 (tpp) cc_final: 0.8593 (tmm) REVERT: D 47 GLU cc_start: 0.8664 (mp0) cc_final: 0.8390 (mp0) REVERT: E 38 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.7536 (ptp90) REVERT: E 89 GLU cc_start: 0.9188 (pm20) cc_final: 0.8877 (pm20) REVERT: A 676 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7565 (mm-40) REVERT: A 682 MET cc_start: 0.7286 (mmp) cc_final: 0.6465 (ptm) REVERT: A 690 MET cc_start: 0.7685 (tpt) cc_final: 0.7419 (tpt) REVERT: A 748 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8330 (pmm) REVERT: A 836 MET cc_start: 0.8544 (ptp) cc_final: 0.8291 (pmm) REVERT: F 637 GLN cc_start: 0.8440 (pm20) cc_final: 0.8102 (pm20) REVERT: F 775 TRP cc_start: 0.5520 (m100) cc_final: 0.5011 (m-90) outliers start: 41 outliers final: 26 residues processed: 142 average time/residue: 0.5193 time to fit residues: 79.6683 Evaluate side-chains 131 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 825 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 101 optimal weight: 50.0000 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 0.0670 chunk 97 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 GLN ** A 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 734 HIS ** 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 = 0.4048 r_free = 0.4048 target = 0.122403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.071633 restraints weight = 22143.482| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.81 r_work: 0.2915 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10042 Z= 0.146 Angle : 0.676 16.998 13633 Z= 0.321 Chirality : 0.043 0.202 1558 Planarity : 0.004 0.052 1728 Dihedral : 4.349 57.483 1367 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.66 % Allowed : 29.55 % Favored : 66.79 % 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 aren not related in a simple way. whole: 1.04 (0.24), residues: 1240 helix: 1.84 (0.22), residues: 587 sheet: -0.08 (0.35), residues: 219 loop : -0.42 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 725 TYR 0.021 0.001 TYR F 699 PHE 0.025 0.001 PHE A 770 TRP 0.031 0.001 TRP F 698 HIS 0.013 0.002 HIS F 734 Details of bonding type rmsd covalent geometry : bond 0.00340 (10040) covalent geometry : angle 0.67637 (13629) SS BOND : bond 0.00200 ( 2) SS BOND : angle 0.56888 ( 4) hydrogen bonds : bond 0.03546 ( 564) hydrogen bonds : angle 4.23140 ( 1635) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: B 214 TYR cc_start: 0.8223 (t80) cc_final: 0.7853 (t80) REVERT: C 10 GLU cc_start: 0.8553 (pt0) cc_final: 0.8319 (pt0) REVERT: C 172 GLU cc_start: 0.9293 (tp30) cc_final: 0.9028 (tp30) REVERT: C 215 GLU cc_start: 0.8923 (mp0) cc_final: 0.8373 (mp0) REVERT: C 217 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8382 (pmt) REVERT: C 339 TRP cc_start: 0.8509 (OUTLIER) cc_final: 0.7901 (m100) REVERT: D 21 MET cc_start: 0.9150 (tpp) cc_final: 0.8608 (tmm) REVERT: D 47 GLU cc_start: 0.8631 (mp0) cc_final: 0.8336 (mp0) REVERT: E 43 LYS cc_start: 0.8925 (mmmm) cc_final: 0.8646 (mmmm) REVERT: E 89 GLU cc_start: 0.9197 (pm20) cc_final: 0.8878 (pm20) REVERT: A 676 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7620 (mm-40) REVERT: A 682 MET cc_start: 0.7191 (mmp) cc_final: 0.6511 (ptm) REVERT: A 690 MET cc_start: 0.7740 (tpt) cc_final: 0.7452 (tpt) REVERT: A 748 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8287 (pmm) REVERT: F 637 GLN cc_start: 0.8359 (pm20) cc_final: 0.8024 (pm20) REVERT: F 689 MET cc_start: 0.9359 (tpp) cc_final: 0.8865 (mmp) REVERT: F 775 TRP cc_start: 0.5502 (m100) cc_final: 0.4977 (m-90) outliers start: 39 outliers final: 21 residues processed: 141 average time/residue: 0.5649 time to fit residues: 85.8650 Evaluate side-chains 126 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 825 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 74 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 106 optimal weight: 50.0000 chunk 21 optimal weight: 0.0980 chunk 120 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 592 HIS ** F 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 734 HIS ** 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 = 0.4050 r_free = 0.4050 target = 0.122412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.071703 restraints weight = 21992.192| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.74 r_work: 0.2921 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10042 Z= 0.148 Angle : 0.678 15.288 13633 Z= 0.323 Chirality : 0.043 0.192 1558 Planarity : 0.004 0.050 1728 Dihedral : 4.281 54.070 1367 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.10 % Allowed : 30.49 % Favored : 66.42 % 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 aren not related in a simple way. whole: 1.04 (0.24), residues: 1240 helix: 1.77 (0.22), residues: 589 sheet: -0.06 (0.34), residues: 225 loop : -0.33 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 42 TYR 0.020 0.001 TYR F 699 PHE 0.027 0.001 PHE A 770 TRP 0.036 0.001 TRP F 698 HIS 0.012 0.002 HIS F 592 Details of bonding type rmsd covalent geometry : bond 0.00345 (10040) covalent geometry : angle 0.67764 (13629) SS BOND : bond 0.00222 ( 2) SS BOND : angle 0.57838 ( 4) hydrogen bonds : bond 0.03571 ( 564) hydrogen bonds : angle 4.22778 ( 1635) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: B 214 TYR cc_start: 0.8296 (t80) cc_final: 0.7929 (t80) REVERT: C 10 GLU cc_start: 0.8523 (pt0) cc_final: 0.8313 (pm20) REVERT: C 172 GLU cc_start: 0.9287 (tp30) cc_final: 0.9027 (tp30) REVERT: C 215 GLU cc_start: 0.8938 (mp0) cc_final: 0.8394 (mp0) REVERT: C 217 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8423 (pmt) REVERT: C 339 TRP cc_start: 0.8555 (OUTLIER) cc_final: 0.7985 (m100) REVERT: D 21 MET cc_start: 0.9192 (tpp) cc_final: 0.8667 (tmm) REVERT: D 47 GLU cc_start: 0.8678 (mp0) cc_final: 0.8380 (mp0) REVERT: E 43 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8638 (mmmm) REVERT: E 89 GLU cc_start: 0.9184 (pm20) cc_final: 0.8867 (pm20) REVERT: A 676 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7635 (mm-40) REVERT: A 690 MET cc_start: 0.7807 (tpt) cc_final: 0.7518 (tpt) REVERT: A 748 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8348 (pmm) REVERT: A 760 LYS cc_start: 0.6421 (OUTLIER) cc_final: 0.6010 (tttt) REVERT: A 793 LEU cc_start: 0.8374 (tt) cc_final: 0.8140 (tm) REVERT: F 637 GLN cc_start: 0.8390 (pm20) cc_final: 0.8055 (pm20) REVERT: F 689 MET cc_start: 0.9347 (tpp) cc_final: 0.8830 (mmp) REVERT: F 775 TRP cc_start: 0.5458 (m100) cc_final: 0.4919 (m-90) outliers start: 33 outliers final: 25 residues processed: 134 average time/residue: 0.5675 time to fit residues: 82.1886 Evaluate side-chains 130 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 825 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 33 optimal weight: 0.7980 chunk 98 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 592 HIS ** F 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 734 HIS ** 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 = 0.4041 r_free = 0.4041 target = 0.121786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.071116 restraints weight = 21825.867| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.80 r_work: 0.2906 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10042 Z= 0.161 Angle : 0.693 16.353 13633 Z= 0.331 Chirality : 0.043 0.188 1558 Planarity : 0.004 0.062 1728 Dihedral : 4.343 59.322 1367 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.19 % Allowed : 30.58 % Favored : 66.23 % 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 aren not related in a simple way. whole: 1.07 (0.24), residues: 1240 helix: 1.83 (0.22), residues: 588 sheet: -0.06 (0.34), residues: 225 loop : -0.36 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 42 TYR 0.020 0.001 TYR F 699 PHE 0.027 0.001 PHE A 770 TRP 0.038 0.001 TRP F 698 HIS 0.012 0.002 HIS F 592 Details of bonding type rmsd covalent geometry : bond 0.00376 (10040) covalent geometry : angle 0.69351 (13629) SS BOND : bond 0.00261 ( 2) SS BOND : angle 0.64370 ( 4) hydrogen bonds : bond 0.03522 ( 564) hydrogen bonds : angle 4.23162 ( 1635) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.425 Fit side-chains REVERT: B 214 TYR cc_start: 0.8257 (t80) cc_final: 0.7979 (t80) REVERT: C 10 GLU cc_start: 0.8550 (pt0) cc_final: 0.8320 (pt0) REVERT: C 172 GLU cc_start: 0.9290 (tp30) cc_final: 0.9026 (tp30) REVERT: C 215 GLU cc_start: 0.8926 (mp0) cc_final: 0.8373 (mp0) REVERT: C 217 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8397 (pmt) REVERT: D 21 MET cc_start: 0.9217 (tpp) cc_final: 0.8705 (tmm) REVERT: D 47 GLU cc_start: 0.8680 (mp0) cc_final: 0.8388 (mp0) REVERT: E 43 LYS cc_start: 0.8935 (mmmm) cc_final: 0.8639 (mmmm) REVERT: E 89 GLU cc_start: 0.9173 (pm20) cc_final: 0.8844 (pm20) REVERT: A 676 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7598 (mm-40) REVERT: A 682 MET cc_start: 0.7196 (mmp) cc_final: 0.6424 (ptm) REVERT: A 690 MET cc_start: 0.7816 (tpt) cc_final: 0.7540 (tpt) REVERT: A 748 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8325 (pmm) REVERT: F 689 MET cc_start: 0.9348 (tpp) cc_final: 0.8846 (mmp) REVERT: F 775 TRP cc_start: 0.5428 (m100) cc_final: 0.4880 (m-90) outliers start: 34 outliers final: 25 residues processed: 128 average time/residue: 0.5651 time to fit residues: 77.8918 Evaluate side-chains 125 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 825 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 79 optimal weight: 0.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 592 HIS ** F 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 734 HIS ** 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 = 0.4040 r_free = 0.4040 target = 0.122031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.071101 restraints weight = 22189.020| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.77 r_work: 0.2914 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10042 Z= 0.143 Angle : 0.683 12.043 13633 Z= 0.327 Chirality : 0.042 0.160 1558 Planarity : 0.004 0.055 1728 Dihedral : 4.323 57.351 1367 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.81 % Allowed : 30.68 % Favored : 66.51 % 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 aren not related in a simple way. whole: 1.04 (0.24), residues: 1240 helix: 1.79 (0.22), residues: 588 sheet: -0.05 (0.34), residues: 225 loop : -0.37 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 42 TYR 0.020 0.001 TYR F 699 PHE 0.026 0.001 PHE A 770 TRP 0.037 0.001 TRP F 698 HIS 0.012 0.002 HIS F 592 Details of bonding type rmsd covalent geometry : bond 0.00330 (10040) covalent geometry : angle 0.68296 (13629) SS BOND : bond 0.00223 ( 2) SS BOND : angle 0.52040 ( 4) hydrogen bonds : bond 0.03489 ( 564) hydrogen bonds : angle 4.19629 ( 1635) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4687.24 seconds wall clock time: 80 minutes 34.36 seconds (4834.36 seconds total)