Starting phenix.real_space_refine on Wed Mar 4 02:25:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bzf_30252/03_2026/7bzf_30252.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bzf_30252/03_2026/7bzf_30252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bzf_30252/03_2026/7bzf_30252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bzf_30252/03_2026/7bzf_30252.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bzf_30252/03_2026/7bzf_30252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bzf_30252/03_2026/7bzf_30252.map" } resolution = 3.26 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= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 19 5.49 5 S 70 5.16 5 C 6245 2.51 5 N 1669 2.21 5 O 1927 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9932 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7333 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 883} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 873 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 519 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "D" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 802 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 209 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "G" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 194 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2450 SG CYS A 301 79.275 41.008 52.381 1.00 28.24 S ATOM 2523 SG CYS A 310 76.742 41.105 49.964 1.00 25.23 S ATOM 3925 SG CYS A 487 89.052 47.626 68.104 1.00 30.40 S ATOM 5178 SG CYS A 645 90.808 48.944 65.420 1.00 35.57 S ATOM 5184 SG CYS A 646 90.164 45.454 65.537 1.00 35.17 S Time building chain proxies: 2.10, per 1000 atoms: 0.21 Number of scatterers: 9932 At special positions: 0 Unit cell: (104.14, 103.32, 124.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 70 16.00 P 19 15.00 O 1927 8.00 N 1669 7.00 C 6245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 420.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " Number of angles added : 3 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2302 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 43.8% alpha, 11.4% beta 9 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 removed outlier: 3.753A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 198 removed outlier: 3.684A pdb=" N ALA A 195 " --> pdb=" O GLN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.508A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.627A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 303 through 318 removed outlier: 4.070A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 removed outlier: 3.645A pdb=" N ASP A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.785A pdb=" N ASP A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA A 423 " --> pdb=" O PHE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.598A pdb=" N TYR A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.346A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.812A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.640A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 708 removed outlier: 3.915A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.921A pdb=" N ILE A 715 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 790 removed outlier: 4.126A pdb=" N SER A 784 " --> pdb=" O LYS A 780 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 843 Processing helix chain 'A' and resid 855 through 864 removed outlier: 3.899A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 862 " --> pdb=" O ARG A 858 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 863 " --> pdb=" O PHE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 874 through 896 removed outlier: 3.591A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 926 removed outlier: 3.924A pdb=" N TYR A 925 " --> pdb=" O GLU A 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.893A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.342A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.570A pdb=" N TYR B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.689A pdb=" N LEU B 180 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 26 through 41 Processing helix chain 'C' and resid 44 through 62 removed outlier: 4.047A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 94 Processing helix chain 'D' and resid 100 through 112 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 3.509A pdb=" N GLN A 57 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N PHE A 56 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER A 68 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLU A 58 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 66 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 38 removed outlier: 3.505A pdb=" N ILE A 37 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.282A pdb=" N PHE A 102 " --> pdb=" O HIS A 113 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS A 113 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 104 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 111 " --> pdb=" O PHE A 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.527A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.570A pdb=" N VAL A 342 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 3.554A pdb=" N MET A 542 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR B 187 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA B 191 " --> pdb=" O TRP B 154 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N TRP B 154 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 612 through 616 removed outlier: 3.525A pdb=" N PHE A 766 " --> pdb=" O HIS A 613 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 754 " --> pdb=" O CYS A 765 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 612 through 616 removed outlier: 3.525A pdb=" N PHE A 766 " --> pdb=" O HIS A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AB1, first strand: chain 'D' and resid 115 through 116 removed outlier: 3.597A pdb=" N THR D 187 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 142 through 143 379 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3113 1.34 - 1.46: 1710 1.46 - 1.57: 5220 1.57 - 1.69: 36 1.69 - 1.81: 105 Bond restraints: 10184 Sorted by residual: bond pdb=" C TRP B 182 " pdb=" N PRO B 183 " ideal model delta sigma weight residual 1.335 1.350 -0.015 8.70e-03 1.32e+04 3.10e+00 bond pdb=" CA SER A 709 " pdb=" C SER A 709 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.80e-02 3.09e+03 1.80e+00 bond pdb=" N ILE A 847 " pdb=" CA ILE A 847 " ideal model delta sigma weight residual 1.474 1.456 0.018 1.57e-02 4.06e+03 1.33e+00 bond pdb=" CA VAL A 844 " pdb=" CB VAL A 844 " ideal model delta sigma weight residual 1.550 1.539 0.012 1.03e-02 9.43e+03 1.28e+00 bond pdb=" CA VAL D 167 " pdb=" CB VAL D 167 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.05e-02 9.07e+03 1.24e+00 ... (remaining 10179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 13723 2.10 - 4.19: 172 4.19 - 6.29: 19 6.29 - 8.38: 1 8.38 - 10.48: 1 Bond angle restraints: 13916 Sorted by residual: angle pdb=" C LEU A 119 " pdb=" N THR A 120 " pdb=" CA THR A 120 " ideal model delta sigma weight residual 121.54 127.94 -6.40 1.91e+00 2.74e-01 1.12e+01 angle pdb=" C TYR A 787 " pdb=" N TYR A 788 " pdb=" CA TYR A 788 " ideal model delta sigma weight residual 122.26 117.24 5.02 1.73e+00 3.34e-01 8.43e+00 angle pdb=" C TRP A 916 " pdb=" N GLU A 917 " pdb=" CA GLU A 917 " ideal model delta sigma weight residual 121.95 132.43 -10.48 3.74e+00 7.15e-02 7.84e+00 angle pdb=" C ASP A 846 " pdb=" N ILE A 847 " pdb=" CA ILE A 847 " ideal model delta sigma weight residual 121.65 119.11 2.54 9.40e-01 1.13e+00 7.33e+00 angle pdb=" N ILE A 847 " pdb=" CA ILE A 847 " pdb=" C ILE A 847 " ideal model delta sigma weight residual 106.21 109.10 -2.89 1.07e+00 8.73e-01 7.30e+00 ... (remaining 13911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.37: 5848 28.37 - 56.73: 215 56.73 - 85.10: 33 85.10 - 113.46: 3 113.46 - 141.83: 1 Dihedral angle restraints: 6100 sinusoidal: 2541 harmonic: 3559 Sorted by residual: dihedral pdb=" CA ILE A 106 " pdb=" C ILE A 106 " pdb=" N ASP A 107 " pdb=" CA ASP A 107 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ASP A 107 " pdb=" C ASP A 107 " pdb=" N GLY A 108 " pdb=" CA GLY A 108 " ideal model delta harmonic sigma weight residual -180.00 -152.19 -27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ILE A 757 " pdb=" C ILE A 757 " pdb=" N LEU A 758 " pdb=" CA LEU A 758 " ideal model delta harmonic sigma weight residual 180.00 154.74 25.26 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 6097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1311 0.056 - 0.111: 263 0.111 - 0.167: 17 0.167 - 0.222: 1 0.222 - 0.278: 1 Chirality restraints: 1593 Sorted by residual: chirality pdb=" CB THR A 120 " pdb=" CA THR A 120 " pdb=" OG1 THR A 120 " pdb=" CG2 THR A 120 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C3' G F -3 " pdb=" C4' G F -3 " pdb=" O3' G F -3 " pdb=" C2' G F -3 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CA TRP D 182 " pdb=" N TRP D 182 " pdb=" C TRP D 182 " pdb=" CB TRP D 182 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.61e-01 ... (remaining 1590 not shown) Planarity restraints: 1712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 177 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.38e+00 pdb=" N PRO B 178 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 178 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 178 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 182 " 0.026 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO D 183 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 183 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 183 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G F -1 " -0.019 2.00e-02 2.50e+03 7.91e-03 1.88e+00 pdb=" N9 G F -1 " 0.018 2.00e-02 2.50e+03 pdb=" C8 G F -1 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G F -1 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G F -1 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G F -1 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G F -1 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G F -1 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G F -1 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G F -1 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G F -1 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G F -1 " 0.003 2.00e-02 2.50e+03 ... (remaining 1709 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 964 2.74 - 3.28: 10318 3.28 - 3.82: 16222 3.82 - 4.36: 20084 4.36 - 4.90: 33800 Nonbonded interactions: 81388 Sorted by model distance: nonbonded pdb=" OG SER A 239 " pdb=" OD1 ASP A 465 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR A 294 " pdb=" OD1 ASN A 314 " model vdw 2.233 3.040 nonbonded pdb=" OD2 ASP A 390 " pdb=" OH TYR A 674 " model vdw 2.237 3.040 nonbonded pdb=" OG SER A 433 " pdb=" O VAL A 435 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR A 420 " pdb=" OG SER C 4 " model vdw 2.259 3.040 ... (remaining 81383 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 84 through 122 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB )) or resid 128 through 188 or (resid 189 and (name N o \ r name CA or name C or name O or name CB )) or resid 190 through 191)) selection = (chain 'D' and (resid 84 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 191)) } 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: 1.750 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 11.540 Find NCS groups from input model: 0.080 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 : 0.012 0.692 10191 Z= 0.404 Angle : 0.726 28.251 13919 Z= 0.360 Chirality : 0.043 0.278 1593 Planarity : 0.003 0.039 1712 Dihedral : 15.055 141.826 3798 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.42 (0.19), residues: 1188 helix: -1.96 (0.19), residues: 500 sheet: -3.57 (0.36), residues: 133 loop : -3.74 (0.20), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 18 TYR 0.013 0.001 TYR A 921 PHE 0.015 0.001 PHE A 753 TRP 0.021 0.001 TRP D 182 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00344 (10184) covalent geometry : angle 0.61030 (13916) hydrogen bonds : bond 0.12949 ( 399) hydrogen bonds : angle 6.20992 ( 1111) metal coordination : bond 0.43123 ( 7) metal coordination : angle 26.81661 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 452 ASP cc_start: 0.7776 (t70) cc_final: 0.7492 (t70) REVERT: D 106 ILE cc_start: 0.5964 (mm) cc_final: 0.5570 (mt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1212 time to fit residues: 27.1439 Evaluate side-chains 120 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0000 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 81 GLN A 113 HIS A 133 HIS A 312 ASN A 356 ASN A 439 HIS A 572 HIS A 650 HIS A 789 GLN B 108 ASN B 168 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN D 104 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.159878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.135794 restraints weight = 15864.417| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.45 r_work: 0.3643 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10191 Z= 0.141 Angle : 0.594 7.482 13919 Z= 0.311 Chirality : 0.043 0.240 1593 Planarity : 0.004 0.060 1712 Dihedral : 12.114 146.561 1600 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 1.04 % Allowed : 11.97 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.22), residues: 1188 helix: -0.74 (0.22), residues: 491 sheet: -2.83 (0.40), residues: 127 loop : -3.16 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 331 TYR 0.015 0.001 TYR A 887 PHE 0.016 0.001 PHE A 741 TRP 0.013 0.001 TRP D 182 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00318 (10184) covalent geometry : angle 0.58760 (13916) hydrogen bonds : bond 0.03796 ( 399) hydrogen bonds : angle 5.05236 ( 1111) metal coordination : bond 0.01189 ( 7) metal coordination : angle 6.07816 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 197 ARG cc_start: 0.5727 (tpp-160) cc_final: 0.5477 (tpp-160) REVERT: A 331 ARG cc_start: 0.7513 (ttm-80) cc_final: 0.7268 (ttt-90) REVERT: A 452 ASP cc_start: 0.8474 (t70) cc_final: 0.8104 (t70) REVERT: A 500 LYS cc_start: 0.7575 (mmtt) cc_final: 0.7374 (mttm) REVERT: A 583 ARG cc_start: 0.8677 (mpt90) cc_final: 0.8398 (mmt180) REVERT: A 601 MET cc_start: 0.7596 (mtp) cc_final: 0.7386 (mtm) REVERT: A 818 MET cc_start: 0.8668 (ttp) cc_final: 0.8450 (ttt) REVERT: A 821 LYS cc_start: 0.8781 (tttm) cc_final: 0.8505 (tptp) REVERT: A 855 MET cc_start: 0.4940 (tpp) cc_final: 0.4542 (tpp) REVERT: A 919 GLU cc_start: 0.8074 (mp0) cc_final: 0.7787 (mp0) REVERT: D 94 MET cc_start: 0.6430 (mtt) cc_final: 0.6068 (mtp) REVERT: D 106 ILE cc_start: 0.5578 (mm) cc_final: 0.5220 (mt) outliers start: 11 outliers final: 8 residues processed: 144 average time/residue: 0.1022 time to fit residues: 20.6410 Evaluate side-chains 129 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain D residue 153 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 0.0870 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 HIS A 752 HIS C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.162486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.138129 restraints weight = 15854.718| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.47 r_work: 0.3676 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10191 Z= 0.113 Angle : 0.535 5.712 13919 Z= 0.282 Chirality : 0.041 0.237 1593 Planarity : 0.003 0.054 1712 Dihedral : 11.933 147.472 1600 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.61 % Allowed : 14.91 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.23), residues: 1188 helix: -0.08 (0.24), residues: 485 sheet: -2.12 (0.45), residues: 122 loop : -2.84 (0.22), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 132 TYR 0.014 0.001 TYR A 887 PHE 0.015 0.001 PHE A 741 TRP 0.011 0.001 TRP D 182 HIS 0.008 0.001 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00254 (10184) covalent geometry : angle 0.53175 (13916) hydrogen bonds : bond 0.03312 ( 399) hydrogen bonds : angle 4.72399 ( 1111) metal coordination : bond 0.00651 ( 7) metal coordination : angle 3.88140 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.305 Fit side-chains REVERT: A 160 LYS cc_start: 0.7699 (tppt) cc_final: 0.7096 (ptmt) REVERT: A 197 ARG cc_start: 0.5657 (tpp-160) cc_final: 0.5379 (tpp-160) REVERT: A 452 ASP cc_start: 0.8381 (t70) cc_final: 0.7987 (t70) REVERT: A 583 ARG cc_start: 0.8623 (mpt90) cc_final: 0.8324 (mmt180) REVERT: A 821 LYS cc_start: 0.8725 (tttm) cc_final: 0.8446 (tptp) REVERT: A 919 GLU cc_start: 0.8031 (mp0) cc_final: 0.7651 (mp0) REVERT: D 94 MET cc_start: 0.6245 (mtt) cc_final: 0.5916 (mtp) REVERT: D 106 ILE cc_start: 0.5501 (mm) cc_final: 0.5152 (mt) outliers start: 17 outliers final: 10 residues processed: 147 average time/residue: 0.1066 time to fit residues: 21.7905 Evaluate side-chains 132 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 164 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 1 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 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 = 0.4048 r_free = 0.4048 target = 0.161506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.137032 restraints weight = 15958.902| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.48 r_work: 0.3657 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10191 Z= 0.137 Angle : 0.549 5.704 13919 Z= 0.288 Chirality : 0.042 0.247 1593 Planarity : 0.003 0.049 1712 Dihedral : 11.819 145.735 1600 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.37 % Allowed : 15.10 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.24), residues: 1188 helix: 0.16 (0.24), residues: 486 sheet: -1.94 (0.46), residues: 123 loop : -2.60 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 80 TYR 0.013 0.001 TYR A 887 PHE 0.014 0.001 PHE A 741 TRP 0.009 0.001 TRP D 182 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00314 (10184) covalent geometry : angle 0.54633 (13916) hydrogen bonds : bond 0.03435 ( 399) hydrogen bonds : angle 4.65309 ( 1111) metal coordination : bond 0.00687 ( 7) metal coordination : angle 3.48572 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 102 PHE cc_start: 0.6541 (p90) cc_final: 0.6077 (p90) REVERT: A 197 ARG cc_start: 0.5670 (tpp-160) cc_final: 0.5365 (tpp-160) REVERT: A 452 ASP cc_start: 0.8392 (t70) cc_final: 0.8003 (t70) REVERT: A 583 ARG cc_start: 0.8638 (mpt90) cc_final: 0.8319 (mmt180) REVERT: A 880 VAL cc_start: 0.8190 (t) cc_final: 0.7904 (t) REVERT: A 919 GLU cc_start: 0.8037 (mp0) cc_final: 0.7632 (mp0) REVERT: B 80 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7668 (mtm-85) REVERT: D 94 MET cc_start: 0.6246 (mtt) cc_final: 0.5979 (mtp) REVERT: D 106 ILE cc_start: 0.5532 (mm) cc_final: 0.5162 (mt) outliers start: 25 outliers final: 18 residues processed: 139 average time/residue: 0.0995 time to fit residues: 19.6245 Evaluate side-chains 145 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 114 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 26 optimal weight: 0.0070 overall best weight: 1.3004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 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 = 0.4043 r_free = 0.4043 target = 0.161109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.136648 restraints weight = 15840.644| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.48 r_work: 0.3661 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10191 Z= 0.141 Angle : 0.553 6.865 13919 Z= 0.289 Chirality : 0.042 0.241 1593 Planarity : 0.003 0.046 1712 Dihedral : 11.751 145.182 1600 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.28 % Allowed : 16.62 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.24), residues: 1188 helix: 0.23 (0.24), residues: 486 sheet: -1.93 (0.46), residues: 128 loop : -2.48 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 331 TYR 0.013 0.001 TYR A 887 PHE 0.015 0.001 PHE A 741 TRP 0.008 0.001 TRP D 182 HIS 0.003 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00328 (10184) covalent geometry : angle 0.55079 (13916) hydrogen bonds : bond 0.03437 ( 399) hydrogen bonds : angle 4.64367 ( 1111) metal coordination : bond 0.00704 ( 7) metal coordination : angle 3.27757 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 102 PHE cc_start: 0.6594 (p90) cc_final: 0.6123 (p90) REVERT: A 144 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7283 (mt-10) REVERT: A 197 ARG cc_start: 0.5662 (tpp-160) cc_final: 0.5356 (tpp-160) REVERT: A 452 ASP cc_start: 0.8361 (t70) cc_final: 0.7989 (t70) REVERT: A 552 ASN cc_start: 0.7729 (p0) cc_final: 0.7266 (t0) REVERT: A 583 ARG cc_start: 0.8629 (mpt90) cc_final: 0.8330 (mmt180) REVERT: A 608 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7458 (m-30) REVERT: A 880 VAL cc_start: 0.8167 (t) cc_final: 0.7895 (t) REVERT: A 919 GLU cc_start: 0.7976 (mp0) cc_final: 0.7536 (mp0) REVERT: C 52 MET cc_start: 0.6958 (tpp) cc_final: 0.6747 (tpp) outliers start: 24 outliers final: 18 residues processed: 138 average time/residue: 0.1013 time to fit residues: 19.5320 Evaluate side-chains 137 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain D residue 114 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 99 optimal weight: 0.1980 chunk 115 optimal weight: 0.0980 chunk 116 optimal weight: 0.0000 chunk 83 optimal weight: 0.7980 chunk 7 optimal weight: 0.0770 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 105 optimal weight: 2.9990 overall best weight: 0.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 347 HIS ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.167334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.142828 restraints weight = 15825.469| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.51 r_work: 0.3722 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10191 Z= 0.095 Angle : 0.506 8.087 13919 Z= 0.264 Chirality : 0.040 0.216 1593 Planarity : 0.003 0.038 1712 Dihedral : 11.599 148.511 1600 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.90 % Allowed : 17.00 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.24), residues: 1188 helix: 0.62 (0.24), residues: 485 sheet: -1.99 (0.44), residues: 137 loop : -2.25 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 365 TYR 0.014 0.001 TYR A 887 PHE 0.015 0.001 PHE A 741 TRP 0.008 0.001 TRP C 29 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00202 (10184) covalent geometry : angle 0.50469 (13916) hydrogen bonds : bond 0.02779 ( 399) hydrogen bonds : angle 4.42569 ( 1111) metal coordination : bond 0.00528 ( 7) metal coordination : angle 2.25556 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 160 LYS cc_start: 0.7871 (tppt) cc_final: 0.7251 (ptmt) REVERT: A 452 ASP cc_start: 0.8322 (t70) cc_final: 0.7940 (t70) REVERT: A 546 TYR cc_start: 0.6100 (t80) cc_final: 0.5852 (t80) REVERT: A 552 ASN cc_start: 0.7691 (p0) cc_final: 0.7257 (t0) REVERT: A 583 ARG cc_start: 0.8530 (mpt90) cc_final: 0.8267 (mmt180) REVERT: A 665 GLU cc_start: 0.8213 (pm20) cc_final: 0.7062 (pm20) REVERT: A 805 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6946 (tp) REVERT: A 919 GLU cc_start: 0.7987 (mp0) cc_final: 0.7536 (mp0) REVERT: B 80 ARG cc_start: 0.8153 (mtp-110) cc_final: 0.7832 (ttm170) outliers start: 20 outliers final: 12 residues processed: 153 average time/residue: 0.0953 time to fit residues: 20.5760 Evaluate side-chains 139 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 164 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 8 optimal weight: 0.0980 chunk 24 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 116 optimal weight: 0.2980 chunk 84 optimal weight: 0.0000 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 177 ASN A 347 HIS B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.164430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.139727 restraints weight = 15799.800| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.50 r_work: 0.3686 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10191 Z= 0.115 Angle : 0.527 6.735 13919 Z= 0.275 Chirality : 0.041 0.235 1593 Planarity : 0.003 0.039 1712 Dihedral : 11.560 146.758 1600 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.99 % Allowed : 17.38 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.24), residues: 1188 helix: 0.57 (0.24), residues: 491 sheet: -1.56 (0.48), residues: 122 loop : -2.26 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.012 0.001 TYR A 87 PHE 0.019 0.001 PHE A 101 TRP 0.007 0.001 TRP D 182 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00263 (10184) covalent geometry : angle 0.52578 (13916) hydrogen bonds : bond 0.03048 ( 399) hydrogen bonds : angle 4.41142 ( 1111) metal coordination : bond 0.00494 ( 7) metal coordination : angle 2.59057 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 102 PHE cc_start: 0.6026 (p90) cc_final: 0.5569 (p90) REVERT: A 160 LYS cc_start: 0.7796 (tppt) cc_final: 0.7208 (ptmt) REVERT: A 452 ASP cc_start: 0.8353 (t70) cc_final: 0.7969 (t70) REVERT: A 546 TYR cc_start: 0.6477 (t80) cc_final: 0.6156 (t80) REVERT: A 552 ASN cc_start: 0.7563 (p0) cc_final: 0.7270 (t0) REVERT: A 583 ARG cc_start: 0.8546 (mpt90) cc_final: 0.8253 (mmt180) REVERT: A 665 GLU cc_start: 0.8260 (pm20) cc_final: 0.7104 (pm20) REVERT: A 807 LYS cc_start: 0.7333 (mmtt) cc_final: 0.7108 (mmtp) REVERT: A 880 VAL cc_start: 0.7972 (t) cc_final: 0.7756 (t) REVERT: A 919 GLU cc_start: 0.7978 (mp0) cc_final: 0.7531 (mp0) REVERT: B 80 ARG cc_start: 0.8155 (mtp-110) cc_final: 0.7802 (ttm170) outliers start: 21 outliers final: 17 residues processed: 138 average time/residue: 0.1011 time to fit residues: 19.6983 Evaluate side-chains 141 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 114 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 0.0010 chunk 68 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN ** C 36 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 = 0.4077 r_free = 0.4077 target = 0.163482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138154 restraints weight = 15941.346| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.57 r_work: 0.3672 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10191 Z= 0.116 Angle : 0.525 6.452 13919 Z= 0.273 Chirality : 0.041 0.232 1593 Planarity : 0.003 0.035 1712 Dihedral : 11.530 146.769 1600 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.61 % Allowed : 18.33 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.24), residues: 1188 helix: 0.64 (0.24), residues: 485 sheet: -1.67 (0.45), residues: 132 loop : -2.16 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 836 TYR 0.013 0.001 TYR A 87 PHE 0.014 0.001 PHE A 741 TRP 0.006 0.001 TRP D 182 HIS 0.003 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00264 (10184) covalent geometry : angle 0.52365 (13916) hydrogen bonds : bond 0.03109 ( 399) hydrogen bonds : angle 4.40680 ( 1111) metal coordination : bond 0.00482 ( 7) metal coordination : angle 2.48513 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.357 Fit side-chains REVERT: A 102 PHE cc_start: 0.6083 (p90) cc_final: 0.5755 (p90) REVERT: A 144 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7235 (mt-10) REVERT: A 331 ARG cc_start: 0.7819 (ttt-90) cc_final: 0.7589 (ttt-90) REVERT: A 418 ASP cc_start: 0.7408 (t0) cc_final: 0.6955 (t70) REVERT: A 452 ASP cc_start: 0.8340 (t70) cc_final: 0.7968 (t70) REVERT: A 546 TYR cc_start: 0.6731 (t80) cc_final: 0.6214 (t80) REVERT: A 552 ASN cc_start: 0.7721 (p0) cc_final: 0.7388 (t0) REVERT: A 583 ARG cc_start: 0.8549 (mpt90) cc_final: 0.8308 (mmt180) REVERT: A 665 GLU cc_start: 0.8235 (pm20) cc_final: 0.7146 (pm20) REVERT: A 880 VAL cc_start: 0.8013 (t) cc_final: 0.7798 (t) REVERT: A 919 GLU cc_start: 0.7923 (mp0) cc_final: 0.7509 (mp0) REVERT: B 80 ARG cc_start: 0.8031 (mtp-110) cc_final: 0.7720 (ttm170) outliers start: 17 outliers final: 17 residues processed: 145 average time/residue: 0.1010 time to fit residues: 20.4448 Evaluate side-chains 145 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 846 ASP Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 164 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 42 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 87 optimal weight: 0.0970 chunk 62 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 HIS ** C 36 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 = 0.4078 r_free = 0.4078 target = 0.163761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.138928 restraints weight = 15841.345| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.55 r_work: 0.3682 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10191 Z= 0.106 Angle : 0.534 8.325 13919 Z= 0.276 Chirality : 0.041 0.226 1593 Planarity : 0.003 0.033 1712 Dihedral : 11.498 147.658 1600 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.09 % Allowed : 18.33 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.24), residues: 1188 helix: 0.66 (0.24), residues: 490 sheet: -1.62 (0.45), residues: 132 loop : -2.13 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 836 TYR 0.012 0.001 TYR A 87 PHE 0.015 0.001 PHE A 741 TRP 0.007 0.001 TRP C 29 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00243 (10184) covalent geometry : angle 0.53337 (13916) hydrogen bonds : bond 0.03006 ( 399) hydrogen bonds : angle 4.35801 ( 1111) metal coordination : bond 0.00387 ( 7) metal coordination : angle 2.34965 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.394 Fit side-chains REVERT: A 102 PHE cc_start: 0.6027 (p90) cc_final: 0.5732 (p90) REVERT: A 144 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7129 (mt-10) REVERT: A 418 ASP cc_start: 0.7350 (t0) cc_final: 0.6912 (t70) REVERT: A 452 ASP cc_start: 0.8324 (t70) cc_final: 0.7957 (t70) REVERT: A 546 TYR cc_start: 0.6814 (t80) cc_final: 0.6301 (t80) REVERT: A 552 ASN cc_start: 0.7699 (p0) cc_final: 0.7413 (t0) REVERT: A 583 ARG cc_start: 0.8540 (mpt90) cc_final: 0.8329 (mmt180) REVERT: A 665 GLU cc_start: 0.8185 (pm20) cc_final: 0.7158 (pm20) REVERT: A 919 GLU cc_start: 0.7915 (mp0) cc_final: 0.7508 (mp0) REVERT: B 80 ARG cc_start: 0.7934 (mtp-110) cc_final: 0.7674 (ttm170) outliers start: 22 outliers final: 18 residues processed: 142 average time/residue: 0.0948 time to fit residues: 19.0554 Evaluate side-chains 147 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain D residue 114 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 109 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 HIS C 36 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.160911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136206 restraints weight = 15677.805| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.46 r_work: 0.3644 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10191 Z= 0.174 Angle : 0.598 8.522 13919 Z= 0.311 Chirality : 0.043 0.251 1593 Planarity : 0.003 0.034 1712 Dihedral : 11.626 144.592 1600 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.80 % Allowed : 18.71 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.24), residues: 1188 helix: 0.51 (0.24), residues: 485 sheet: -1.56 (0.47), residues: 122 loop : -2.18 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 836 TYR 0.016 0.002 TYR A 87 PHE 0.016 0.002 PHE A 101 TRP 0.010 0.001 TRP B 154 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00408 (10184) covalent geometry : angle 0.59675 (13916) hydrogen bonds : bond 0.03728 ( 399) hydrogen bonds : angle 4.58546 ( 1111) metal coordination : bond 0.00943 ( 7) metal coordination : angle 3.05101 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.351 Fit side-chains REVERT: A 102 PHE cc_start: 0.6381 (p90) cc_final: 0.5970 (p90) REVERT: A 418 ASP cc_start: 0.7565 (t0) cc_final: 0.7111 (t70) REVERT: A 452 ASP cc_start: 0.8341 (t70) cc_final: 0.7875 (t70) REVERT: A 552 ASN cc_start: 0.7808 (p0) cc_final: 0.7400 (t0) REVERT: A 662 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8350 (p) REVERT: A 665 GLU cc_start: 0.8299 (pm20) cc_final: 0.7180 (pm20) REVERT: A 756 MET cc_start: 0.8383 (tpp) cc_final: 0.8108 (tpp) REVERT: A 880 VAL cc_start: 0.8096 (t) cc_final: 0.7876 (t) REVERT: A 919 GLU cc_start: 0.7932 (mp0) cc_final: 0.7516 (mp0) REVERT: B 80 ARG cc_start: 0.8082 (mtp-110) cc_final: 0.7718 (ttm170) outliers start: 19 outliers final: 18 residues processed: 141 average time/residue: 0.0929 time to fit residues: 18.5653 Evaluate side-chains 149 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 114 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 117 optimal weight: 0.0670 chunk 72 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 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 = 0.4065 r_free = 0.4065 target = 0.163043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138399 restraints weight = 15836.608| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.49 r_work: 0.3674 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10191 Z= 0.125 Angle : 0.558 8.264 13919 Z= 0.290 Chirality : 0.042 0.233 1593 Planarity : 0.003 0.033 1712 Dihedral : 11.570 146.659 1600 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.99 % Allowed : 18.71 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.24), residues: 1188 helix: 0.60 (0.24), residues: 485 sheet: -1.68 (0.44), residues: 132 loop : -2.08 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 836 TYR 0.015 0.001 TYR A 453 PHE 0.016 0.001 PHE A 101 TRP 0.007 0.001 TRP C 29 HIS 0.003 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00287 (10184) covalent geometry : angle 0.55679 (13916) hydrogen bonds : bond 0.03281 ( 399) hydrogen bonds : angle 4.48752 ( 1111) metal coordination : bond 0.00502 ( 7) metal coordination : angle 2.63835 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2100.72 seconds wall clock time: 36 minutes 53.12 seconds (2213.12 seconds total)