Starting phenix.real_space_refine on Mon Jul 28 07:56:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bzf_30252/07_2025/7bzf_30252.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bzf_30252/07_2025/7bzf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7bzf_30252/07_2025/7bzf_30252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bzf_30252/07_2025/7bzf_30252.map" model { file = "/net/cci-nas-00/data/ceres_data/7bzf_30252/07_2025/7bzf_30252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bzf_30252/07_2025/7bzf_30252.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.059 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'PHE:plan': 1, 'GLU:plan': 1, 'TRP:plan': 1, 'ASP: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: 6.69, per 1000 atoms: 0.67 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: 2.66 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 3.46 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: 3.54 Time building geometry restraints manager: 3.19 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: 1.240 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.680 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.670 ------------------------------------------------------------------------------- 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 : 11.67 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.021 0.001 TRP D 182 HIS 0.005 0.001 HIS A 113 PHE 0.015 0.001 PHE A 753 TYR 0.013 0.001 TYR A 921 ARG 0.002 0.000 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.12949 ( 399) hydrogen bonds : angle 6.20992 ( 1111) metal coordination : bond 0.43123 ( 7) metal coordination : angle 26.81661 ( 3) covalent geometry : bond 0.00344 (10184) covalent geometry : angle 0.61030 (13916) *********************** 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 : 1.066 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: 0.2923 time to fit residues: 65.6864 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 : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 7.9990 chunk 90 optimal weight: 0.0010 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 0.0770 chunk 56 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.6146 ------------------------------------------------------------------------------- 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.161275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.137169 restraints weight = 15749.081| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.46 r_work: 0.3658 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10191 Z= 0.123 Angle : 0.576 7.727 13919 Z= 0.302 Chirality : 0.042 0.233 1593 Planarity : 0.004 0.059 1712 Dihedral : 12.117 147.759 1600 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.14 % Allowed : 11.40 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.22), residues: 1188 helix: -0.76 (0.22), residues: 503 sheet: -2.81 (0.40), residues: 127 loop : -3.16 (0.22), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 182 HIS 0.005 0.001 HIS A 295 PHE 0.016 0.001 PHE A 741 TYR 0.015 0.001 TYR A 887 ARG 0.005 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 399) hydrogen bonds : angle 5.00640 ( 1111) metal coordination : bond 0.01755 ( 7) metal coordination : angle 6.10142 ( 3) covalent geometry : bond 0.00270 (10184) covalent geometry : angle 0.56864 (13916) *********************** 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 152 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 197 ARG cc_start: 0.5741 (tpp-160) cc_final: 0.5487 (tpp-160) REVERT: A 452 ASP cc_start: 0.8451 (t70) cc_final: 0.8087 (t70) REVERT: A 583 ARG cc_start: 0.8652 (mpt90) cc_final: 0.8291 (mmt180) REVERT: A 818 MET cc_start: 0.8697 (ttp) cc_final: 0.8483 (ttt) REVERT: A 821 LYS cc_start: 0.8786 (tttm) cc_final: 0.8555 (tptp) REVERT: A 855 MET cc_start: 0.4947 (tpp) cc_final: 0.4543 (tpp) REVERT: A 919 GLU cc_start: 0.8066 (mp0) cc_final: 0.7775 (mp0) REVERT: D 94 MET cc_start: 0.6359 (mtt) cc_final: 0.6000 (mtp) REVERT: D 106 ILE cc_start: 0.5556 (mm) cc_final: 0.5209 (mt) outliers start: 12 outliers final: 9 residues processed: 145 average time/residue: 0.2574 time to fit residues: 53.2355 Evaluate side-chains 130 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 672 SER 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 65 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 82 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 572 HIS B 109 ASN C 31 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 = 0.4043 r_free = 0.4043 target = 0.161076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136686 restraints weight = 16016.519| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.47 r_work: 0.3652 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10191 Z= 0.134 Angle : 0.554 5.673 13919 Z= 0.292 Chirality : 0.042 0.243 1593 Planarity : 0.003 0.056 1712 Dihedral : 11.927 146.240 1600 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 1.71 % Allowed : 15.29 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.23), residues: 1188 helix: -0.11 (0.23), residues: 487 sheet: -2.20 (0.44), residues: 123 loop : -2.86 (0.22), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 182 HIS 0.005 0.001 HIS A 599 PHE 0.015 0.001 PHE A 741 TYR 0.014 0.001 TYR A 887 ARG 0.002 0.000 ARG A 33 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 399) hydrogen bonds : angle 4.77490 ( 1111) metal coordination : bond 0.00743 ( 7) metal coordination : angle 3.96643 ( 3) covalent geometry : bond 0.00307 (10184) covalent geometry : angle 0.55111 (13916) *********************** 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 150 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 1.504 Fit side-chains REVERT: A 102 PHE cc_start: 0.6606 (p90) cc_final: 0.6112 (p90) REVERT: A 160 LYS cc_start: 0.7792 (tppt) cc_final: 0.7183 (ptmt) REVERT: A 197 ARG cc_start: 0.5729 (tpp-160) cc_final: 0.5456 (tpp-160) REVERT: A 340 PHE cc_start: 0.8739 (m-80) cc_final: 0.8528 (m-10) REVERT: A 452 ASP cc_start: 0.8390 (t70) cc_final: 0.8011 (t70) REVERT: A 583 ARG cc_start: 0.8643 (mpt90) cc_final: 0.8419 (mmt180) REVERT: A 919 GLU cc_start: 0.8027 (mp0) cc_final: 0.7646 (mp0) REVERT: D 94 MET cc_start: 0.6309 (mtt) cc_final: 0.5972 (mtp) REVERT: D 106 ILE cc_start: 0.5527 (mm) cc_final: 0.5174 (mt) outliers start: 18 outliers final: 10 residues processed: 143 average time/residue: 0.2851 time to fit residues: 56.3309 Evaluate side-chains 133 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 1.645 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 80 optimal weight: 0.2980 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.162194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.137774 restraints weight = 15807.769| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.51 r_work: 0.3664 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1872 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= 0.122 Angle : 0.537 6.234 13919 Z= 0.283 Chirality : 0.041 0.237 1593 Planarity : 0.003 0.048 1712 Dihedral : 11.822 145.994 1600 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.99 % Allowed : 15.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.24), residues: 1188 helix: 0.16 (0.24), residues: 486 sheet: -1.98 (0.46), residues: 124 loop : -2.57 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 182 HIS 0.004 0.001 HIS A 309 PHE 0.015 0.001 PHE A 741 TYR 0.014 0.001 TYR A 887 ARG 0.005 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 399) hydrogen bonds : angle 4.65164 ( 1111) metal coordination : bond 0.00580 ( 7) metal coordination : angle 3.38066 ( 3) covalent geometry : bond 0.00278 (10184) covalent geometry : angle 0.53512 (13916) *********************** 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: 21 poor density : 128 time to evaluate : 1.229 Fit side-chains REVERT: A 102 PHE cc_start: 0.6481 (p90) cc_final: 0.6009 (p90) REVERT: A 197 ARG cc_start: 0.5629 (tpp-160) cc_final: 0.5339 (tpp-160) REVERT: A 391 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8209 (mmtm) REVERT: A 452 ASP cc_start: 0.8346 (t70) cc_final: 0.7958 (t70) REVERT: A 583 ARG cc_start: 0.8643 (mpt90) cc_final: 0.8340 (mmt180) REVERT: A 821 LYS cc_start: 0.8892 (tttm) cc_final: 0.8578 (tptp) REVERT: A 880 VAL cc_start: 0.8196 (t) cc_final: 0.7918 (t) REVERT: A 919 GLU cc_start: 0.8035 (mp0) cc_final: 0.7628 (mp0) REVERT: D 94 MET cc_start: 0.6263 (mtt) cc_final: 0.5989 (mtp) REVERT: D 106 ILE cc_start: 0.5541 (mm) cc_final: 0.5171 (mt) outliers start: 21 outliers final: 15 residues processed: 142 average time/residue: 0.3244 time to fit residues: 65.3864 Evaluate side-chains 141 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 15 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 0.0770 chunk 18 optimal weight: 0.9980 overall best weight: 1.4144 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.160783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136296 restraints weight = 15817.888| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.48 r_work: 0.3648 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10191 Z= 0.149 Angle : 0.564 6.796 13919 Z= 0.295 Chirality : 0.042 0.247 1593 Planarity : 0.003 0.044 1712 Dihedral : 11.775 144.415 1600 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.18 % Allowed : 16.90 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.24), residues: 1188 helix: 0.20 (0.24), residues: 486 sheet: -1.94 (0.47), residues: 128 loop : -2.44 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.003 0.001 HIS A 309 PHE 0.015 0.001 PHE A 741 TYR 0.016 0.002 TYR A 453 ARG 0.002 0.000 ARG A 33 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 399) hydrogen bonds : angle 4.66716 ( 1111) metal coordination : bond 0.00752 ( 7) metal coordination : angle 3.28712 ( 3) covalent geometry : bond 0.00347 (10184) covalent geometry : angle 0.56200 (13916) *********************** 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: 23 poor density : 126 time to evaluate : 1.312 Fit side-chains REVERT: A 102 PHE cc_start: 0.6603 (p90) cc_final: 0.6152 (p90) REVERT: A 144 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7286 (mt-10) REVERT: A 197 ARG cc_start: 0.5703 (tpp-160) cc_final: 0.5410 (tpp-160) REVERT: A 340 PHE cc_start: 0.8753 (m-10) cc_final: 0.8512 (m-10) REVERT: A 452 ASP cc_start: 0.8355 (t70) cc_final: 0.7977 (t70) REVERT: A 552 ASN cc_start: 0.7680 (p0) cc_final: 0.7209 (t0) REVERT: A 583 ARG cc_start: 0.8635 (mpt90) cc_final: 0.8339 (mmt180) REVERT: A 608 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7488 (m-30) REVERT: A 821 LYS cc_start: 0.8886 (tttm) cc_final: 0.8612 (tptp) REVERT: A 880 VAL cc_start: 0.8179 (t) cc_final: 0.7907 (t) REVERT: A 919 GLU cc_start: 0.7961 (mp0) cc_final: 0.7534 (mp0) outliers start: 23 outliers final: 19 residues processed: 138 average time/residue: 0.3585 time to fit residues: 70.1752 Evaluate side-chains 140 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 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 856 ILE Chi-restraints excluded: chain A residue 928 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 4 optimal weight: 0.0000 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.161037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.136592 restraints weight = 15858.411| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.48 r_work: 0.3648 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10191 Z= 0.144 Angle : 0.561 7.826 13919 Z= 0.292 Chirality : 0.042 0.243 1593 Planarity : 0.003 0.040 1712 Dihedral : 11.746 144.865 1600 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.56 % Allowed : 17.09 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.24), residues: 1188 helix: 0.20 (0.24), residues: 494 sheet: -1.96 (0.46), residues: 128 loop : -2.42 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.004 0.001 HIS A 82 PHE 0.015 0.001 PHE A 741 TYR 0.015 0.001 TYR A 286 ARG 0.004 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 399) hydrogen bonds : angle 4.64434 ( 1111) metal coordination : bond 0.00673 ( 7) metal coordination : angle 3.04503 ( 3) covalent geometry : bond 0.00332 (10184) covalent geometry : angle 0.55894 (13916) *********************** 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 156 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 1.058 Fit side-chains REVERT: A 102 PHE cc_start: 0.6660 (p90) cc_final: 0.6166 (p90) REVERT: A 144 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7296 (mt-10) REVERT: A 160 LYS cc_start: 0.7855 (tppt) cc_final: 0.7183 (ptmt) REVERT: A 197 ARG cc_start: 0.5712 (tpp-160) cc_final: 0.5425 (tpp-160) REVERT: A 340 PHE cc_start: 0.8739 (m-10) cc_final: 0.8484 (m-10) REVERT: A 452 ASP cc_start: 0.8329 (t70) cc_final: 0.7954 (t70) REVERT: A 546 TYR cc_start: 0.6684 (t80) cc_final: 0.6206 (t80) REVERT: A 552 ASN cc_start: 0.7718 (p0) cc_final: 0.7255 (t0) REVERT: A 583 ARG cc_start: 0.8631 (mpt90) cc_final: 0.8346 (mmt180) REVERT: A 608 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7500 (m-30) REVERT: A 665 GLU cc_start: 0.8310 (pm20) cc_final: 0.7177 (pm20) REVERT: A 821 LYS cc_start: 0.8875 (tttm) cc_final: 0.8578 (tptp) REVERT: A 855 MET cc_start: 0.5033 (tpp) cc_final: 0.4213 (tpp) REVERT: A 880 VAL cc_start: 0.8159 (t) cc_final: 0.7875 (t) REVERT: A 919 GLU cc_start: 0.7918 (mp0) cc_final: 0.7507 (mp0) outliers start: 27 outliers final: 20 residues processed: 143 average time/residue: 0.2368 time to fit residues: 47.9813 Evaluate side-chains 146 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 410 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 493 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 799 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 864 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 112 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 104 optimal weight: 0.0470 chunk 114 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.0040 chunk 103 optimal weight: 1.9990 overall best weight: 0.7694 ------------------------------------------------------------------------------- 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 A 752 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.163452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138858 restraints weight = 15946.145| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.51 r_work: 0.3676 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2270 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= 0.112 Angle : 0.534 8.631 13919 Z= 0.279 Chirality : 0.041 0.231 1593 Planarity : 0.003 0.036 1712 Dihedral : 11.647 146.687 1600 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.71 % Allowed : 18.04 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.24), residues: 1188 helix: 0.38 (0.24), residues: 491 sheet: -1.98 (0.44), residues: 137 loop : -2.28 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 29 HIS 0.004 0.001 HIS A 309 PHE 0.015 0.001 PHE A 741 TYR 0.012 0.001 TYR A 286 ARG 0.002 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 399) hydrogen bonds : angle 4.50694 ( 1111) metal coordination : bond 0.00443 ( 7) metal coordination : angle 2.55870 ( 3) covalent geometry : bond 0.00252 (10184) covalent geometry : angle 0.53317 (13916) *********************** 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 147 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.063 Fit side-chains REVERT: A 102 PHE cc_start: 0.6341 (p90) cc_final: 0.5874 (p90) REVERT: A 144 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7267 (mt-10) REVERT: A 391 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8179 (mmtm) REVERT: A 452 ASP cc_start: 0.8354 (t70) cc_final: 0.7965 (t70) REVERT: A 546 TYR cc_start: 0.6752 (t80) cc_final: 0.6171 (t80) REVERT: A 552 ASN cc_start: 0.7713 (p0) cc_final: 0.7286 (t0) REVERT: A 583 ARG cc_start: 0.8560 (mpt90) cc_final: 0.8290 (mmt180) REVERT: A 665 GLU cc_start: 0.8283 (pm20) cc_final: 0.7170 (pm20) REVERT: A 821 LYS cc_start: 0.8857 (tttm) cc_final: 0.8555 (tptp) REVERT: A 919 GLU cc_start: 0.7934 (mp0) cc_final: 0.7502 (mp0) outliers start: 18 outliers final: 15 residues processed: 139 average time/residue: 0.2354 time to fit residues: 45.8860 Evaluate side-chains 136 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 62 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.163077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.138621 restraints weight = 15935.295| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.49 r_work: 0.3674 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10191 Z= 0.121 Angle : 0.550 8.607 13919 Z= 0.283 Chirality : 0.041 0.236 1593 Planarity : 0.003 0.037 1712 Dihedral : 11.610 146.474 1600 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.18 % Allowed : 18.61 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.24), residues: 1188 helix: 0.48 (0.24), residues: 485 sheet: -1.93 (0.43), residues: 139 loop : -2.16 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 617 HIS 0.003 0.001 HIS A 309 PHE 0.015 0.001 PHE A 741 TYR 0.013 0.001 TYR A 286 ARG 0.002 0.000 ARG A 33 Details of bonding type rmsd hydrogen bonds : bond 0.03218 ( 399) hydrogen bonds : angle 4.48932 ( 1111) metal coordination : bond 0.00476 ( 7) metal coordination : angle 2.54977 ( 3) covalent geometry : bond 0.00278 (10184) covalent geometry : angle 0.54890 (13916) *********************** 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 146 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.167 Fit side-chains REVERT: A 102 PHE cc_start: 0.6364 (p90) cc_final: 0.5901 (p90) REVERT: A 144 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7254 (mt-10) REVERT: A 391 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8170 (mmtm) REVERT: A 452 ASP cc_start: 0.8306 (t70) cc_final: 0.7915 (t70) REVERT: A 552 ASN cc_start: 0.7714 (p0) cc_final: 0.7311 (t0) REVERT: A 583 ARG cc_start: 0.8538 (mpt90) cc_final: 0.8286 (mmt180) REVERT: A 665 GLU cc_start: 0.8274 (pm20) cc_final: 0.7170 (pm20) REVERT: A 821 LYS cc_start: 0.8853 (tttm) cc_final: 0.8547 (tptp) REVERT: A 919 GLU cc_start: 0.7907 (mp0) cc_final: 0.7463 (mp0) outliers start: 23 outliers final: 18 residues processed: 136 average time/residue: 0.2639 time to fit residues: 50.3716 Evaluate side-chains 138 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 437 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 90 optimal weight: 0.0970 chunk 39 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 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 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 = 0.4084 r_free = 0.4084 target = 0.164727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140241 restraints weight = 15795.540| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.50 r_work: 0.3695 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10191 Z= 0.106 Angle : 0.533 7.376 13919 Z= 0.275 Chirality : 0.041 0.227 1593 Planarity : 0.003 0.034 1712 Dihedral : 11.531 147.541 1600 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.80 % Allowed : 19.09 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.24), residues: 1188 helix: 0.60 (0.24), residues: 484 sheet: -1.82 (0.44), residues: 137 loop : -2.08 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 29 HIS 0.004 0.001 HIS A 309 PHE 0.015 0.001 PHE A 741 TYR 0.011 0.001 TYR A 286 ARG 0.003 0.000 ARG A 836 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 399) hydrogen bonds : angle 4.41734 ( 1111) metal coordination : bond 0.00377 ( 7) metal coordination : angle 2.25247 ( 3) covalent geometry : bond 0.00238 (10184) covalent geometry : angle 0.53185 (13916) *********************** 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 150 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.099 Fit side-chains REVERT: A 102 PHE cc_start: 0.6207 (p90) cc_final: 0.5812 (p90) REVERT: A 144 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7146 (mt-10) REVERT: A 331 ARG cc_start: 0.7802 (ttt-90) cc_final: 0.7585 (ttt-90) REVERT: A 391 LYS cc_start: 0.8428 (mmtt) cc_final: 0.8178 (mmtm) REVERT: A 418 ASP cc_start: 0.7389 (t0) cc_final: 0.6906 (t70) REVERT: A 452 ASP cc_start: 0.8326 (t70) cc_final: 0.7920 (t70) REVERT: A 552 ASN cc_start: 0.7693 (p0) cc_final: 0.7410 (t0) REVERT: A 583 ARG cc_start: 0.8529 (mpt90) cc_final: 0.8280 (mmt180) REVERT: A 665 GLU cc_start: 0.8227 (pm20) cc_final: 0.7122 (pm20) REVERT: A 821 LYS cc_start: 0.8816 (tttm) cc_final: 0.8416 (tptp) REVERT: A 919 GLU cc_start: 0.7903 (mp0) cc_final: 0.7459 (mp0) outliers start: 19 outliers final: 16 residues processed: 143 average time/residue: 0.2399 time to fit residues: 48.4664 Evaluate side-chains 148 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 437 LEU Chi-restraints excluded: chain A residue 493 VAL 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 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: 2.9990 chunk 67 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 381 HIS 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 = 0.161222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.136723 restraints weight = 15901.630| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.48 r_work: 0.3653 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10191 Z= 0.157 Angle : 0.582 7.622 13919 Z= 0.300 Chirality : 0.043 0.245 1593 Planarity : 0.003 0.034 1712 Dihedral : 11.628 145.336 1600 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.09 % Allowed : 19.28 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.24), residues: 1188 helix: 0.54 (0.24), residues: 479 sheet: -1.71 (0.45), residues: 134 loop : -2.11 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 154 HIS 0.003 0.001 HIS A 82 PHE 0.015 0.001 PHE A 741 TYR 0.014 0.002 TYR A 286 ARG 0.004 0.000 ARG A 836 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 399) hydrogen bonds : angle 4.57462 ( 1111) metal coordination : bond 0.00802 ( 7) metal coordination : angle 2.84083 ( 3) covalent geometry : bond 0.00367 (10184) covalent geometry : angle 0.58084 (13916) ********************** 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: 22 poor density : 129 time to evaluate : 1.099 Fit side-chains REVERT: A 331 ARG cc_start: 0.7922 (ttt-90) cc_final: 0.7672 (ttt-90) REVERT: A 418 ASP cc_start: 0.7556 (t0) cc_final: 0.7096 (t70) REVERT: A 452 ASP cc_start: 0.8327 (t70) cc_final: 0.7938 (t70) REVERT: A 552 ASN cc_start: 0.7788 (p0) cc_final: 0.7412 (t0) REVERT: A 665 GLU cc_start: 0.8311 (pm20) cc_final: 0.7197 (pm20) REVERT: A 756 MET cc_start: 0.8389 (tpp) cc_final: 0.8140 (tpp) REVERT: A 821 LYS cc_start: 0.8841 (tttm) cc_final: 0.8454 (tptp) REVERT: A 919 GLU cc_start: 0.7879 (mp0) cc_final: 0.7452 (mp0) outliers start: 22 outliers final: 20 residues processed: 141 average time/residue: 0.2310 time to fit residues: 46.1260 Evaluate side-chains 145 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 437 LEU 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 820 VAL Chi-restraints excluded: chain A residue 864 ILE 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 118 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.163814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139372 restraints weight = 15828.052| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.50 r_work: 0.3684 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10191 Z= 0.115 Angle : 0.545 7.425 13919 Z= 0.281 Chirality : 0.041 0.228 1593 Planarity : 0.003 0.034 1712 Dihedral : 11.555 147.436 1600 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.99 % Allowed : 19.47 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.24), residues: 1188 helix: 0.66 (0.24), residues: 478 sheet: -1.84 (0.43), residues: 139 loop : -1.94 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 29 HIS 0.004 0.001 HIS A 82 PHE 0.014 0.001 PHE A 741 TYR 0.012 0.001 TYR A 286 ARG 0.003 0.000 ARG A 836 Details of bonding type rmsd hydrogen bonds : bond 0.03156 ( 399) hydrogen bonds : angle 4.47801 ( 1111) metal coordination : bond 0.00427 ( 7) metal coordination : angle 2.40876 ( 3) covalent geometry : bond 0.00261 (10184) covalent geometry : angle 0.54363 (13916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5158.97 seconds wall clock time: 94 minutes 5.20 seconds (5645.20 seconds total)