Starting phenix.real_space_refine on Fri Feb 14 11:45:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bzf_30252/02_2025/7bzf_30252.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bzf_30252/02_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_30252/02_2025/7bzf_30252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bzf_30252/02_2025/7bzf_30252.map" model { file = "/net/cci-nas-00/data/ceres_data/7bzf_30252/02_2025/7bzf_30252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bzf_30252/02_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-5592/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: 5.93, per 1000 atoms: 0.60 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: 2.36 Conformation dependent library (CDL) restraints added in 1.3 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: 3.18 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: 3.32 Time building geometry restraints manager: 2.76 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.040 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.640 ------------------------------------------------------------------------------- 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 : 0.003 0.033 10184 Z= 0.224 Angle : 0.610 10.475 13916 Z= 0.347 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 *********************** 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 : 1.001 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: 0.2758 time to fit residues: 61.2220 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 : 1.155 ------------------------------------------------------------------------------- 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: 0.0010 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 0.0770 chunk 56 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 overall best weight: 0.3950 ------------------------------------------------------------------------------- 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 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 = 0.4060 r_free = 0.4060 target = 0.162548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.138515 restraints weight = 15738.728| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.45 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: 0.7442 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10184 Z= 0.164 Angle : 0.563 7.587 13916 Z= 0.298 Chirality : 0.042 0.230 1593 Planarity : 0.004 0.058 1712 Dihedral : 12.121 148.666 1600 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.04 % Allowed : 11.68 % Favored : 87.27 % 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: -2.99 (0.22), residues: 1188 helix: -0.67 (0.22), residues: 503 sheet: -2.76 (0.40), residues: 127 loop : -3.11 (0.22), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 182 HIS 0.006 0.001 HIS A 295 PHE 0.015 0.001 PHE A 741 TYR 0.015 0.001 TYR A 887 ARG 0.004 0.000 ARG A 249 *********************** 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 156 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 197 ARG cc_start: 0.5698 (tpp-160) cc_final: 0.5443 (tpp-160) REVERT: A 452 ASP cc_start: 0.8424 (t70) cc_final: 0.8040 (t70) REVERT: A 583 ARG cc_start: 0.8642 (mpt90) cc_final: 0.8305 (mmt180) REVERT: A 818 MET cc_start: 0.8652 (ttp) cc_final: 0.8445 (ttt) REVERT: A 821 LYS cc_start: 0.8764 (tttm) cc_final: 0.8492 (tptp) REVERT: A 855 MET cc_start: 0.4941 (tpp) cc_final: 0.4527 (tpp) REVERT: A 919 GLU cc_start: 0.8028 (mp0) cc_final: 0.7721 (mp0) REVERT: D 94 MET cc_start: 0.6346 (mtt) cc_final: 0.5995 (mtp) REVERT: D 106 ILE cc_start: 0.5554 (mm) cc_final: 0.5207 (mt) outliers start: 11 outliers final: 7 residues processed: 149 average time/residue: 0.2331 time to fit residues: 48.5508 Evaluate side-chains 129 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 82 optimal weight: 0.1980 chunk 24 optimal weight: 0.0980 chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 0.1980 chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 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 = 0.4085 r_free = 0.4085 target = 0.165085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.140746 restraints weight = 15939.751| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.49 r_work: 0.3695 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10184 Z= 0.142 Angle : 0.517 5.633 13916 Z= 0.274 Chirality : 0.041 0.229 1593 Planarity : 0.003 0.050 1712 Dihedral : 11.877 148.280 1600 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.99 % Allowed : 13.39 % Favored : 84.62 % 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: -2.15 (0.23), residues: 1188 helix: 0.05 (0.24), residues: 486 sheet: -2.14 (0.44), residues: 122 loop : -2.65 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 598 HIS 0.004 0.001 HIS A 309 PHE 0.015 0.001 PHE A 741 TYR 0.015 0.001 TYR A 887 ARG 0.005 0.000 ARG A 331 *********************** 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 149 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.065 Fit side-chains REVERT: A 102 PHE cc_start: 0.6251 (p90) cc_final: 0.5741 (p90) REVERT: A 160 LYS cc_start: 0.7738 (tppt) cc_final: 0.7147 (ptmt) REVERT: A 197 ARG cc_start: 0.5645 (tpp-160) cc_final: 0.5344 (tpp-160) REVERT: A 452 ASP cc_start: 0.8335 (t70) cc_final: 0.7941 (t70) REVERT: A 583 ARG cc_start: 0.8608 (mpt90) cc_final: 0.8199 (mmt180) REVERT: A 608 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7415 (m-30) REVERT: A 756 MET cc_start: 0.8355 (tpt) cc_final: 0.7587 (ttt) REVERT: A 821 LYS cc_start: 0.8704 (tttm) cc_final: 0.8441 (tptp) REVERT: A 919 GLU cc_start: 0.8019 (mp0) cc_final: 0.7621 (mp0) REVERT: D 94 MET cc_start: 0.6269 (mtt) cc_final: 0.5931 (mtp) REVERT: D 106 ILE cc_start: 0.5482 (mm) cc_final: 0.5134 (mt) REVERT: D 117 LEU cc_start: 0.7286 (mm) cc_final: 0.7062 (mm) outliers start: 21 outliers final: 10 residues processed: 142 average time/residue: 0.2453 time to fit residues: 48.1469 Evaluate side-chains 130 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 42 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 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 = 0.4029 r_free = 0.4029 target = 0.159821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.134797 restraints weight = 15817.503| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.59 r_work: 0.3625 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10184 Z= 0.263 Angle : 0.576 5.740 13916 Z= 0.303 Chirality : 0.043 0.255 1593 Planarity : 0.004 0.059 1712 Dihedral : 11.835 144.120 1600 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.28 % Allowed : 15.19 % 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: -2.13 (0.23), residues: 1188 helix: 0.07 (0.24), residues: 488 sheet: -2.16 (0.44), residues: 128 loop : -2.63 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 154 HIS 0.003 0.001 HIS A 599 PHE 0.014 0.002 PHE A 741 TYR 0.013 0.002 TYR A 530 ARG 0.006 0.000 ARG A 331 *********************** 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 151 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 102 PHE cc_start: 0.6597 (p90) cc_final: 0.6168 (p90) REVERT: A 144 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7341 (mt-10) REVERT: A 331 ARG cc_start: 0.8066 (ttt180) cc_final: 0.7672 (ttt-90) REVERT: A 452 ASP cc_start: 0.8340 (t70) cc_final: 0.7965 (t70) REVERT: A 583 ARG cc_start: 0.8653 (mpt90) cc_final: 0.8329 (mmt180) REVERT: A 756 MET cc_start: 0.8394 (tpt) cc_final: 0.7821 (tpp) REVERT: A 880 VAL cc_start: 0.8256 (t) cc_final: 0.7975 (t) REVERT: A 919 GLU cc_start: 0.8042 (mp0) cc_final: 0.7635 (mp0) REVERT: B 80 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7700 (mtm-85) REVERT: D 94 MET cc_start: 0.6261 (mtt) cc_final: 0.5962 (mtp) REVERT: D 106 ILE cc_start: 0.5540 (mm) cc_final: 0.5170 (mt) outliers start: 24 outliers final: 15 residues processed: 140 average time/residue: 0.2352 time to fit residues: 46.1662 Evaluate side-chains 138 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 350 GLU Chi-restraints excluded: chain A residue 410 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 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 80 ARG 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: 0.5980 chunk 42 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 22 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 0.0970 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 168 ASN ** 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 = 0.164338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139679 restraints weight = 15710.800| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.49 r_work: 0.3688 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10184 Z= 0.151 Angle : 0.521 7.180 13916 Z= 0.274 Chirality : 0.041 0.227 1593 Planarity : 0.003 0.040 1712 Dihedral : 11.705 146.836 1600 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.90 % Allowed : 16.62 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.77 (0.24), residues: 1188 helix: 0.29 (0.24), residues: 491 sheet: -1.88 (0.47), residues: 127 loop : -2.38 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 182 HIS 0.004 0.001 HIS A 309 PHE 0.014 0.001 PHE A 741 TYR 0.014 0.001 TYR A 887 ARG 0.002 0.000 ARG A 33 *********************** 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 150 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 102 PHE cc_start: 0.6297 (p90) cc_final: 0.5858 (p90) REVERT: A 331 ARG cc_start: 0.7944 (ttt180) cc_final: 0.7370 (ttt-90) REVERT: A 452 ASP cc_start: 0.8300 (t70) cc_final: 0.7911 (t70) REVERT: A 546 TYR cc_start: 0.6719 (t80) cc_final: 0.6314 (t80) REVERT: A 583 ARG cc_start: 0.8598 (mpt90) cc_final: 0.8388 (mmt180) REVERT: A 608 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7518 (m-30) REVERT: A 665 GLU cc_start: 0.8272 (pm20) cc_final: 0.7056 (pm20) REVERT: A 756 MET cc_start: 0.8361 (tpt) cc_final: 0.8132 (tpp) REVERT: A 880 VAL cc_start: 0.8047 (t) cc_final: 0.7767 (t) REVERT: A 919 GLU cc_start: 0.7967 (mp0) cc_final: 0.7538 (mp0) REVERT: B 80 ARG cc_start: 0.8154 (mtp-110) cc_final: 0.7771 (ttm170) REVERT: D 94 MET cc_start: 0.6264 (mtt) cc_final: 0.6007 (mtp) outliers start: 20 outliers final: 11 residues processed: 141 average time/residue: 0.2528 time to fit residues: 49.2175 Evaluate side-chains 132 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 608 ASP Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 681 SER 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 16 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 114 optimal weight: 8.9990 chunk 87 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 0.0670 chunk 27 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- 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** ** 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 = 0.4081 r_free = 0.4081 target = 0.164626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.139999 restraints weight = 15794.488| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.51 r_work: 0.3694 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10184 Z= 0.155 Angle : 0.525 8.733 13916 Z= 0.272 Chirality : 0.041 0.232 1593 Planarity : 0.003 0.038 1712 Dihedral : 11.607 146.705 1600 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.18 % Allowed : 16.33 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.51 (0.24), residues: 1188 helix: 0.52 (0.24), residues: 485 sheet: -1.81 (0.46), residues: 127 loop : -2.21 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 182 HIS 0.004 0.001 HIS A 309 PHE 0.014 0.001 PHE A 741 TYR 0.013 0.001 TYR A 286 ARG 0.002 0.000 ARG A 365 *********************** 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 154 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 102 PHE cc_start: 0.6173 (p90) cc_final: 0.5766 (p90) REVERT: A 160 LYS cc_start: 0.7908 (tppt) cc_final: 0.7690 (tppt) REVERT: A 331 ARG cc_start: 0.7942 (ttt180) cc_final: 0.7474 (ttt-90) REVERT: A 452 ASP cc_start: 0.8330 (t70) cc_final: 0.7926 (t70) REVERT: A 546 TYR cc_start: 0.6875 (t80) cc_final: 0.6497 (t80) REVERT: A 583 ARG cc_start: 0.8561 (mpt90) cc_final: 0.8340 (mmt180) REVERT: A 665 GLU cc_start: 0.8253 (pm20) cc_final: 0.7108 (pm20) REVERT: A 756 MET cc_start: 0.8316 (tpt) cc_final: 0.8101 (tpp) REVERT: A 919 GLU cc_start: 0.7960 (mp0) cc_final: 0.7508 (mp0) REVERT: B 80 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7781 (ttm170) REVERT: C 3 MET cc_start: 0.6524 (mmm) cc_final: 0.5834 (tpt) REVERT: D 94 MET cc_start: 0.6452 (mtt) cc_final: 0.6203 (mtp) outliers start: 23 outliers final: 14 residues processed: 144 average time/residue: 0.2465 time to fit residues: 49.4599 Evaluate side-chains 138 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 548 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 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 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 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: 3.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 26 optimal weight: 0.0060 chunk 73 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.161486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136300 restraints weight = 15995.044| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.62 r_work: 0.3642 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10184 Z= 0.220 Angle : 0.563 6.855 13916 Z= 0.293 Chirality : 0.042 0.244 1593 Planarity : 0.003 0.036 1712 Dihedral : 11.630 144.765 1600 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 1.90 % Allowed : 17.38 % Favored : 80.72 % 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: -1.63 (0.24), residues: 1188 helix: 0.34 (0.24), residues: 492 sheet: -1.79 (0.46), residues: 129 loop : -2.25 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 154 HIS 0.003 0.001 HIS A 309 PHE 0.014 0.001 PHE A 741 TYR 0.015 0.001 TYR A 286 ARG 0.002 0.000 ARG A 33 *********************** 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 149 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.027 Fit side-chains REVERT: A 102 PHE cc_start: 0.6501 (p90) cc_final: 0.6062 (p90) REVERT: A 144 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7331 (mt-10) REVERT: A 331 ARG cc_start: 0.8054 (ttt180) cc_final: 0.7595 (ttt-90) REVERT: A 452 ASP cc_start: 0.8330 (t70) cc_final: 0.7938 (t70) REVERT: A 583 ARG cc_start: 0.8588 (mpt90) cc_final: 0.8249 (mmt180) REVERT: A 665 GLU cc_start: 0.8305 (pm20) cc_final: 0.7191 (pm20) REVERT: A 880 VAL cc_start: 0.8083 (t) cc_final: 0.7869 (t) REVERT: A 919 GLU cc_start: 0.8006 (mp0) cc_final: 0.7588 (mp0) REVERT: B 80 ARG cc_start: 0.8175 (mtp-110) cc_final: 0.7777 (ttm170) REVERT: C 3 MET cc_start: 0.6530 (mmm) cc_final: 0.5909 (tpt) outliers start: 20 outliers final: 16 residues processed: 139 average time/residue: 0.2614 time to fit residues: 49.5932 Evaluate side-chains 135 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 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 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 62 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 33 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.163044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.138247 restraints weight = 15907.890| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.50 r_work: 0.3672 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10184 Z= 0.180 Angle : 0.541 6.740 13916 Z= 0.281 Chirality : 0.041 0.234 1593 Planarity : 0.003 0.033 1712 Dihedral : 11.599 146.072 1600 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.71 % Allowed : 17.76 % Favored : 80.53 % 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: -1.54 (0.24), residues: 1188 helix: 0.43 (0.24), residues: 491 sheet: -1.83 (0.43), residues: 145 loop : -2.17 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 182 HIS 0.004 0.001 HIS A 82 PHE 0.014 0.001 PHE A 741 TYR 0.013 0.001 TYR A 286 ARG 0.002 0.000 ARG A 33 *********************** 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 145 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.103 Fit side-chains REVERT: A 102 PHE cc_start: 0.6311 (p90) cc_final: 0.5872 (p90) REVERT: A 144 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7267 (mt-10) REVERT: A 331 ARG cc_start: 0.8013 (ttt180) cc_final: 0.7558 (ttt-90) REVERT: A 418 ASP cc_start: 0.7434 (t0) cc_final: 0.6979 (t70) REVERT: A 452 ASP cc_start: 0.8345 (t70) cc_final: 0.7933 (t70) REVERT: A 583 ARG cc_start: 0.8568 (mpt90) cc_final: 0.8274 (mmt180) REVERT: A 665 GLU cc_start: 0.8263 (pm20) cc_final: 0.7096 (pm20) REVERT: A 880 VAL cc_start: 0.7974 (t) cc_final: 0.7727 (t) REVERT: A 919 GLU cc_start: 0.7943 (mp0) cc_final: 0.7509 (mp0) REVERT: B 80 ARG cc_start: 0.8170 (mtp-110) cc_final: 0.7766 (ttm170) outliers start: 18 outliers final: 16 residues processed: 137 average time/residue: 0.2526 time to fit residues: 48.2093 Evaluate side-chains 138 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 35 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 0.0980 chunk 90 optimal weight: 0.1980 chunk 39 optimal weight: 0.0980 chunk 64 optimal weight: 0.0670 overall best weight: 0.2318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 177 ASN A 347 HIS ** 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 = 0.4110 r_free = 0.4110 target = 0.166516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.141198 restraints weight = 15870.459| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.58 r_work: 0.3711 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10184 Z= 0.139 Angle : 0.521 9.176 13916 Z= 0.269 Chirality : 0.040 0.218 1593 Planarity : 0.003 0.033 1712 Dihedral : 11.441 148.536 1600 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.42 % Allowed : 18.42 % Favored : 80.15 % 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: -1.18 (0.25), residues: 1188 helix: 0.76 (0.24), residues: 485 sheet: -1.82 (0.44), residues: 132 loop : -1.94 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 29 HIS 0.004 0.001 HIS A 309 PHE 0.014 0.001 PHE A 741 TYR 0.011 0.001 TYR A 887 ARG 0.004 0.000 ARG A 836 *********************** 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 156 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 1.016 Fit side-chains REVERT: A 102 PHE cc_start: 0.5891 (p90) cc_final: 0.5545 (p90) REVERT: A 331 ARG cc_start: 0.7938 (ttt180) cc_final: 0.7511 (ttt-90) REVERT: A 418 ASP cc_start: 0.7412 (t0) cc_final: 0.6950 (t70) REVERT: A 452 ASP cc_start: 0.8293 (t70) cc_final: 0.7901 (t70) REVERT: A 583 ARG cc_start: 0.8495 (mpt90) cc_final: 0.8269 (mmt180) REVERT: A 665 GLU cc_start: 0.8187 (pm20) cc_final: 0.7136 (pm20) REVERT: A 919 GLU cc_start: 0.7939 (mp0) cc_final: 0.7525 (mp0) REVERT: B 80 ARG cc_start: 0.8081 (mtp-110) cc_final: 0.7750 (ttm170) outliers start: 15 outliers final: 13 residues processed: 151 average time/residue: 0.2313 time to fit residues: 49.3581 Evaluate side-chains 147 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 77 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 HIS ** 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 = 0.4076 r_free = 0.4076 target = 0.163308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.138242 restraints weight = 15874.013| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.54 r_work: 0.3675 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10184 Z= 0.187 Angle : 0.544 8.307 13916 Z= 0.281 Chirality : 0.042 0.233 1593 Planarity : 0.003 0.033 1712 Dihedral : 11.463 147.183 1600 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.42 % Allowed : 18.80 % Favored : 79.77 % 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: -1.13 (0.25), residues: 1188 helix: 0.83 (0.24), residues: 479 sheet: -1.54 (0.45), residues: 134 loop : -1.97 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 154 HIS 0.003 0.001 HIS A 82 PHE 0.015 0.001 PHE A 741 TYR 0.016 0.001 TYR A 289 ARG 0.003 0.000 ARG A 836 ********************** 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 148 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.066 Fit side-chains REVERT: A 102 PHE cc_start: 0.6061 (p90) cc_final: 0.5719 (p90) REVERT: A 144 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7171 (mt-10) REVERT: A 331 ARG cc_start: 0.8054 (ttt180) cc_final: 0.7513 (ttt-90) REVERT: A 418 ASP cc_start: 0.7481 (t0) cc_final: 0.7048 (t70) REVERT: A 452 ASP cc_start: 0.8342 (t70) cc_final: 0.7946 (t70) REVERT: A 583 ARG cc_start: 0.8549 (mpt90) cc_final: 0.8314 (mmt180) REVERT: A 662 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8436 (p) REVERT: A 665 GLU cc_start: 0.8241 (pm20) cc_final: 0.7177 (pm20) REVERT: A 919 GLU cc_start: 0.7912 (mp0) cc_final: 0.7503 (mp0) REVERT: B 80 ARG cc_start: 0.8073 (mtp-110) cc_final: 0.7744 (ttm170) outliers start: 15 outliers final: 13 residues processed: 142 average time/residue: 0.2291 time to fit residues: 46.1999 Evaluate side-chains 142 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 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 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: 0.0670 chunk 109 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 95 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- 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** ** 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 = 0.4083 r_free = 0.4083 target = 0.163898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138415 restraints weight = 15955.973| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.59 r_work: 0.3674 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10184 Z= 0.178 Angle : 0.545 8.081 13916 Z= 0.282 Chirality : 0.042 0.230 1593 Planarity : 0.003 0.033 1712 Dihedral : 11.449 147.362 1600 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.52 % Allowed : 18.99 % 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 (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: -1.18 (0.25), residues: 1188 helix: 0.73 (0.24), residues: 485 sheet: -1.60 (0.43), residues: 144 loop : -1.97 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 182 HIS 0.003 0.001 HIS A 82 PHE 0.015 0.001 PHE A 741 TYR 0.014 0.001 TYR A 289 ARG 0.003 0.000 ARG A 836 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4538.82 seconds wall clock time: 81 minutes 28.90 seconds (4888.90 seconds total)