Starting phenix.real_space_refine on Sun Oct 12 08:42:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8urb_42488/10_2025/8urb_42488.cif Found real_map, /net/cci-nas-00/data/ceres_data/8urb_42488/10_2025/8urb_42488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8urb_42488/10_2025/8urb_42488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8urb_42488/10_2025/8urb_42488.map" model { file = "/net/cci-nas-00/data/ceres_data/8urb_42488/10_2025/8urb_42488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8urb_42488/10_2025/8urb_42488.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.049 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 41 5.49 5 S 82 5.16 5 C 7239 2.51 5 N 1974 2.21 5 O 2316 1.98 5 H 11060 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22714 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 14521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 921, 14521 Classifications: {'peptide': 921} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 895} Chain: "B" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2901 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} Chain: "C" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1072 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2909 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 178} Chain: "I" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 639 Classifications: {'RNA': 20} Modifications used: {'3*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "J" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 670 Classifications: {'RNA': 21} Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 9} Link IDs: {'rna3p': 20} 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 4641 SG CYS A 296 33.356 94.490 113.706 1.00 58.21 S ATOM 4707 SG CYS A 301 35.192 97.441 115.219 1.00 43.72 S ATOM 4771 SG CYS A 305 35.279 94.028 116.947 1.00 43.40 S ATOM 7554 SG CYS A 482 32.799 95.250 91.808 1.00 41.59 S ATOM 10058 SG CYS A 640 33.477 98.838 92.934 1.00 58.82 S ATOM 10069 SG CYS A 641 31.431 96.466 95.177 1.00 46.50 S Time building chain proxies: 4.27, per 1000 atoms: 0.19 Number of scatterers: 22714 At special positions: 0 Unit cell: (92.568, 122.36, 169.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 82 16.00 P 41 15.00 O 2316 8.00 N 1974 7.00 C 7239 6.00 H 11060 1.00 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: 2.08 Conformation dependent library (CDL) restraints added in 580.2 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 290 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 296 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 305 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 637 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 482 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 641 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 640 " Number of angles added : 6 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2578 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 13 sheets defined 56.8% alpha, 12.2% beta 18 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 4.18 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.760A pdb=" N ARG A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.578A pdb=" N ARG A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 removed outlier: 3.720A pdb=" N LEU A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 164 through 171 removed outlier: 3.733A pdb=" N LEU A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 removed outlier: 3.592A pdb=" N LYS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 228 through 235 removed outlier: 3.828A pdb=" N MET A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 242 Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.678A pdb=" N GLU A 267 " --> pdb=" O ASP A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 298 through 313 removed outlier: 3.690A pdb=" N PHE A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 362 through 372 Processing helix chain 'A' and resid 372 through 379 removed outlier: 4.491A pdb=" N LEU A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 422 Processing helix chain 'A' and resid 442 through 449 Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 460 through 474 removed outlier: 4.797A pdb=" N VAL A 466 " --> pdb=" O CYS A 462 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.711A pdb=" N VAL A 488 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 Processing helix chain 'A' and resid 506 through 514 removed outlier: 4.022A pdb=" N TYR A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 Processing helix chain 'A' and resid 556 through 577 removed outlier: 3.513A pdb=" N THR A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N HIS A 570 " --> pdb=" O TYR A 566 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 622 through 634 Processing helix chain 'A' and resid 642 through 657 removed outlier: 3.571A pdb=" N GLU A 653 " --> pdb=" O ARG A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 703 removed outlier: 4.040A pdb=" N SER A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 728 Processing helix chain 'A' and resid 733 through 747 removed outlier: 3.734A pdb=" N VAL A 737 " --> pdb=" O ASP A 733 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS A 746 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 769 Processing helix chain 'A' and resid 773 through 785 removed outlier: 3.911A pdb=" N ALA A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 794 removed outlier: 3.649A pdb=" N CYS A 794 " --> pdb=" O ALA A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 803 removed outlier: 4.055A pdb=" N LYS A 802 " --> pdb=" O ASP A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 837 removed outlier: 3.737A pdb=" N ILE A 832 " --> pdb=" O ASP A 828 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY A 836 " --> pdb=" O ILE A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 854 removed outlier: 4.322A pdb=" N ALA A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL A 848 " --> pdb=" O THR A 845 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 849 " --> pdb=" O ASP A 846 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU A 852 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 853 " --> pdb=" O LEU A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 867 Processing helix chain 'A' and resid 869 through 899 removed outlier: 3.589A pdb=" N VAL A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 876 " --> pdb=" O TYR A 872 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A 877 " --> pdb=" O LYS A 873 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 879 " --> pdb=" O VAL A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.237A pdb=" N TYR A 916 " --> pdb=" O ASP A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 921 No H-bonds generated for 'chain 'A' and resid 919 through 921' Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 31 through 96 removed outlier: 3.975A pdb=" N GLN B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR B 55 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.565A pdb=" N THR B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.901A pdb=" N ARG B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.626A pdb=" N VAL B 172 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 178 removed outlier: 3.744A pdb=" N GLU B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 10 Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.739A pdb=" N ALA C 24 " --> pdb=" O ASN C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 42 Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.501A pdb=" N GLU C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS C 62 " --> pdb=" O PHE C 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 25 Processing helix chain 'D' and resid 26 through 28 No H-bonds generated for 'chain 'D' and resid 26 through 28' Processing helix chain 'D' and resid 31 through 80 Processing helix chain 'D' and resid 82 through 98 removed outlier: 3.598A pdb=" N SER D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG D 96 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG D 97 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 98 " --> pdb=" O MET D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.792A pdb=" N ILE D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 170 removed outlier: 3.796A pdb=" N VAL D 169 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 180 removed outlier: 3.603A pdb=" N GLU D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 5.279A pdb=" N PHE A 63 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP A 112 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 65 " --> pdb=" O ARG A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.988A pdb=" N VAL A 29 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 48 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 218 removed outlier: 3.557A pdb=" N ILE A 225 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 227 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 333 through 338 removed outlier: 9.864A pdb=" N SER A 358 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP A 329 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 338 removed outlier: 3.518A pdb=" N VAL B 115 " --> pdb=" O CYS A 325 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 340 through 343 Processing sheet with id=AA8, first strand: chain 'A' and resid 382 through 385 removed outlier: 6.670A pdb=" N ALA A 382 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N VAL B 131 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A 384 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ILE B 156 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 409 through 410 Processing sheet with id=AB1, first strand: chain 'A' and resid 551 through 554 removed outlier: 3.685A pdb=" N GLN A 536 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR A 535 " --> pdb=" O TYR A 663 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 748 through 753 Processing sheet with id=AB3, first strand: chain 'A' and resid 811 through 817 Processing sheet with id=AB4, first strand: chain 'D' and resid 115 through 116 removed outlier: 3.810A pdb=" N VAL D 115 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP D 158 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE D 156 " --> pdb=" O GLU D 189 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1569 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 5.87 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11004 1.03 - 1.23: 77 1.23 - 1.42: 5214 1.42 - 1.62: 6624 1.62 - 1.81: 120 Bond restraints: 23039 Sorted by residual: bond pdb=" N ASP A 331 " pdb=" H ASP A 331 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.85e+01 bond pdb=" N ASP B 24 " pdb=" H ASP B 24 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" N ASN B 28 " pdb=" H ASN B 28 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" ND2 ASN B 28 " pdb="HD22 ASN B 28 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.07e+01 bond pdb=" ND2 ASN B 28 " pdb="HD21 ASN B 28 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 6.03e+01 ... (remaining 23034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 40963 1.67 - 3.33: 476 3.33 - 5.00: 37 5.00 - 6.66: 2 6.66 - 8.33: 1 Bond angle restraints: 41479 Sorted by residual: angle pdb=" CA GLU B 144 " pdb=" CB GLU B 144 " pdb=" CG GLU B 144 " ideal model delta sigma weight residual 114.10 122.43 -8.33 2.00e+00 2.50e-01 1.73e+01 angle pdb=" N ASP A 331 " pdb=" CA ASP A 331 " pdb=" C ASP A 331 " ideal model delta sigma weight residual 112.86 109.31 3.55 1.22e+00 6.72e-01 8.46e+00 angle pdb=" CA ASP A 331 " pdb=" C ASP A 331 " pdb=" O ASP A 331 " ideal model delta sigma weight residual 120.32 117.02 3.30 1.18e+00 7.18e-01 7.82e+00 angle pdb=" CA ARG D 96 " pdb=" CB ARG D 96 " pdb=" CG ARG D 96 " ideal model delta sigma weight residual 114.10 119.60 -5.50 2.00e+00 2.50e-01 7.57e+00 angle pdb=" N VAL A 393 " pdb=" CA VAL A 393 " pdb=" C VAL A 393 " ideal model delta sigma weight residual 106.42 110.54 -4.12 1.51e+00 4.39e-01 7.43e+00 ... (remaining 41474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 10017 21.39 - 42.78: 627 42.78 - 64.17: 200 64.17 - 85.56: 53 85.56 - 106.95: 5 Dihedral angle restraints: 10902 sinusoidal: 6133 harmonic: 4769 Sorted by residual: dihedral pdb=" CA TYR A 854 " pdb=" C TYR A 854 " pdb=" N VAL A 855 " pdb=" CA VAL A 855 " ideal model delta harmonic sigma weight residual 180.00 155.02 24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA GLU D 171 " pdb=" C GLU D 171 " pdb=" N VAL D 172 " pdb=" CA VAL D 172 " ideal model delta harmonic sigma weight residual -180.00 -159.96 -20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ASP A 860 " pdb=" CB ASP A 860 " pdb=" CG ASP A 860 " pdb=" OD1 ASP A 860 " ideal model delta sinusoidal sigma weight residual -30.00 -88.33 58.33 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 10899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1237 0.027 - 0.054: 428 0.054 - 0.081: 106 0.081 - 0.108: 69 0.108 - 0.135: 28 Chirality restraints: 1868 Sorted by residual: chirality pdb=" CA VAL A 52 " pdb=" N VAL A 52 " pdb=" C VAL A 52 " pdb=" CB VAL A 52 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA VAL A 661 " pdb=" N VAL A 661 " pdb=" C VAL A 661 " pdb=" CB VAL A 661 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE A 104 " pdb=" N ILE A 104 " pdb=" C ILE A 104 " pdb=" CB ILE A 104 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 1865 not shown) Planarity restraints: 3294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 28 " 0.089 2.00e-02 2.50e+03 8.39e-02 1.06e+02 pdb=" CG ASN B 28 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN B 28 " -0.081 2.00e-02 2.50e+03 pdb=" ND2 ASN B 28 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN B 28 " -0.115 2.00e-02 2.50e+03 pdb="HD22 ASN B 28 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 24 " -0.021 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" N ALA B 25 " 0.069 2.00e-02 2.50e+03 pdb=" CA ALA B 25 " -0.018 2.00e-02 2.50e+03 pdb=" H ALA B 25 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 24 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.84e+00 pdb=" C ASP B 24 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP B 24 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA B 25 " -0.018 2.00e-02 2.50e+03 ... (remaining 3291 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1317 2.21 - 2.81: 44949 2.81 - 3.40: 57451 3.40 - 4.00: 75372 4.00 - 4.60: 117376 Nonbonded interactions: 296465 Sorted by model distance: nonbonded pdb=" O ARG A 83 " pdb="HE21 GLN A 193 " model vdw 1.612 2.450 nonbonded pdb=" HG1 THR D 132 " pdb=" O LEU D 184 " model vdw 1.622 2.450 nonbonded pdb=" OE1 GLN A 204 " pdb=" HH TYR A 231 " model vdw 1.632 2.450 nonbonded pdb=" O PHE A 910 " pdb=" HH TYR A 916 " model vdw 1.634 2.450 nonbonded pdb=" H ASP D 161 " pdb=" O GLY D 164 " model vdw 1.648 2.450 ... (remaining 296460 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 11 through 192) selection = (chain 'D' and resid 11 through 192) } 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 31.000 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 : 0.002 0.034 11987 Z= 0.119 Angle : 0.519 8.326 16420 Z= 0.303 Chirality : 0.035 0.135 1868 Planarity : 0.003 0.058 1949 Dihedral : 15.021 106.954 4603 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.17 % Allowed : 7.56 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.23), residues: 1351 helix: -0.16 (0.21), residues: 620 sheet: -0.38 (0.42), residues: 137 loop : -0.50 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 143 TYR 0.012 0.001 TYR A 854 PHE 0.011 0.001 PHE A 898 TRP 0.013 0.001 TRP A 911 HIS 0.002 0.001 HIS A 567 Details of bonding type rmsd covalent geometry : bond 0.00238 (11979) covalent geometry : angle 0.51842 (16414) hydrogen bonds : bond 0.26211 ( 603) hydrogen bonds : angle 7.96493 ( 1649) metal coordination : bond 0.00776 ( 8) metal coordination : angle 1.40213 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 157 ILE cc_start: 0.8421 (mt) cc_final: 0.8202 (mt) outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.3656 time to fit residues: 53.0137 Evaluate side-chains 107 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 154 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** D 176 ASN ** 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 = 0.3982 r_free = 0.3982 target = 0.162862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.116780 restraints weight = 40880.596| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.03 r_work: 0.3286 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11987 Z= 0.264 Angle : 0.618 5.658 16420 Z= 0.345 Chirality : 0.042 0.148 1868 Planarity : 0.004 0.039 1949 Dihedral : 11.075 106.744 2075 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.18 % Allowed : 7.81 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.22), residues: 1351 helix: 0.15 (0.20), residues: 677 sheet: -0.40 (0.44), residues: 128 loop : -0.93 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 143 TYR 0.023 0.002 TYR A 743 PHE 0.017 0.002 PHE A 736 TRP 0.017 0.002 TRP A 911 HIS 0.006 0.001 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00618 (11979) covalent geometry : angle 0.61633 (16414) hydrogen bonds : bond 0.07665 ( 603) hydrogen bonds : angle 5.33821 ( 1649) metal coordination : bond 0.01903 ( 8) metal coordination : angle 2.71804 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 GLU cc_start: 0.7523 (tp30) cc_final: 0.6936 (tp30) outliers start: 14 outliers final: 6 residues processed: 119 average time/residue: 0.3098 time to fit residues: 50.2081 Evaluate side-chains 111 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain D residue 15 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 18 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 114 optimal weight: 0.0470 chunk 90 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 ASN ** D 176 ASN ** 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 = 0.4038 r_free = 0.4038 target = 0.168030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121206 restraints weight = 40238.986| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.16 r_work: 0.3341 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11987 Z= 0.113 Angle : 0.486 5.814 16420 Z= 0.267 Chirality : 0.036 0.144 1868 Planarity : 0.003 0.033 1949 Dihedral : 10.938 105.585 2073 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.76 % Allowed : 9.40 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.22), residues: 1351 helix: 0.76 (0.20), residues: 670 sheet: -0.35 (0.40), residues: 138 loop : -0.79 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.014 0.001 TYR A 783 PHE 0.014 0.001 PHE A 898 TRP 0.011 0.001 TRP A 911 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00240 (11979) covalent geometry : angle 0.48495 (16414) hydrogen bonds : bond 0.05305 ( 603) hydrogen bonds : angle 4.57300 ( 1649) metal coordination : bond 0.00736 ( 8) metal coordination : angle 1.89461 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 TRP cc_start: 0.9103 (OUTLIER) cc_final: 0.8749 (m100) REVERT: D 96 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7855 (tpt170) outliers start: 9 outliers final: 4 residues processed: 115 average time/residue: 0.3057 time to fit residues: 48.0508 Evaluate side-chains 105 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain D residue 161 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 14 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.163481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116286 restraints weight = 40855.529| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.14 r_work: 0.3275 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11987 Z= 0.220 Angle : 0.547 5.117 16420 Z= 0.301 Chirality : 0.039 0.147 1868 Planarity : 0.004 0.033 1949 Dihedral : 10.916 106.231 2073 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.68 % Allowed : 9.74 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.22), residues: 1351 helix: 0.66 (0.20), residues: 676 sheet: -0.60 (0.41), residues: 140 loop : -1.03 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 143 TYR 0.023 0.002 TYR A 743 PHE 0.013 0.002 PHE A 736 TRP 0.015 0.001 TRP A 911 HIS 0.005 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00525 (11979) covalent geometry : angle 0.54534 (16414) hydrogen bonds : bond 0.05673 ( 603) hydrogen bonds : angle 4.60404 ( 1649) metal coordination : bond 0.01452 ( 8) metal coordination : angle 2.21213 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8212 (ptm) cc_final: 0.7898 (ptm) REVERT: A 745 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7736 (mtm110) REVERT: A 919 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7910 (mtt) REVERT: D 96 ARG cc_start: 0.8250 (tpp80) cc_final: 0.7937 (tpt170) outliers start: 20 outliers final: 11 residues processed: 111 average time/residue: 0.2842 time to fit residues: 44.0650 Evaluate side-chains 110 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 10 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 4 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 120 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.165166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117977 restraints weight = 40360.362| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.14 r_work: 0.3301 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11987 Z= 0.144 Angle : 0.490 4.671 16420 Z= 0.268 Chirality : 0.037 0.146 1868 Planarity : 0.003 0.032 1949 Dihedral : 10.898 106.197 2073 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.68 % Allowed : 10.66 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.23), residues: 1351 helix: 0.84 (0.21), residues: 669 sheet: -0.64 (0.41), residues: 140 loop : -0.99 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.016 0.001 TYR A 743 PHE 0.011 0.001 PHE A 736 TRP 0.012 0.001 TRP A 911 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00335 (11979) covalent geometry : angle 0.48896 (16414) hydrogen bonds : bond 0.04906 ( 603) hydrogen bonds : angle 4.37803 ( 1649) metal coordination : bond 0.01070 ( 8) metal coordination : angle 2.03834 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.8798 (p) cc_final: 0.8560 (p) REVERT: A 236 MET cc_start: 0.8491 (mtt) cc_final: 0.8203 (mtt) REVERT: A 239 MET cc_start: 0.8225 (ptm) cc_final: 0.7956 (ptm) REVERT: A 511 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8399 (m-80) REVERT: A 745 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7719 (mtm110) REVERT: A 919 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7921 (mtt) REVERT: B 62 MET cc_start: 0.7920 (tpp) cc_final: 0.7709 (tpp) REVERT: B 154 TRP cc_start: 0.9128 (OUTLIER) cc_final: 0.8713 (m100) REVERT: C 13 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7767 (tt) REVERT: D 96 ARG cc_start: 0.8218 (tpp80) cc_final: 0.7907 (tpt170) outliers start: 20 outliers final: 13 residues processed: 119 average time/residue: 0.2697 time to fit residues: 45.3679 Evaluate side-chains 118 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 161 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 125 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.164442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.117154 restraints weight = 40655.746| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.15 r_work: 0.3292 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11987 Z= 0.159 Angle : 0.498 4.698 16420 Z= 0.272 Chirality : 0.037 0.147 1868 Planarity : 0.003 0.032 1949 Dihedral : 10.889 106.268 2073 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.93 % Allowed : 10.66 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.23), residues: 1351 helix: 0.90 (0.21), residues: 663 sheet: -0.69 (0.41), residues: 140 loop : -1.07 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 619 TYR 0.018 0.001 TYR A 743 PHE 0.012 0.001 PHE A 213 TRP 0.013 0.001 TRP A 911 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00375 (11979) covalent geometry : angle 0.49670 (16414) hydrogen bonds : bond 0.04876 ( 603) hydrogen bonds : angle 4.32915 ( 1649) metal coordination : bond 0.01196 ( 8) metal coordination : angle 2.09226 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8494 (mtt) cc_final: 0.8221 (mtt) REVERT: A 239 MET cc_start: 0.8356 (ptm) cc_final: 0.7965 (ptm) REVERT: A 511 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: A 745 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7746 (mtm110) REVERT: A 919 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7928 (mtt) REVERT: B 62 MET cc_start: 0.7922 (tpp) cc_final: 0.7703 (tpp) REVERT: B 154 TRP cc_start: 0.9130 (OUTLIER) cc_final: 0.8701 (m100) REVERT: C 13 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7825 (tt) outliers start: 23 outliers final: 16 residues processed: 124 average time/residue: 0.2686 time to fit residues: 46.9480 Evaluate side-chains 122 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 13 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 28 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 75 optimal weight: 0.4980 chunk 112 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.166979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.119845 restraints weight = 40514.508| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.18 r_work: 0.3326 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11987 Z= 0.100 Angle : 0.455 4.412 16420 Z= 0.247 Chirality : 0.036 0.144 1868 Planarity : 0.003 0.029 1949 Dihedral : 10.853 105.631 2073 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.60 % Allowed : 11.50 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.23), residues: 1351 helix: 1.12 (0.21), residues: 664 sheet: -0.66 (0.40), residues: 140 loop : -0.92 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 190 TYR 0.013 0.001 TYR A 783 PHE 0.007 0.001 PHE A 736 TRP 0.011 0.001 TRP A 911 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00217 (11979) covalent geometry : angle 0.45362 (16414) hydrogen bonds : bond 0.04167 ( 603) hydrogen bonds : angle 4.10036 ( 1649) metal coordination : bond 0.00877 ( 8) metal coordination : angle 1.84355 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8286 (ptm) cc_final: 0.7873 (ptm) REVERT: A 511 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: A 745 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7774 (mtm110) REVERT: A 919 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7941 (mtt) REVERT: B 62 MET cc_start: 0.7900 (tpp) cc_final: 0.7656 (tpp) REVERT: B 154 TRP cc_start: 0.9124 (OUTLIER) cc_final: 0.8680 (m100) REVERT: C 13 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7814 (tt) outliers start: 19 outliers final: 12 residues processed: 127 average time/residue: 0.2770 time to fit residues: 49.3221 Evaluate side-chains 120 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 13 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 118 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.163805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.117940 restraints weight = 39887.527| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.02 r_work: 0.3322 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11987 Z= 0.145 Angle : 0.481 4.927 16420 Z= 0.263 Chirality : 0.037 0.145 1868 Planarity : 0.003 0.033 1949 Dihedral : 10.844 105.850 2073 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.85 % Allowed : 11.59 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.23), residues: 1351 helix: 1.15 (0.21), residues: 664 sheet: -0.62 (0.41), residues: 145 loop : -0.95 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 190 TYR 0.018 0.001 TYR A 743 PHE 0.011 0.001 PHE A 213 TRP 0.012 0.001 TRP A 911 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00340 (11979) covalent geometry : angle 0.47931 (16414) hydrogen bonds : bond 0.04461 ( 603) hydrogen bonds : angle 4.12892 ( 1649) metal coordination : bond 0.01074 ( 8) metal coordination : angle 1.89583 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8374 (ptm) cc_final: 0.7985 (ptm) REVERT: A 366 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8005 (mt) REVERT: A 511 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.8386 (m-80) REVERT: A 745 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7687 (mtm110) REVERT: A 919 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7912 (mtt) REVERT: B 62 MET cc_start: 0.7824 (tpp) cc_final: 0.7516 (tpp) REVERT: B 154 TRP cc_start: 0.9148 (OUTLIER) cc_final: 0.8632 (m100) REVERT: C 13 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7728 (tt) outliers start: 22 outliers final: 16 residues processed: 122 average time/residue: 0.2958 time to fit residues: 50.2100 Evaluate side-chains 126 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 161 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 30 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 118 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.167431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119887 restraints weight = 41793.129| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.13 r_work: 0.3294 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11987 Z= 0.179 Angle : 0.508 5.616 16420 Z= 0.279 Chirality : 0.038 0.144 1868 Planarity : 0.003 0.034 1949 Dihedral : 10.874 106.258 2073 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.10 % Allowed : 12.01 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.23), residues: 1351 helix: 1.03 (0.21), residues: 671 sheet: -0.67 (0.40), residues: 145 loop : -1.12 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 190 TYR 0.020 0.001 TYR A 743 PHE 0.013 0.001 PHE A 213 TRP 0.012 0.001 TRP A 911 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00430 (11979) covalent geometry : angle 0.50659 (16414) hydrogen bonds : bond 0.04788 ( 603) hydrogen bonds : angle 4.19459 ( 1649) metal coordination : bond 0.01324 ( 8) metal coordination : angle 2.21170 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8429 (ptm) cc_final: 0.8073 (ptm) REVERT: A 511 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.8412 (m-80) REVERT: A 745 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7631 (mtm110) REVERT: A 919 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7929 (mtt) REVERT: B 62 MET cc_start: 0.7846 (tpp) cc_final: 0.7527 (tpp) REVERT: B 154 TRP cc_start: 0.9175 (OUTLIER) cc_final: 0.8593 (m100) REVERT: C 13 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7771 (tt) outliers start: 25 outliers final: 19 residues processed: 125 average time/residue: 0.2752 time to fit residues: 47.8894 Evaluate side-chains 126 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 161 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 103 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.166797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.119724 restraints weight = 40515.603| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.13 r_work: 0.3328 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11987 Z= 0.105 Angle : 0.459 6.322 16420 Z= 0.250 Chirality : 0.036 0.142 1868 Planarity : 0.003 0.029 1949 Dihedral : 10.861 105.955 2073 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.85 % Allowed : 12.43 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.23), residues: 1351 helix: 1.27 (0.21), residues: 661 sheet: -0.87 (0.38), residues: 157 loop : -0.88 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 619 TYR 0.014 0.001 TYR A 783 PHE 0.008 0.001 PHE A 736 TRP 0.012 0.001 TRP A 911 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00235 (11979) covalent geometry : angle 0.45715 (16414) hydrogen bonds : bond 0.04070 ( 603) hydrogen bonds : angle 4.00132 ( 1649) metal coordination : bond 0.00973 ( 8) metal coordination : angle 1.95488 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8144 (mtpp) cc_final: 0.7590 (mttp) REVERT: A 239 MET cc_start: 0.8340 (ptm) cc_final: 0.7950 (ptm) REVERT: A 366 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7996 (mt) REVERT: A 511 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.8320 (m-80) REVERT: A 745 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7724 (mtm110) REVERT: A 919 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7941 (mtt) REVERT: B 62 MET cc_start: 0.7820 (tpp) cc_final: 0.7490 (tpp) REVERT: B 154 TRP cc_start: 0.9161 (OUTLIER) cc_final: 0.8644 (m100) REVERT: C 13 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7719 (tt) outliers start: 22 outliers final: 16 residues processed: 124 average time/residue: 0.2874 time to fit residues: 49.0203 Evaluate side-chains 127 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 162 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 114 optimal weight: 0.0980 chunk 3 optimal weight: 0.0980 chunk 63 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.166742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119645 restraints weight = 40379.389| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.15 r_work: 0.3328 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 11987 Z= 0.135 Angle : 0.747 59.181 16420 Z= 0.465 Chirality : 0.036 0.142 1868 Planarity : 0.003 0.029 1949 Dihedral : 10.860 105.952 2073 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.18 % Allowed : 12.09 % Favored : 85.73 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.23), residues: 1351 helix: 1.28 (0.21), residues: 661 sheet: -0.86 (0.38), residues: 157 loop : -0.88 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 619 TYR 0.014 0.001 TYR A 783 PHE 0.008 0.001 PHE A 736 TRP 0.011 0.001 TRP A 911 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00262 (11979) covalent geometry : angle 0.74661 (16414) hydrogen bonds : bond 0.04046 ( 603) hydrogen bonds : angle 3.99918 ( 1649) metal coordination : bond 0.00961 ( 8) metal coordination : angle 1.94818 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5823.25 seconds wall clock time: 99 minutes 26.91 seconds (5966.91 seconds total)