Starting phenix.real_space_refine on Thu Mar 5 12:27:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s7b_24882/03_2026/7s7b_24882.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s7b_24882/03_2026/7s7b_24882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s7b_24882/03_2026/7s7b_24882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s7b_24882/03_2026/7s7b_24882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s7b_24882/03_2026/7s7b_24882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s7b_24882/03_2026/7s7b_24882.map" } resolution = 4.06 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= -0.009 sd= 1.240 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 22 5.49 5 S 134 5.16 5 C 14071 2.51 5 N 3795 2.21 5 O 4193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22217 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7376 Classifications: {'peptide': 924} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 882} Chain breaks: 2 Chain: "B" Number of atoms: 2847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2847 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 22, 'TRANS': 328} Chain breaks: 4 Chain: "C" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 644 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "D" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 236 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 6, 'rna3p': 4} Chain breaks: 1 Chain: "E" Number of atoms: 7376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7376 Classifications: {'peptide': 924} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 882} Chain breaks: 2 Chain: "F" Number of atoms: 2856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2856 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain breaks: 4 Chain: "G" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 644 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "H" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 236 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 6, 'rna3p': 4} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8786 SG CYS B 229 69.092 81.069 150.591 1.00230.03 S ATOM 8811 SG CYS B 232 68.012 81.919 147.188 1.00229.84 S ATOM 8889 SG CYS B 242 70.870 83.686 148.641 1.00233.19 S ATOM 19898 SG CYS F 229 30.303 83.287 78.681 1.00219.13 S ATOM 19923 SG CYS F 232 32.475 84.891 81.330 1.00222.29 S ATOM 20001 SG CYS F 242 29.074 86.148 80.707 1.00223.04 S Time building chain proxies: 5.32, per 1000 atoms: 0.24 Number of scatterers: 22217 At special positions: 0 Unit cell: (104.448, 154.496, 228.48, 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 134 16.00 P 22 15.00 O 4193 8.00 N 3795 7.00 C 14071 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: 1.79 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 900 " pdb="ZN ZN B 900 " - pdb=" NE2 HIS B 237 " pdb="ZN ZN B 900 " - pdb=" SG CYS B 229 " pdb="ZN ZN B 900 " - pdb=" SG CYS B 232 " pdb="ZN ZN B 900 " - pdb=" SG CYS B 242 " pdb=" ZN F 900 " pdb="ZN ZN F 900 " - pdb=" NE2 HIS F 237 " pdb="ZN ZN F 900 " - pdb=" SG CYS F 229 " pdb="ZN ZN F 900 " - pdb=" SG CYS F 242 " pdb="ZN ZN F 900 " - pdb=" SG CYS F 232 " Number of angles added : 6 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5142 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 15 sheets defined 49.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 141 through 153 removed outlier: 3.586A pdb=" N ASN A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 181 removed outlier: 3.831A pdb=" N ALA A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 206 Processing helix chain 'A' and resid 229 through 239 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.531A pdb=" N ARG A 258 " --> pdb=" O HIS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.668A pdb=" N GLU A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 301 removed outlier: 3.663A pdb=" N PHE A 292 " --> pdb=" O ASN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 356 Processing helix chain 'A' and resid 372 through 384 Processing helix chain 'A' and resid 395 through 406 Processing helix chain 'A' and resid 413 through 429 Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 438 through 451 removed outlier: 3.598A pdb=" N VAL A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Proline residue: A 446 - end of helix Processing helix chain 'A' and resid 460 through 473 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 566 through 576 Processing helix chain 'A' and resid 580 through 588 removed outlier: 3.971A pdb=" N MET A 584 " --> pdb=" O ASN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 615 removed outlier: 3.765A pdb=" N HIS A 594 " --> pdb=" O TYR A 590 " (cutoff:3.500A) Proline residue: A 599 - end of helix Processing helix chain 'A' and resid 619 through 645 Processing helix chain 'A' and resid 646 through 651 removed outlier: 3.589A pdb=" N LEU A 651 " --> pdb=" O PRO A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 654 No H-bonds generated for 'chain 'A' and resid 652 through 654' Processing helix chain 'A' and resid 754 through 770 removed outlier: 3.993A pdb=" N LEU A 760 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 806 removed outlier: 3.873A pdb=" N LYS A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 843 removed outlier: 3.910A pdb=" N VAL A 818 " --> pdb=" O ASN A 814 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 861 Processing helix chain 'A' and resid 871 through 880 removed outlier: 3.967A pdb=" N GLU A 879 " --> pdb=" O ARG A 875 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 894 Processing helix chain 'A' and resid 901 through 913 Processing helix chain 'A' and resid 929 through 949 Processing helix chain 'A' and resid 954 through 962 removed outlier: 4.319A pdb=" N PHE A 962 " --> pdb=" O TYR A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 976 Processing helix chain 'A' and resid 978 through 984 Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1016 through 1030 Processing helix chain 'B' and resid 47 through 74 Processing helix chain 'B' and resid 102 through 130 removed outlier: 5.882A pdb=" N GLN B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLU B 111 " --> pdb=" O GLN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 166 Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 277 through 281 removed outlier: 4.106A pdb=" N GLU B 280 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 Processing helix chain 'B' and resid 307 through 317 removed outlier: 4.120A pdb=" N TYR B 311 " --> pdb=" O PRO B 307 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 326 removed outlier: 3.607A pdb=" N LEU B 323 " --> pdb=" O PRO B 319 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU B 325 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 326 " --> pdb=" O TRP B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 364 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 662 through 667 removed outlier: 3.686A pdb=" N PHE B 666 " --> pdb=" O ASP B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 692 Processing helix chain 'B' and resid 695 through 700 Processing helix chain 'C' and resid 22 through 34 removed outlier: 3.872A pdb=" N GLN C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 70 Processing helix chain 'E' and resid 141 through 153 removed outlier: 3.621A pdb=" N ASN E 153 " --> pdb=" O GLN E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 181 removed outlier: 3.963A pdb=" N ALA E 171 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 207 Processing helix chain 'E' and resid 229 through 239 Processing helix chain 'E' and resid 241 through 245 removed outlier: 4.345A pdb=" N GLU E 245 " --> pdb=" O GLU E 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 241 through 245' Processing helix chain 'E' and resid 254 through 259 removed outlier: 3.654A pdb=" N ARG E 258 " --> pdb=" O HIS E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 273 removed outlier: 3.765A pdb=" N GLU E 267 " --> pdb=" O GLY E 263 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 273 " --> pdb=" O THR E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 301 removed outlier: 3.765A pdb=" N PHE E 292 " --> pdb=" O ASN E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 356 Processing helix chain 'E' and resid 372 through 384 Processing helix chain 'E' and resid 395 through 406 Processing helix chain 'E' and resid 413 through 429 Processing helix chain 'E' and resid 432 through 437 Processing helix chain 'E' and resid 438 through 451 removed outlier: 3.816A pdb=" N LEU E 445 " --> pdb=" O VAL E 441 " (cutoff:3.500A) Proline residue: E 446 - end of helix Processing helix chain 'E' and resid 460 through 473 Processing helix chain 'E' and resid 483 through 488 Processing helix chain 'E' and resid 513 through 522 Processing helix chain 'E' and resid 544 through 554 Processing helix chain 'E' and resid 566 through 576 Processing helix chain 'E' and resid 580 through 588 removed outlier: 4.044A pdb=" N MET E 584 " --> pdb=" O ASN E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 615 Proline residue: E 599 - end of helix Processing helix chain 'E' and resid 619 through 645 removed outlier: 3.584A pdb=" N VAL E 623 " --> pdb=" O ASN E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 651 Processing helix chain 'E' and resid 652 through 654 No H-bonds generated for 'chain 'E' and resid 652 through 654' Processing helix chain 'E' and resid 752 through 770 removed outlier: 3.973A pdb=" N ARG E 756 " --> pdb=" O PRO E 752 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN E 757 " --> pdb=" O VAL E 753 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 807 removed outlier: 3.894A pdb=" N LYS E 791 " --> pdb=" O ASP E 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 812 removed outlier: 4.468A pdb=" N ASN E 811 " --> pdb=" O HIS E 807 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP E 812 " --> pdb=" O PRO E 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 807 through 812' Processing helix chain 'E' and resid 814 through 843 removed outlier: 3.927A pdb=" N VAL E 818 " --> pdb=" O ASN E 814 " (cutoff:3.500A) Processing helix chain 'E' and resid 847 through 861 Processing helix chain 'E' and resid 871 through 880 removed outlier: 4.123A pdb=" N GLU E 879 " --> pdb=" O ARG E 875 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE E 880 " --> pdb=" O VAL E 876 " (cutoff:3.500A) Processing helix chain 'E' and resid 885 through 894 Processing helix chain 'E' and resid 895 through 899 removed outlier: 3.951A pdb=" N ASP E 899 " --> pdb=" O LEU E 896 " (cutoff:3.500A) Processing helix chain 'E' and resid 901 through 913 Processing helix chain 'E' and resid 929 through 949 Processing helix chain 'E' and resid 954 through 962 removed outlier: 4.332A pdb=" N PHE E 962 " --> pdb=" O TYR E 958 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 976 Processing helix chain 'E' and resid 978 through 984 Processing helix chain 'E' and resid 989 through 1015 Processing helix chain 'E' and resid 1016 through 1030 Processing helix chain 'F' and resid 47 through 75 Processing helix chain 'F' and resid 76 through 78 No H-bonds generated for 'chain 'F' and resid 76 through 78' Processing helix chain 'F' and resid 102 through 108 Processing helix chain 'F' and resid 108 through 130 Processing helix chain 'F' and resid 158 through 166 Processing helix chain 'F' and resid 278 through 282 removed outlier: 3.845A pdb=" N ARG F 282 " --> pdb=" O VAL F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 300 Processing helix chain 'F' and resid 307 through 317 removed outlier: 4.061A pdb=" N TYR F 311 " --> pdb=" O PRO F 307 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG F 312 " --> pdb=" O PRO F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 326 removed outlier: 4.078A pdb=" N GLU F 325 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 364 removed outlier: 3.733A pdb=" N LEU F 364 " --> pdb=" O LEU F 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 361 through 364' Processing helix chain 'F' and resid 395 through 403 removed outlier: 4.118A pdb=" N LEU F 403 " --> pdb=" O PHE F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 667 removed outlier: 3.661A pdb=" N PHE F 666 " --> pdb=" O ASP F 662 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA F 667 " --> pdb=" O MET F 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 662 through 667' Processing helix chain 'F' and resid 683 through 692 removed outlier: 3.596A pdb=" N LEU F 692 " --> pdb=" O ILE F 688 " (cutoff:3.500A) Processing helix chain 'F' and resid 695 through 700 Processing helix chain 'G' and resid 22 through 34 removed outlier: 3.911A pdb=" N GLN G 32 " --> pdb=" O GLU G 28 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY G 34 " --> pdb=" O PHE G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 70 removed outlier: 4.278A pdb=" N TYR G 65 " --> pdb=" O VAL G 61 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 102 removed outlier: 3.633A pdb=" N TYR A 308 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 157 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ARG A 184 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL A 249 " --> pdb=" O ARG A 184 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 186 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE A 251 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR A 188 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 189 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 212 Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 455 removed outlier: 6.683A pdb=" N GLY A 453 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE A 390 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 496 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N MET A 538 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A 498 " --> pdb=" O MET A 538 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLN A 317 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU A 537 " --> pdb=" O GLN A 317 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A 319 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL A 539 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE A 321 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE A 320 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU A 330 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LEU A 328 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU A 328 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 502 through 504 Processing sheet with id=AA5, first strand: chain 'A' and resid 727 through 732 removed outlier: 5.821A pdb=" N LEU A 699 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL A 674 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP A 668 " --> pdb=" O ASN A 664 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASN A 664 " --> pdb=" O ASP A 668 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY A 670 " --> pdb=" O VAL A 662 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 662 " --> pdb=" O GLY A 670 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS A 663 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU A 736 " --> pdb=" O LYS A 663 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 179 through 182 removed outlier: 4.762A pdb=" N PHE F 99 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER B 171 " --> pdb=" O ILE F 97 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE F 97 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU B 173 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU F 95 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE B 97 " --> pdb=" O SER F 171 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER F 171 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE B 99 " --> pdb=" O VAL F 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AA8, first strand: chain 'C' and resid 36 through 40 removed outlier: 6.644A pdb=" N ASN C 56 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL C 39 " --> pdb=" O PHE C 54 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N PHE C 54 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 99 through 102 removed outlier: 3.533A pdb=" N TYR E 308 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL E 157 " --> pdb=" O PHE E 281 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER E 283 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL E 159 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA E 247 " --> pdb=" O HIS E 278 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL E 280 " --> pdb=" O ALA E 247 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL E 249 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU E 282 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE E 251 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG E 184 " --> pdb=" O TRP E 248 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE E 250 " --> pdb=" O ARG E 184 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE E 186 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ASP E 252 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR E 188 " --> pdb=" O ASP E 252 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 211 through 212 Processing sheet with id=AB2, first strand: chain 'E' and resid 453 through 455 removed outlier: 6.707A pdb=" N GLY E 453 " --> pdb=" O PHE E 480 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL E 496 " --> pdb=" O ILE E 536 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N MET E 538 " --> pdb=" O VAL E 496 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE E 498 " --> pdb=" O MET E 538 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLN E 317 " --> pdb=" O VAL E 535 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU E 537 " --> pdb=" O GLN E 317 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TYR E 319 " --> pdb=" O LEU E 537 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL E 539 " --> pdb=" O TYR E 319 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE E 321 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE E 320 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU E 330 " --> pdb=" O ILE E 320 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU E 328 " --> pdb=" O PRO E 322 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU E 328 " --> pdb=" O TYR F 336 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 502 through 504 Processing sheet with id=AB4, first strand: chain 'E' and resid 727 through 732 removed outlier: 3.539A pdb=" N ASN E 676 " --> pdb=" O GLU E 697 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU E 699 " --> pdb=" O VAL E 674 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL E 674 " --> pdb=" O LEU E 699 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP E 668 " --> pdb=" O ASN E 664 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASN E 664 " --> pdb=" O ASP E 668 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY E 670 " --> pdb=" O VAL E 662 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL E 662 " --> pdb=" O GLY E 670 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS E 663 " --> pdb=" O LEU E 736 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU E 736 " --> pdb=" O LYS E 663 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 327 through 328 Processing sheet with id=AB6, first strand: chain 'G' and resid 36 through 40 removed outlier: 3.569A pdb=" N ILE G 80 " --> pdb=" O ILE G 73 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE G 73 " --> pdb=" O ILE G 80 " (cutoff:3.500A) 979 hydrogen bonds defined for protein. 2832 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.82 Time building geometry restraints manager: 2.44 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: 7206 1.34 - 1.45: 2775 1.45 - 1.57: 12462 1.57 - 1.69: 40 1.69 - 1.81: 218 Bond restraints: 22701 Sorted by residual: bond pdb=" C MET A 543 " pdb=" N SER A 544 " ideal model delta sigma weight residual 1.340 1.276 0.065 5.87e-02 2.90e+02 1.22e+00 bond pdb=" CB TRP A 266 " pdb=" CG TRP A 266 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.77e-01 bond pdb=" CG GLN A 655 " pdb=" CD GLN A 655 " ideal model delta sigma weight residual 1.516 1.494 0.022 2.50e-02 1.60e+03 7.43e-01 bond pdb=" CB ARG E 743 " pdb=" CG ARG E 743 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.32e-01 bond pdb=" CG GLN E 655 " pdb=" CD GLN E 655 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 6.89e-01 ... (remaining 22696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 29778 1.07 - 2.14: 744 2.14 - 3.22: 95 3.22 - 4.29: 93 4.29 - 5.36: 6 Bond angle restraints: 30716 Sorted by residual: angle pdb=" N ASP A1033 " pdb=" CA ASP A1033 " pdb=" C ASP A1033 " ideal model delta sigma weight residual 111.37 115.19 -3.82 1.64e+00 3.72e-01 5.42e+00 angle pdb=" N ILE B 94 " pdb=" CA ILE B 94 " pdb=" C ILE B 94 " ideal model delta sigma weight residual 109.34 104.73 4.61 2.08e+00 2.31e-01 4.91e+00 angle pdb=" N GLN F 107 " pdb=" CA GLN F 107 " pdb=" C GLN F 107 " ideal model delta sigma weight residual 111.36 113.77 -2.41 1.09e+00 8.42e-01 4.88e+00 angle pdb=" N ASP E1033 " pdb=" CA ASP E1033 " pdb=" C ASP E1033 " ideal model delta sigma weight residual 111.02 113.31 -2.29 1.22e+00 6.72e-01 3.53e+00 angle pdb=" N TYR A 590 " pdb=" CA TYR A 590 " pdb=" C TYR A 590 " ideal model delta sigma weight residual 113.18 110.80 2.38 1.33e+00 5.65e-01 3.20e+00 ... (remaining 30711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.79: 13363 20.79 - 41.59: 473 41.59 - 62.38: 73 62.38 - 83.17: 9 83.17 - 103.96: 2 Dihedral angle restraints: 13920 sinusoidal: 6003 harmonic: 7917 Sorted by residual: dihedral pdb=" CA ARG A1032 " pdb=" C ARG A1032 " pdb=" N ASP A1033 " pdb=" CA ASP A1033 " ideal model delta harmonic sigma weight residual 180.00 -152.89 -27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ARG E1032 " pdb=" C ARG E1032 " pdb=" N ASP E1033 " pdb=" CA ASP E1033 " ideal model delta harmonic sigma weight residual 180.00 -153.63 -26.37 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ASP E1033 " pdb=" C ASP E1033 " pdb=" N ILE E1034 " pdb=" CA ILE E1034 " ideal model delta harmonic sigma weight residual -180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 13917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2149 0.028 - 0.057: 846 0.057 - 0.085: 211 0.085 - 0.114: 159 0.114 - 0.142: 50 Chirality restraints: 3415 Sorted by residual: chirality pdb=" CA ILE B 94 " pdb=" N ILE B 94 " pdb=" C ILE B 94 " pdb=" CB ILE B 94 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA GLN A 387 " pdb=" N GLN A 387 " pdb=" C GLN A 387 " pdb=" CB GLN A 387 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE B 660 " pdb=" N ILE B 660 " pdb=" C ILE B 660 " pdb=" CB ILE B 660 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 3412 not shown) Planarity restraints: 3898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 387 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.19e+00 pdb=" N PRO E 388 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 388 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 388 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR F 311 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" C TYR F 311 " 0.027 2.00e-02 2.50e+03 pdb=" O TYR F 311 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG F 312 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 200 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO B 201 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 201 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 201 " -0.021 5.00e-02 4.00e+02 ... (remaining 3895 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 262 2.55 - 3.14: 19687 3.14 - 3.73: 33684 3.73 - 4.31: 46329 4.31 - 4.90: 78312 Nonbonded interactions: 178274 Sorted by model distance: nonbonded pdb=" OG1 THR A 228 " pdb=" OP1 A D 46 " model vdw 1.963 3.040 nonbonded pdb=" OE2 GLU E 267 " pdb=" OG SER E 561 " model vdw 1.976 3.040 nonbonded pdb=" O THR E 972 " pdb=" OG1 THR E 975 " model vdw 2.022 3.040 nonbonded pdb=" O THR A 972 " pdb=" OG1 THR A 975 " model vdw 2.067 3.040 nonbonded pdb=" N GLU E 230 " pdb=" OE1 GLU E 230 " model vdw 2.098 3.120 ... (remaining 178269 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 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 46 through 216 or resid 228 through 900)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.760 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.040 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 : 0.004 0.074 22709 Z= 0.163 Angle : 0.467 6.167 30722 Z= 0.243 Chirality : 0.039 0.142 3415 Planarity : 0.003 0.045 3898 Dihedral : 10.889 103.962 8778 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 1.54 % Allowed : 5.81 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.17), residues: 2673 helix: 1.80 (0.15), residues: 1211 sheet: -0.78 (0.36), residues: 242 loop : -1.09 (0.19), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 526 TYR 0.012 0.001 TYR E 612 PHE 0.011 0.001 PHE E 770 TRP 0.008 0.001 TRP E 295 HIS 0.003 0.001 HIS F 109 Details of bonding type rmsd covalent geometry : bond 0.00368 (22701) covalent geometry : angle 0.46341 (30716) hydrogen bonds : bond 0.15567 ( 979) hydrogen bonds : angle 6.00997 ( 2832) metal coordination : bond 0.04453 ( 8) metal coordination : angle 4.02088 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 445 time to evaluate : 0.864 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: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.8696 (mmt) cc_final: 0.8246 (mmp) REVERT: A 387 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7496 (mp10) REVERT: A 529 MET cc_start: 0.8243 (ptp) cc_final: 0.7935 (ptp) REVERT: A 643 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7147 (t80) REVERT: A 837 ARG cc_start: 0.8519 (ttp80) cc_final: 0.8258 (tmm-80) REVERT: A 891 MET cc_start: 0.8946 (mtm) cc_final: 0.8673 (mtm) REVERT: B 57 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7187 (mm-30) REVERT: B 124 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7546 (tm-30) REVERT: B 163 LYS cc_start: 0.8383 (mttt) cc_final: 0.8171 (tttp) REVERT: B 303 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8506 (p0) REVERT: B 382 TRP cc_start: 0.9339 (p-90) cc_final: 0.9020 (p90) REVERT: C 30 PHE cc_start: 0.9189 (m-10) cc_final: 0.8944 (m-10) REVERT: C 57 PHE cc_start: 0.7806 (m-80) cc_final: 0.7493 (m-10) REVERT: C 59 HIS cc_start: 0.8630 (m-70) cc_final: 0.8252 (m-70) REVERT: C 74 LYS cc_start: 0.8673 (tppp) cc_final: 0.8359 (mmmm) REVERT: E 172 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8639 (mt-10) REVERT: E 240 SER cc_start: 0.8953 (t) cc_final: 0.8464 (t) REVERT: E 387 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7632 (mp10) REVERT: E 393 SER cc_start: 0.8896 (t) cc_final: 0.8693 (p) REVERT: E 395 SER cc_start: 0.8842 (t) cc_final: 0.8323 (p) REVERT: E 398 ASP cc_start: 0.8797 (m-30) cc_final: 0.8127 (m-30) REVERT: E 408 LYS cc_start: 0.9062 (ptmm) cc_final: 0.8439 (ptmm) REVERT: E 473 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7785 (mm-30) REVERT: E 500 ASN cc_start: 0.8445 (t0) cc_final: 0.8146 (t0) REVERT: E 529 MET cc_start: 0.8215 (ptp) cc_final: 0.7982 (ptm) REVERT: E 537 LEU cc_start: 0.9602 (tp) cc_final: 0.9390 (tt) REVERT: E 542 LYS cc_start: 0.9108 (mtmt) cc_final: 0.8673 (mtmm) REVERT: E 620 GLU cc_start: 0.7522 (pt0) cc_final: 0.7059 (mp0) REVERT: E 713 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8426 (tp30) REVERT: E 725 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7359 (tm-30) REVERT: E 754 ASP cc_start: 0.8457 (t0) cc_final: 0.8153 (t0) REVERT: E 772 ASP cc_start: 0.7931 (p0) cc_final: 0.7289 (p0) REVERT: E 778 ASP cc_start: 0.8872 (t0) cc_final: 0.8594 (t0) REVERT: E 878 CYS cc_start: 0.8567 (m) cc_final: 0.8137 (m) REVERT: E 890 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8599 (mm-30) REVERT: E 1001 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8027 (tm-30) REVERT: E 1002 GLU cc_start: 0.8896 (pt0) cc_final: 0.8566 (pt0) REVERT: F 55 GLN cc_start: 0.7721 (tp40) cc_final: 0.7272 (pp30) REVERT: F 161 ASN cc_start: 0.7844 (m-40) cc_final: 0.7577 (m-40) REVERT: F 163 LYS cc_start: 0.8171 (mttt) cc_final: 0.7958 (pttp) REVERT: F 185 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8430 (pt0) REVERT: F 274 TYR cc_start: 0.8672 (p90) cc_final: 0.8458 (p90) REVERT: F 390 MET cc_start: 0.2414 (ttp) cc_final: 0.2021 (ttt) REVERT: F 677 ASN cc_start: 0.9095 (m-40) cc_final: 0.8866 (m110) REVERT: G 11 THR cc_start: 0.5863 (p) cc_final: 0.5650 (p) REVERT: G 31 HIS cc_start: 0.8600 (t70) cc_final: 0.8211 (p90) REVERT: G 52 PHE cc_start: 0.3927 (OUTLIER) cc_final: 0.3658 (p90) outliers start: 37 outliers final: 14 residues processed: 475 average time/residue: 0.1656 time to fit residues: 118.4574 Evaluate side-chains 344 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 324 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 0.0870 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN B 231 ASN B 391 GLN ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 HIS E 426 ASN E 519 GLN E 795 GLN ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 915 GLN F 102 ASN F 109 HIS F 126 GLN F 228 HIS F 238 GLN F 271 GLN ** F 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.115026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.089404 restraints weight = 49139.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.089355 restraints weight = 45755.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.090276 restraints weight = 42920.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.090838 restraints weight = 28909.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091943 restraints weight = 25595.949| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 0.050 22709 Z= 0.156 Angle : 0.626 12.185 30722 Z= 0.317 Chirality : 0.044 0.190 3415 Planarity : 0.005 0.107 3898 Dihedral : 7.827 100.246 3189 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.17), residues: 2673 helix: 1.66 (0.15), residues: 1244 sheet: -0.37 (0.37), residues: 232 loop : -1.02 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 282 TYR 0.022 0.001 TYR E 402 PHE 0.018 0.002 PHE C 52 TRP 0.019 0.001 TRP A 266 HIS 0.011 0.001 HIS E 807 Details of bonding type rmsd covalent geometry : bond 0.00359 (22701) covalent geometry : angle 0.62557 (30716) hydrogen bonds : bond 0.04523 ( 979) hydrogen bonds : angle 4.63644 ( 2832) metal coordination : bond 0.00797 ( 8) metal coordination : angle 1.69269 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 413 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 935 MET cc_start: 0.8623 (tmm) cc_final: 0.8276 (tmm) REVERT: B 49 LEU cc_start: 0.7811 (mt) cc_final: 0.7599 (mt) REVERT: B 57 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7439 (mm-30) REVERT: B 382 TRP cc_start: 0.8975 (p-90) cc_final: 0.8510 (p90) REVERT: B 663 MET cc_start: 0.8187 (ttm) cc_final: 0.7943 (ttt) REVERT: E 96 MET cc_start: 0.4978 (mpp) cc_final: 0.3939 (mpp) REVERT: E 240 SER cc_start: 0.8304 (t) cc_final: 0.7425 (t) REVERT: E 406 MET cc_start: 0.8817 (mmp) cc_final: 0.8559 (mmp) REVERT: E 480 PHE cc_start: 0.9241 (m-80) cc_final: 0.9037 (m-10) REVERT: E 497 LEU cc_start: 0.9606 (tp) cc_final: 0.9290 (tt) REVERT: E 500 ASN cc_start: 0.8618 (t0) cc_final: 0.8357 (t0) REVERT: E 536 ILE cc_start: 0.9505 (mt) cc_final: 0.9305 (mt) REVERT: E 542 LYS cc_start: 0.8900 (mtmt) cc_final: 0.8597 (mtmm) REVERT: E 680 LYS cc_start: 0.7742 (tmtt) cc_final: 0.7313 (tptp) REVERT: E 725 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7640 (tp30) REVERT: E 754 ASP cc_start: 0.7989 (t0) cc_final: 0.7751 (t0) REVERT: E 772 ASP cc_start: 0.7548 (p0) cc_final: 0.6844 (p0) REVERT: E 778 ASP cc_start: 0.8835 (t0) cc_final: 0.8502 (t0) REVERT: E 878 CYS cc_start: 0.8570 (m) cc_final: 0.8230 (m) REVERT: E 890 GLU cc_start: 0.8232 (mm-30) cc_final: 0.8004 (mm-30) REVERT: E 987 ASP cc_start: 0.8569 (p0) cc_final: 0.8246 (p0) REVERT: E 1001 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8047 (tm-30) REVERT: E 1002 GLU cc_start: 0.8407 (pt0) cc_final: 0.8129 (pt0) REVERT: F 57 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8217 (pt0) REVERT: F 161 ASN cc_start: 0.7854 (m-40) cc_final: 0.7567 (m-40) outliers start: 2 outliers final: 1 residues processed: 415 average time/residue: 0.1491 time to fit residues: 97.5392 Evaluate side-chains 313 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 98 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 116 optimal weight: 7.9990 chunk 12 optimal weight: 0.4980 chunk 140 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN B 231 ASN ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 HIS E 405 GLN ** E 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN F 102 ASN F 126 GLN F 228 HIS F 296 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.114763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.088907 restraints weight = 48997.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.089889 restraints weight = 41954.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.089767 restraints weight = 47485.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.091008 restraints weight = 28705.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.092303 restraints weight = 23348.645| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22709 Z= 0.152 Angle : 0.582 11.915 30722 Z= 0.297 Chirality : 0.043 0.187 3415 Planarity : 0.004 0.083 3898 Dihedral : 7.809 105.314 3189 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.17 % Allowed : 2.62 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.17), residues: 2673 helix: 1.66 (0.15), residues: 1245 sheet: -0.40 (0.37), residues: 232 loop : -1.03 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 50 TYR 0.022 0.001 TYR E 402 PHE 0.029 0.001 PHE C 52 TRP 0.005 0.001 TRP E 295 HIS 0.006 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00353 (22701) covalent geometry : angle 0.58169 (30716) hydrogen bonds : bond 0.04084 ( 979) hydrogen bonds : angle 4.42045 ( 2832) metal coordination : bond 0.01027 ( 8) metal coordination : angle 2.00628 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 379 time to evaluate : 0.726 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: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.7719 (mt) cc_final: 0.7497 (mt) REVERT: B 57 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7586 (mm-30) REVERT: B 128 LYS cc_start: 0.8122 (mptt) cc_final: 0.7727 (tptt) REVERT: B 382 TRP cc_start: 0.9027 (p-90) cc_final: 0.8544 (p90) REVERT: B 663 MET cc_start: 0.8201 (ttm) cc_final: 0.7963 (ttt) REVERT: C 32 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8581 (mm-40) REVERT: C 62 SER cc_start: 0.8043 (t) cc_final: 0.7691 (t) REVERT: E 197 GLN cc_start: 0.8760 (mt0) cc_final: 0.8315 (mt0) REVERT: E 240 SER cc_start: 0.8217 (t) cc_final: 0.7487 (t) REVERT: E 267 GLU cc_start: 0.8224 (mt-10) cc_final: 0.8012 (mt-10) REVERT: E 406 MET cc_start: 0.8893 (mmp) cc_final: 0.8657 (mmp) REVERT: E 408 LYS cc_start: 0.9034 (ptmt) cc_final: 0.8806 (ptmm) REVERT: E 500 ASN cc_start: 0.8642 (t0) cc_final: 0.8308 (t0) REVERT: E 542 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8486 (mtmm) REVERT: E 680 LYS cc_start: 0.7691 (tmtt) cc_final: 0.7255 (tptp) REVERT: E 725 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7622 (tp30) REVERT: E 772 ASP cc_start: 0.7521 (p0) cc_final: 0.6856 (p0) REVERT: E 778 ASP cc_start: 0.8883 (t0) cc_final: 0.8535 (t0) REVERT: E 878 CYS cc_start: 0.8467 (m) cc_final: 0.8146 (m) REVERT: E 987 ASP cc_start: 0.8425 (p0) cc_final: 0.8222 (p0) REVERT: E 999 ARG cc_start: 0.8409 (mmm-85) cc_final: 0.8144 (mmm-85) REVERT: E 1001 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7964 (tm-30) REVERT: E 1002 GLU cc_start: 0.8442 (pt0) cc_final: 0.8098 (pt0) REVERT: E 1007 MET cc_start: 0.8840 (mmm) cc_final: 0.8613 (mmm) REVERT: F 66 GLU cc_start: 0.6884 (mp0) cc_final: 0.6623 (mp0) REVERT: F 133 LYS cc_start: 0.5734 (tmmt) cc_final: 0.5457 (mmtt) REVERT: F 161 ASN cc_start: 0.7795 (m-40) cc_final: 0.7545 (m-40) REVERT: F 163 LYS cc_start: 0.8348 (tttm) cc_final: 0.8138 (tttm) REVERT: F 239 MET cc_start: 0.6502 (mmm) cc_final: 0.5965 (mmm) REVERT: F 399 PHE cc_start: 0.7405 (t80) cc_final: 0.7117 (t80) outliers start: 4 outliers final: 1 residues processed: 380 average time/residue: 0.1473 time to fit residues: 89.1223 Evaluate side-chains 306 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 305 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 135 optimal weight: 4.9990 chunk 177 optimal weight: 0.1980 chunk 259 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 190 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 HIS ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 GLN E 591 GLN ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN F 126 GLN F 228 HIS F 275 HIS F 330 ASN G 59 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.113931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.088365 restraints weight = 49610.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.088302 restraints weight = 46285.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.089114 restraints weight = 44475.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.089629 restraints weight = 30170.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.090820 restraints weight = 26686.803| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22709 Z= 0.182 Angle : 0.579 11.486 30722 Z= 0.296 Chirality : 0.043 0.209 3415 Planarity : 0.004 0.062 3898 Dihedral : 7.828 105.645 3189 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.12 % Allowed : 2.53 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.17), residues: 2673 helix: 1.62 (0.15), residues: 1245 sheet: -0.29 (0.37), residues: 232 loop : -1.03 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 50 TYR 0.020 0.001 TYR G 65 PHE 0.017 0.001 PHE G 52 TRP 0.006 0.001 TRP E 511 HIS 0.005 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00435 (22701) covalent geometry : angle 0.57888 (30716) hydrogen bonds : bond 0.04008 ( 979) hydrogen bonds : angle 4.41610 ( 2832) metal coordination : bond 0.00406 ( 8) metal coordination : angle 1.47948 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 365 time to evaluate : 0.917 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: A 935 MET cc_start: 0.8517 (tmm) cc_final: 0.8240 (tmm) REVERT: B 49 LEU cc_start: 0.7728 (mt) cc_final: 0.7500 (mt) REVERT: B 57 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7591 (mm-30) REVERT: B 128 LYS cc_start: 0.8059 (mptt) cc_final: 0.7690 (tptt) REVERT: B 382 TRP cc_start: 0.8998 (p-90) cc_final: 0.8481 (p90) REVERT: B 663 MET cc_start: 0.8204 (ttm) cc_final: 0.7978 (ttt) REVERT: C 62 SER cc_start: 0.8059 (t) cc_final: 0.7722 (t) REVERT: E 240 SER cc_start: 0.8266 (t) cc_final: 0.7606 (t) REVERT: E 408 LYS cc_start: 0.9082 (ptmt) cc_final: 0.8858 (ptmm) REVERT: E 500 ASN cc_start: 0.8597 (t0) cc_final: 0.8370 (t0) REVERT: E 519 GLN cc_start: 0.8625 (tp40) cc_final: 0.8291 (tp40) REVERT: E 542 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8508 (mtmm) REVERT: E 543 MET cc_start: 0.8776 (tpt) cc_final: 0.8507 (tpt) REVERT: E 584 MET cc_start: 0.8323 (tpp) cc_final: 0.7925 (tpp) REVERT: E 680 LYS cc_start: 0.7831 (tmtt) cc_final: 0.7350 (tptp) REVERT: E 772 ASP cc_start: 0.7518 (p0) cc_final: 0.6872 (p0) REVERT: E 778 ASP cc_start: 0.8872 (t0) cc_final: 0.8547 (t0) REVERT: E 878 CYS cc_start: 0.8618 (m) cc_final: 0.8244 (m) REVERT: E 987 ASP cc_start: 0.8488 (p0) cc_final: 0.8230 (p0) REVERT: E 999 ARG cc_start: 0.8430 (mmm-85) cc_final: 0.8163 (mmm-85) REVERT: E 1001 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7953 (tm-30) REVERT: E 1007 MET cc_start: 0.8847 (mmm) cc_final: 0.8549 (mmm) REVERT: F 66 GLU cc_start: 0.6883 (mp0) cc_final: 0.6264 (mp0) REVERT: F 133 LYS cc_start: 0.5618 (tmmt) cc_final: 0.5290 (mmtt) REVERT: F 161 ASN cc_start: 0.7843 (m-40) cc_final: 0.7559 (m-40) REVERT: F 163 LYS cc_start: 0.8440 (tttm) cc_final: 0.8178 (tptm) REVERT: F 239 MET cc_start: 0.6645 (mmm) cc_final: 0.6305 (mmm) REVERT: F 399 PHE cc_start: 0.7326 (t80) cc_final: 0.6967 (t80) outliers start: 3 outliers final: 0 residues processed: 366 average time/residue: 0.1494 time to fit residues: 87.1629 Evaluate side-chains 292 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 67 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 189 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 242 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 240 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 210 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN B 275 HIS ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 GLN ** E 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN F 102 ASN F 126 GLN F 228 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.089555 restraints weight = 49067.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.089278 restraints weight = 46002.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.090060 restraints weight = 45514.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.090763 restraints weight = 30509.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091910 restraints weight = 26912.602| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22709 Z= 0.136 Angle : 0.556 11.629 30722 Z= 0.282 Chirality : 0.042 0.207 3415 Planarity : 0.004 0.077 3898 Dihedral : 7.757 106.610 3189 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.08 % Allowed : 1.83 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.17), residues: 2673 helix: 1.67 (0.15), residues: 1247 sheet: -0.24 (0.36), residues: 232 loop : -0.99 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 999 TYR 0.013 0.001 TYR E 402 PHE 0.016 0.001 PHE G 52 TRP 0.005 0.001 TRP A 295 HIS 0.009 0.001 HIS E 807 Details of bonding type rmsd covalent geometry : bond 0.00318 (22701) covalent geometry : angle 0.55622 (30716) hydrogen bonds : bond 0.03713 ( 979) hydrogen bonds : angle 4.26382 ( 2832) metal coordination : bond 0.00338 ( 8) metal coordination : angle 1.27765 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 363 time to evaluate : 0.850 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 935 MET cc_start: 0.8502 (tmm) cc_final: 0.8100 (tmm) REVERT: B 49 LEU cc_start: 0.7720 (mt) cc_final: 0.7499 (mt) REVERT: B 57 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7581 (mm-30) REVERT: B 239 MET cc_start: 0.4313 (tpp) cc_final: 0.1247 (tmm) REVERT: B 382 TRP cc_start: 0.8989 (p-90) cc_final: 0.8451 (p90) REVERT: C 62 SER cc_start: 0.7982 (t) cc_final: 0.7643 (t) REVERT: E 240 SER cc_start: 0.8194 (t) cc_final: 0.7864 (t) REVERT: E 408 LYS cc_start: 0.9046 (ptmt) cc_final: 0.8818 (ptmm) REVERT: E 438 LEU cc_start: 0.9112 (mt) cc_final: 0.8784 (mp) REVERT: E 500 ASN cc_start: 0.8578 (t0) cc_final: 0.8342 (t0) REVERT: E 542 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8485 (mtmm) REVERT: E 543 MET cc_start: 0.8778 (tpt) cc_final: 0.8536 (tpt) REVERT: E 772 ASP cc_start: 0.7524 (p0) cc_final: 0.6885 (p0) REVERT: E 778 ASP cc_start: 0.8788 (t0) cc_final: 0.8471 (t0) REVERT: E 878 CYS cc_start: 0.8500 (m) cc_final: 0.8115 (m) REVERT: E 987 ASP cc_start: 0.8402 (p0) cc_final: 0.8161 (p0) REVERT: E 999 ARG cc_start: 0.8370 (mmm-85) cc_final: 0.8128 (mmm-85) REVERT: E 1001 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7937 (tm-30) REVERT: E 1007 MET cc_start: 0.8828 (mmm) cc_final: 0.8539 (mmm) REVERT: F 66 GLU cc_start: 0.6801 (mp0) cc_final: 0.6598 (mp0) REVERT: F 102 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7547 (p0) REVERT: F 161 ASN cc_start: 0.7838 (m-40) cc_final: 0.7548 (m-40) REVERT: F 163 LYS cc_start: 0.8473 (tttm) cc_final: 0.8190 (tptm) REVERT: F 239 MET cc_start: 0.6784 (mmm) cc_final: 0.6490 (mmm) REVERT: F 399 PHE cc_start: 0.7282 (t80) cc_final: 0.6854 (t80) REVERT: G 31 HIS cc_start: 0.8093 (p90) cc_final: 0.7762 (p90) outliers start: 2 outliers final: 0 residues processed: 364 average time/residue: 0.1390 time to fit residues: 80.7556 Evaluate side-chains 293 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 103 optimal weight: 0.4980 chunk 116 optimal weight: 4.9990 chunk 230 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 GLN ** E 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.115230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.090237 restraints weight = 49213.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.090069 restraints weight = 44786.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.090410 restraints weight = 48929.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.091912 restraints weight = 29636.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.092819 restraints weight = 23661.524| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22709 Z= 0.145 Angle : 0.564 11.246 30722 Z= 0.286 Chirality : 0.043 0.241 3415 Planarity : 0.004 0.062 3898 Dihedral : 7.715 107.613 3189 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.08 % Allowed : 1.37 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2673 helix: 1.66 (0.15), residues: 1247 sheet: -0.22 (0.36), residues: 228 loop : -1.03 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 54 TYR 0.024 0.001 TYR G 65 PHE 0.015 0.001 PHE A 912 TRP 0.005 0.001 TRP F 198 HIS 0.006 0.001 HIS E 807 Details of bonding type rmsd covalent geometry : bond 0.00343 (22701) covalent geometry : angle 0.56385 (30716) hydrogen bonds : bond 0.03686 ( 979) hydrogen bonds : angle 4.23268 ( 2832) metal coordination : bond 0.00390 ( 8) metal coordination : angle 1.45162 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 368 time to evaluate : 0.752 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 935 MET cc_start: 0.8498 (tmm) cc_final: 0.8125 (tmm) REVERT: B 49 LEU cc_start: 0.7782 (mt) cc_final: 0.7576 (mt) REVERT: B 57 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7627 (mm-30) REVERT: B 239 MET cc_start: 0.4289 (tpp) cc_final: 0.1279 (tmm) REVERT: B 382 TRP cc_start: 0.9036 (p-90) cc_final: 0.8492 (p90) REVERT: E 438 LEU cc_start: 0.9109 (mt) cc_final: 0.8788 (mp) REVERT: E 463 LEU cc_start: 0.9168 (mt) cc_final: 0.8932 (mt) REVERT: E 542 LYS cc_start: 0.8772 (mtmt) cc_final: 0.8484 (mtmm) REVERT: E 543 MET cc_start: 0.8786 (tpt) cc_final: 0.8540 (tpt) REVERT: E 584 MET cc_start: 0.8326 (tpp) cc_final: 0.7912 (tpp) REVERT: E 765 GLU cc_start: 0.7696 (tp30) cc_final: 0.7470 (tp30) REVERT: E 772 ASP cc_start: 0.7495 (p0) cc_final: 0.6859 (p0) REVERT: E 778 ASP cc_start: 0.8777 (t0) cc_final: 0.8454 (t0) REVERT: E 878 CYS cc_start: 0.8548 (m) cc_final: 0.8238 (m) REVERT: E 999 ARG cc_start: 0.8440 (mmm-85) cc_final: 0.8153 (mmm-85) REVERT: E 1001 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7940 (tm-30) REVERT: F 52 ARG cc_start: 0.7460 (mmm160) cc_final: 0.6652 (mtt90) REVERT: F 55 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7186 (pp30) REVERT: F 57 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8157 (pt0) REVERT: F 66 GLU cc_start: 0.6915 (mp0) cc_final: 0.6283 (mp0) REVERT: F 161 ASN cc_start: 0.7780 (m-40) cc_final: 0.7540 (m-40) REVERT: F 163 LYS cc_start: 0.8468 (tttm) cc_final: 0.8225 (tttm) REVERT: F 239 MET cc_start: 0.6834 (mmm) cc_final: 0.6514 (mmm) REVERT: F 399 PHE cc_start: 0.7361 (t80) cc_final: 0.6863 (t80) REVERT: G 31 HIS cc_start: 0.8151 (p90) cc_final: 0.6411 (t-90) outliers start: 2 outliers final: 0 residues processed: 369 average time/residue: 0.1423 time to fit residues: 82.8018 Evaluate side-chains 300 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 39 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 GLN ** E 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN F 391 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.114458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.088869 restraints weight = 49407.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.089091 restraints weight = 43257.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.089292 restraints weight = 50296.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.090843 restraints weight = 30536.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.091332 restraints weight = 24208.044| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 22709 Z= 0.179 Angle : 0.584 11.244 30722 Z= 0.295 Chirality : 0.044 0.273 3415 Planarity : 0.004 0.051 3898 Dihedral : 7.723 108.075 3189 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2673 helix: 1.68 (0.15), residues: 1246 sheet: -0.19 (0.37), residues: 228 loop : -1.05 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 54 TYR 0.019 0.001 TYR C 76 PHE 0.019 0.001 PHE E 912 TRP 0.006 0.001 TRP F 198 HIS 0.006 0.001 HIS E 807 Details of bonding type rmsd covalent geometry : bond 0.00431 (22701) covalent geometry : angle 0.58340 (30716) hydrogen bonds : bond 0.03813 ( 979) hydrogen bonds : angle 4.27597 ( 2832) metal coordination : bond 0.00461 ( 8) metal coordination : angle 1.68084 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.876 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7985 (mt-10) REVERT: A 935 MET cc_start: 0.8545 (tmm) cc_final: 0.8132 (tmm) REVERT: B 49 LEU cc_start: 0.7802 (mt) cc_final: 0.7589 (mt) REVERT: B 57 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7626 (mm-30) REVERT: B 239 MET cc_start: 0.4321 (tpp) cc_final: 0.1306 (tmm) REVERT: B 382 TRP cc_start: 0.9075 (p-90) cc_final: 0.8509 (p90) REVERT: B 390 MET cc_start: 0.6488 (mtt) cc_final: 0.6056 (mmm) REVERT: E 500 ASN cc_start: 0.8622 (t0) cc_final: 0.8373 (t0) REVERT: E 542 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8502 (mtmm) REVERT: E 543 MET cc_start: 0.8753 (tpt) cc_final: 0.8519 (tpt) REVERT: E 584 MET cc_start: 0.8373 (tpp) cc_final: 0.7942 (tpp) REVERT: E 680 LYS cc_start: 0.7745 (tmtt) cc_final: 0.7389 (tptp) REVERT: E 765 GLU cc_start: 0.7662 (tp30) cc_final: 0.7434 (tp30) REVERT: E 772 ASP cc_start: 0.7528 (p0) cc_final: 0.6905 (p0) REVERT: E 778 ASP cc_start: 0.8814 (t0) cc_final: 0.8486 (t0) REVERT: E 878 CYS cc_start: 0.8583 (m) cc_final: 0.8227 (m) REVERT: E 999 ARG cc_start: 0.8431 (mmm-85) cc_final: 0.8188 (mmm-85) REVERT: E 1001 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7937 (tm-30) REVERT: E 1007 MET cc_start: 0.8882 (mmm) cc_final: 0.8666 (mmm) REVERT: F 52 ARG cc_start: 0.7672 (mmm160) cc_final: 0.6644 (mtt90) REVERT: F 57 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7987 (pt0) REVERT: F 66 GLU cc_start: 0.6743 (mp0) cc_final: 0.6018 (mp0) REVERT: F 161 ASN cc_start: 0.7825 (m-40) cc_final: 0.7541 (m-40) REVERT: F 239 MET cc_start: 0.6828 (mmm) cc_final: 0.6612 (mmm) REVERT: G 31 HIS cc_start: 0.8011 (p90) cc_final: 0.6477 (t70) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.1440 time to fit residues: 80.7111 Evaluate side-chains 288 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 255 optimal weight: 0.9980 chunk 157 optimal weight: 0.5980 chunk 222 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 247 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 HIS ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS B 231 ASN ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN ** F 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.114535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.089010 restraints weight = 49353.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.089300 restraints weight = 45033.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.089748 restraints weight = 45742.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.090510 restraints weight = 28584.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.091696 restraints weight = 24799.339| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22709 Z= 0.171 Angle : 0.595 11.432 30722 Z= 0.303 Chirality : 0.044 0.315 3415 Planarity : 0.004 0.051 3898 Dihedral : 7.736 107.988 3189 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.04 % Allowed : 1.08 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.17), residues: 2673 helix: 1.59 (0.15), residues: 1243 sheet: 0.07 (0.39), residues: 206 loop : -1.08 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 54 TYR 0.020 0.001 TYR F 274 PHE 0.017 0.001 PHE E 912 TRP 0.005 0.001 TRP F 198 HIS 0.005 0.001 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00411 (22701) covalent geometry : angle 0.59423 (30716) hydrogen bonds : bond 0.03811 ( 979) hydrogen bonds : angle 4.31851 ( 2832) metal coordination : bond 0.00408 ( 8) metal coordination : angle 1.85102 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 343 time to evaluate : 0.683 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: symmetry clash REVERT: A 268 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8007 (mt-10) REVERT: A 921 MET cc_start: 0.8144 (tpp) cc_final: 0.7944 (tpp) REVERT: A 935 MET cc_start: 0.8540 (tmm) cc_final: 0.8229 (tmm) REVERT: B 57 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7603 (mm-30) REVERT: B 239 MET cc_start: 0.4305 (tpp) cc_final: 0.1317 (tmm) REVERT: B 313 MET cc_start: 0.7439 (ppp) cc_final: 0.7047 (tmm) REVERT: B 382 TRP cc_start: 0.9108 (p-90) cc_final: 0.8737 (p90) REVERT: E 192 LYS cc_start: 0.8285 (mttm) cc_final: 0.7871 (mmtm) REVERT: E 473 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6986 (mm-30) REVERT: E 500 ASN cc_start: 0.8664 (t0) cc_final: 0.8348 (t0) REVERT: E 542 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8470 (mtmm) REVERT: E 543 MET cc_start: 0.8733 (tpt) cc_final: 0.8501 (tpt) REVERT: E 584 MET cc_start: 0.8334 (tpp) cc_final: 0.7910 (tpp) REVERT: E 680 LYS cc_start: 0.7723 (tmtt) cc_final: 0.7377 (tptp) REVERT: E 765 GLU cc_start: 0.7669 (tp30) cc_final: 0.7447 (tp30) REVERT: E 772 ASP cc_start: 0.7530 (p0) cc_final: 0.6904 (p0) REVERT: E 778 ASP cc_start: 0.8809 (t0) cc_final: 0.8511 (t0) REVERT: E 878 CYS cc_start: 0.8563 (m) cc_final: 0.8226 (m) REVERT: E 999 ARG cc_start: 0.8405 (mmm-85) cc_final: 0.8148 (mmm-85) REVERT: E 1001 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7916 (tm-30) REVERT: F 55 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7599 (pp30) REVERT: F 66 GLU cc_start: 0.6802 (mp0) cc_final: 0.5992 (mp0) REVERT: F 161 ASN cc_start: 0.7814 (m-40) cc_final: 0.7519 (m-40) REVERT: F 239 MET cc_start: 0.6938 (mmm) cc_final: 0.6720 (mmm) REVERT: F 274 TYR cc_start: 0.8748 (p90) cc_final: 0.8504 (p90) REVERT: G 31 HIS cc_start: 0.8058 (p90) cc_final: 0.7835 (p90) outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.1439 time to fit residues: 78.8357 Evaluate side-chains 293 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 2.9990 chunk 63 optimal weight: 0.0050 chunk 226 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 2 optimal weight: 0.0170 chunk 199 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 221 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 overall best weight: 0.5232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN ** F 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.115857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.090444 restraints weight = 49204.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.090458 restraints weight = 43693.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.090963 restraints weight = 45754.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.091902 restraints weight = 29402.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.092543 restraints weight = 25450.280| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22709 Z= 0.124 Angle : 0.571 11.178 30722 Z= 0.289 Chirality : 0.042 0.231 3415 Planarity : 0.004 0.059 3898 Dihedral : 7.632 107.793 3189 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.17), residues: 2673 helix: 1.55 (0.15), residues: 1259 sheet: 0.17 (0.38), residues: 202 loop : -1.10 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 233 TYR 0.017 0.001 TYR E 402 PHE 0.022 0.001 PHE E 912 TRP 0.006 0.001 TRP E 295 HIS 0.004 0.001 HIS E 807 Details of bonding type rmsd covalent geometry : bond 0.00285 (22701) covalent geometry : angle 0.57074 (30716) hydrogen bonds : bond 0.03555 ( 979) hydrogen bonds : angle 4.20529 ( 2832) metal coordination : bond 0.00414 ( 8) metal coordination : angle 1.24990 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.737 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: symmetry clash REVERT: A 935 MET cc_start: 0.8559 (tmm) cc_final: 0.8215 (tmm) REVERT: B 57 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7581 (mm-30) REVERT: B 239 MET cc_start: 0.4407 (tpp) cc_final: 0.1322 (tmm) REVERT: B 313 MET cc_start: 0.7347 (ppp) cc_final: 0.6975 (tmm) REVERT: B 382 TRP cc_start: 0.8964 (p-90) cc_final: 0.8591 (p90) REVERT: E 500 ASN cc_start: 0.8551 (t0) cc_final: 0.8321 (t0) REVERT: E 542 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8450 (mtmm) REVERT: E 543 MET cc_start: 0.8719 (tpt) cc_final: 0.8458 (tpt) REVERT: E 584 MET cc_start: 0.8280 (tpp) cc_final: 0.7830 (tpp) REVERT: E 765 GLU cc_start: 0.7601 (tp30) cc_final: 0.7392 (tp30) REVERT: E 772 ASP cc_start: 0.7629 (p0) cc_final: 0.6988 (p0) REVERT: E 778 ASP cc_start: 0.8777 (t0) cc_final: 0.8479 (t0) REVERT: E 878 CYS cc_start: 0.8612 (m) cc_final: 0.8393 (m) REVERT: E 967 MET cc_start: 0.8605 (mtp) cc_final: 0.8172 (mtt) REVERT: E 999 ARG cc_start: 0.8409 (mmm-85) cc_final: 0.8102 (mmm-85) REVERT: E 1001 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7829 (tm-30) REVERT: E 1007 MET cc_start: 0.8860 (mmm) cc_final: 0.8412 (mmm) REVERT: F 52 ARG cc_start: 0.7695 (mmm160) cc_final: 0.6677 (mtt90) REVERT: F 66 GLU cc_start: 0.6870 (mp0) cc_final: 0.6509 (mp0) REVERT: F 161 ASN cc_start: 0.7794 (m-40) cc_final: 0.7500 (m-40) REVERT: F 163 LYS cc_start: 0.8500 (tttm) cc_final: 0.8249 (tttm) REVERT: G 31 HIS cc_start: 0.7837 (p90) cc_final: 0.6775 (t-90) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.1430 time to fit residues: 81.8264 Evaluate side-chains 288 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 157 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 243 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 GLN E 519 GLN F 55 GLN F 126 GLN ** F 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.115912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.090761 restraints weight = 49389.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.090498 restraints weight = 43029.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.091003 restraints weight = 47458.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.092244 restraints weight = 29009.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094896 restraints weight = 23805.730| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22709 Z= 0.130 Angle : 0.582 11.074 30722 Z= 0.293 Chirality : 0.043 0.351 3415 Planarity : 0.004 0.053 3898 Dihedral : 7.581 108.015 3189 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.04 % Allowed : 0.21 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.17), residues: 2673 helix: 1.52 (0.15), residues: 1261 sheet: 0.20 (0.38), residues: 202 loop : -1.11 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 697 TYR 0.025 0.001 TYR C 76 PHE 0.021 0.001 PHE C 84 TRP 0.011 0.001 TRP E 266 HIS 0.004 0.001 HIS E 807 Details of bonding type rmsd covalent geometry : bond 0.00303 (22701) covalent geometry : angle 0.58148 (30716) hydrogen bonds : bond 0.03546 ( 979) hydrogen bonds : angle 4.20546 ( 2832) metal coordination : bond 0.00356 ( 8) metal coordination : angle 1.46327 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 348 time to evaluate : 0.866 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: A 935 MET cc_start: 0.8565 (tmm) cc_final: 0.8192 (tmm) REVERT: B 57 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7651 (mm-30) REVERT: B 239 MET cc_start: 0.4310 (tpp) cc_final: 0.1332 (tmm) REVERT: B 313 MET cc_start: 0.7447 (ppp) cc_final: 0.6965 (tmm) REVERT: B 382 TRP cc_start: 0.9041 (p-90) cc_final: 0.8673 (p90) REVERT: E 233 ARG cc_start: 0.8723 (mtp-110) cc_final: 0.8515 (ttp80) REVERT: E 500 ASN cc_start: 0.8526 (t0) cc_final: 0.8311 (t0) REVERT: E 542 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8407 (mtmm) REVERT: E 543 MET cc_start: 0.8728 (tpt) cc_final: 0.8497 (tpt) REVERT: E 584 MET cc_start: 0.8239 (tpp) cc_final: 0.7795 (tpp) REVERT: E 765 GLU cc_start: 0.7719 (tp30) cc_final: 0.7499 (tp30) REVERT: E 772 ASP cc_start: 0.7608 (p0) cc_final: 0.6992 (p0) REVERT: E 778 ASP cc_start: 0.8799 (t0) cc_final: 0.8491 (t0) REVERT: E 878 CYS cc_start: 0.8453 (m) cc_final: 0.8226 (m) REVERT: E 967 MET cc_start: 0.8688 (mtp) cc_final: 0.8231 (mtt) REVERT: E 1001 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7836 (tm-30) REVERT: E 1007 MET cc_start: 0.8857 (mmm) cc_final: 0.8385 (mmm) REVERT: F 52 ARG cc_start: 0.7290 (mmm160) cc_final: 0.6316 (mtt90) REVERT: F 66 GLU cc_start: 0.6954 (mp0) cc_final: 0.6280 (mp0) REVERT: F 161 ASN cc_start: 0.7720 (m-40) cc_final: 0.7402 (m-40) REVERT: F 239 MET cc_start: 0.4741 (mmm) cc_final: 0.4311 (mmm) REVERT: G 31 HIS cc_start: 0.7956 (p90) cc_final: 0.6873 (t-90) outliers start: 1 outliers final: 0 residues processed: 348 average time/residue: 0.1395 time to fit residues: 78.1345 Evaluate side-chains 292 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 187 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 185 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 223 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN ** F 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 698 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.115102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.090093 restraints weight = 49315.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.089956 restraints weight = 43846.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.090574 restraints weight = 47605.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.091692 restraints weight = 29172.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092640 restraints weight = 24634.283| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22709 Z= 0.148 Angle : 0.591 11.008 30722 Z= 0.299 Chirality : 0.043 0.237 3415 Planarity : 0.004 0.048 3898 Dihedral : 7.566 108.010 3189 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.17), residues: 2673 helix: 1.47 (0.15), residues: 1262 sheet: 0.22 (0.38), residues: 202 loop : -1.12 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 233 TYR 0.033 0.001 TYR C 76 PHE 0.014 0.001 PHE E 143 TRP 0.008 0.001 TRP E 266 HIS 0.005 0.001 HIS A 965 Details of bonding type rmsd covalent geometry : bond 0.00350 (22701) covalent geometry : angle 0.59055 (30716) hydrogen bonds : bond 0.03600 ( 979) hydrogen bonds : angle 4.22834 ( 2832) metal coordination : bond 0.00377 ( 8) metal coordination : angle 1.34805 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3204.46 seconds wall clock time: 56 minutes 21.53 seconds (3381.53 seconds total)