Starting phenix.real_space_refine on Sun Sep 13 09:18:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s7b_24882/09_2026/7s7b_24882.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s7b_24882/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7s7b_24882/09_2026/7s7b_24882.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s7b_24882/09_2026/7s7b_24882.cif" model { file = "/net/cci-nas-00/data/ceres_data/7s7b_24882/09_2026/7s7b_24882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s7b_24882/09_2026/7s7b_24882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s7b_24882/09_2026/7s7b_24882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s7b_24882/09_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: 5.43, 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: 1.92 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: 0.69 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: 4.46 Time building geometry restraints manager: 2.55 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: 29631 1.07 - 2.14: 801 2.14 - 3.22: 146 3.22 - 4.29: 118 4.29 - 5.36: 20 Bond angle restraints: 30716 Sorted by residual: angle pdb=" C3' A D 40 " pdb=" C2' A D 40 " pdb=" O2' A D 40 " ideal model delta sigma weight residual 109.80 114.98 -5.18 2.00e+00 2.50e-01 6.71e+00 angle pdb=" C3' A H 40 " pdb=" C2' A H 40 " pdb=" O2' A H 40 " ideal model delta sigma weight residual 109.80 114.83 -5.03 2.00e+00 2.50e-01 6.33e+00 angle pdb=" C3' A H 39 " pdb=" C2' A H 39 " pdb=" O2' A H 39 " ideal model delta sigma weight residual 109.80 114.77 -4.97 2.00e+00 2.50e-01 6.17e+00 angle pdb=" C3' A H 41 " pdb=" C2' A H 41 " pdb=" O2' A H 41 " ideal model delta sigma weight residual 109.80 114.77 -4.97 2.00e+00 2.50e-01 6.17e+00 angle pdb=" C3' A D 39 " pdb=" C2' A D 39 " pdb=" O2' A D 39 " ideal model delta sigma weight residual 109.80 114.76 -4.96 2.00e+00 2.50e-01 6.16e+00 ... (remaining 30711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 12962 16.01 - 32.03: 700 32.03 - 48.04: 153 48.04 - 64.05: 65 64.05 - 80.07: 16 Dihedral angle restraints: 13896 sinusoidal: 5979 harmonic: 7917 Sorted by residual: dihedral pdb=" C4' A H 41 " pdb=" C3' A H 41 " pdb=" C2' A H 41 " pdb=" C1' A H 41 " ideal model delta sinusoidal sigma weight residual 36.34 -37.12 73.47 1 3.10e+00 1.04e-01 7.15e+02 dihedral pdb=" C4' A D 40 " pdb=" C3' A D 40 " pdb=" C2' A D 40 " pdb=" C1' A D 40 " ideal model delta sinusoidal sigma weight residual 36.34 -36.74 73.08 1 3.10e+00 1.04e-01 7.08e+02 dihedral pdb=" C4' A D 41 " pdb=" C3' A D 41 " pdb=" C2' A D 41 " pdb=" C1' A D 41 " ideal model delta sinusoidal sigma weight residual 36.35 -36.65 73.00 1 3.10e+00 1.04e-01 7.07e+02 ... (remaining 13893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2946 0.057 - 0.115: 379 0.115 - 0.172: 45 0.172 - 0.230: 19 0.230 - 0.287: 26 Chirality restraints: 3415 Sorted by residual: chirality pdb=" C2' A D 40 " pdb=" C3' A D 40 " pdb=" O2' A D 40 " pdb=" C1' A D 40 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C2' A D 39 " pdb=" C3' A D 39 " pdb=" O2' A D 39 " pdb=" C1' A D 39 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C2' A D 45 " pdb=" C3' A D 45 " pdb=" O2' A D 45 " pdb=" C1' A D 45 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (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: 5.620 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: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.670 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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= 0.165 Angle : 0.507 6.167 30722 Z= 0.257 Chirality : 0.048 0.287 3415 Planarity : 0.003 0.045 3898 Dihedral : 11.600 80.067 8754 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/Z covalent geometry : bond 0.00372 / 0.16 (22701) covalent geometry : angle 0.50406 / 0.26 (30716) hydrogen bonds : bond 0.15567 / 10.64 ( 979) hydrogen bonds : angle 6.00997 / 4.25 ( 2832) metal coordination : bond 0.04453 / 2.35 ( 8) metal coordination : angle 4.02088 / 1.78 ( 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 : 1.022 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: 0.1790 time to fit residues: 129.1295 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 : 0.878 ------------------------------------------------------------------------------- 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... ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.115146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.089612 restraints weight = 49132.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.090738 restraints weight = 43487.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.090582 restraints weight = 49416.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.092136 restraints weight = 28633.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.093018 restraints weight = 22258.767| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 22709 Z= 0.173 Angle : 0.737 16.213 30722 Z= 0.354 Chirality : 0.060 0.931 3415 Planarity : 0.004 0.096 3898 Dihedral : 8.295 135.211 3165 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.08 % Allowed : 2.66 % Favored : 97.26 % 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: 0.53 (0.17), residues: 2673 helix: 1.73 (0.15), residues: 1240 sheet: -0.35 (0.37), residues: 232 loop : -1.00 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 450 TYR 0.023 0.001 TYR E 402 PHE 0.017 0.002 PHE C 52 TRP 0.018 0.001 TRP A 266 HIS 0.010 0.001 HIS E 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (22701) covalent geometry : angle 0.73706 / 0.35 (30716) hydrogen bonds : bond 0.04663 / 3.13 ( 979) hydrogen bonds : angle 4.66939 / 3.33 ( 2832) metal coordination : bond 0.00644 / 0.28 ( 8) metal coordination : angle 1.68115 / 0.76 ( 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 411 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 409 time to evaluate : 0.938 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 569 MET cc_start: 0.8717 (ttm) cc_final: 0.8353 (ttm) REVERT: A 935 MET cc_start: 0.8636 (tmm) cc_final: 0.8283 (tmm) REVERT: B 49 LEU cc_start: 0.7790 (mt) cc_final: 0.7576 (mt) REVERT: B 57 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7428 (mm-30) REVERT: B 382 TRP cc_start: 0.8993 (p-90) cc_final: 0.8533 (p90) REVERT: B 663 MET cc_start: 0.8209 (ttm) cc_final: 0.7967 (ttt) REVERT: E 96 MET cc_start: 0.5127 (mpp) cc_final: 0.4042 (mpp) REVERT: E 197 GLN cc_start: 0.8674 (mt0) cc_final: 0.8234 (mt0) REVERT: E 240 SER cc_start: 0.8273 (t) cc_final: 0.7452 (t) REVERT: E 406 MET cc_start: 0.8816 (mmp) cc_final: 0.8342 (mmp) REVERT: E 500 ASN cc_start: 0.8591 (t0) cc_final: 0.8360 (t0) REVERT: E 542 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8586 (mtmm) REVERT: E 680 LYS cc_start: 0.7648 (tmtt) cc_final: 0.7256 (tptp) REVERT: E 713 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7916 (tp30) REVERT: E 725 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7666 (tp30) REVERT: E 754 ASP cc_start: 0.7955 (t0) cc_final: 0.7720 (t0) REVERT: E 772 ASP cc_start: 0.7507 (p0) cc_final: 0.6801 (p0) REVERT: E 778 ASP cc_start: 0.8853 (t0) cc_final: 0.8508 (t0) REVERT: E 878 CYS cc_start: 0.8571 (m) cc_final: 0.8279 (m) REVERT: E 890 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7975 (mm-30) REVERT: E 987 ASP cc_start: 0.8555 (p0) cc_final: 0.8229 (p0) REVERT: E 1001 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8081 (tm-30) REVERT: E 1002 GLU cc_start: 0.8192 (pt0) cc_final: 0.7933 (pt0) REVERT: F 57 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8226 (pt0) REVERT: F 161 ASN cc_start: 0.7867 (m-40) cc_final: 0.7585 (m-40) outliers start: 2 outliers final: 2 residues processed: 411 average time/residue: 0.1561 time to fit residues: 101.5531 Evaluate side-chains 315 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 313 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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: 0.0570 chunk 149 optimal weight: 0.0670 chunk 116 optimal weight: 8.9990 chunk 12 optimal weight: 0.0470 chunk 140 optimal weight: 0.7980 chunk 30 optimal weight: 0.0770 chunk 120 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 overall best weight: 0.2092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN B 231 ASN ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 HIS ** 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.116862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.091631 restraints weight = 48651.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.091032 restraints weight = 40704.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091837 restraints weight = 43894.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.092681 restraints weight = 27904.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.093696 restraints weight = 24471.668| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2453 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= 0.123 Angle : 0.621 12.059 30722 Z= 0.306 Chirality : 0.049 0.420 3415 Planarity : 0.004 0.068 3898 Dihedral : 8.569 143.337 3165 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.12 % Allowed : 2.49 % Favored : 97.38 % 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: 0.48 (0.17), residues: 2673 helix: 1.67 (0.15), residues: 1243 sheet: -0.35 (0.37), residues: 228 loop : -1.01 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 50 TYR 0.023 0.001 TYR E 402 PHE 0.017 0.001 PHE G 52 TRP 0.008 0.001 TRP E 266 HIS 0.012 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (22701) covalent geometry : angle 0.62091 / 0.31 (30716) hydrogen bonds : bond 0.03828 / 2.60 ( 979) hydrogen bonds : angle 4.31192 / 3.07 ( 2832) metal coordination : bond 0.00974 / 0.49 ( 8) metal coordination : angle 1.78555 / 0.93 ( 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 400 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 397 time to evaluate : 0.927 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: 0.8153 (mt-10) cc_final: 0.7815 (mt-10) REVERT: A 569 MET cc_start: 0.8943 (ttm) cc_final: 0.8625 (ttm) REVERT: A 935 MET cc_start: 0.8618 (tmm) cc_final: 0.8330 (tmm) REVERT: B 49 LEU cc_start: 0.7658 (mt) cc_final: 0.7421 (mt) REVERT: B 57 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7643 (mm-30) REVERT: B 128 LYS cc_start: 0.8068 (mptt) cc_final: 0.7698 (tptt) REVERT: B 382 TRP cc_start: 0.8992 (p-90) cc_final: 0.8508 (p90) REVERT: B 663 MET cc_start: 0.8177 (ttm) cc_final: 0.7931 (ttt) REVERT: C 32 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8582 (mm-40) REVERT: C 62 SER cc_start: 0.7963 (t) cc_final: 0.7615 (t) REVERT: E 197 GLN cc_start: 0.8593 (mt0) cc_final: 0.8220 (mt0) REVERT: E 233 ARG cc_start: 0.8557 (ttp80) cc_final: 0.7617 (ttp-170) REVERT: E 240 SER cc_start: 0.8143 (t) cc_final: 0.7686 (t) REVERT: E 406 MET cc_start: 0.8992 (mmp) cc_final: 0.8607 (mmp) REVERT: E 408 LYS cc_start: 0.8983 (ptmt) cc_final: 0.8768 (ptmm) REVERT: E 500 ASN cc_start: 0.8552 (t0) cc_final: 0.8307 (t0) REVERT: E 542 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8466 (mtmm) REVERT: E 680 LYS cc_start: 0.7666 (tmtt) cc_final: 0.7236 (tptp) REVERT: E 713 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7877 (tp30) REVERT: E 725 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7529 (tp30) REVERT: E 772 ASP cc_start: 0.7597 (p0) cc_final: 0.6921 (p0) REVERT: E 778 ASP cc_start: 0.8833 (t0) cc_final: 0.8470 (t0) REVERT: E 878 CYS cc_start: 0.8478 (m) cc_final: 0.8143 (m) REVERT: E 987 ASP cc_start: 0.8364 (p0) cc_final: 0.8155 (p0) REVERT: E 1001 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7922 (tm-30) REVERT: E 1002 GLU cc_start: 0.7899 (pt0) cc_final: 0.7582 (pt0) REVERT: F 66 GLU cc_start: 0.6808 (mp0) cc_final: 0.6540 (mp0) REVERT: F 161 ASN cc_start: 0.7716 (m-40) cc_final: 0.7479 (m-40) REVERT: F 239 MET cc_start: 0.6216 (mmm) cc_final: 0.5742 (mmm) outliers start: 3 outliers final: 1 residues processed: 398 average time/residue: 0.1565 time to fit residues: 99.0991 Evaluate side-chains 296 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 295 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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: 0.7980 chunk 259 optimal weight: 0.0770 chunk 91 optimal weight: 0.3980 chunk 122 optimal weight: 0.6980 chunk 174 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 61 optimal weight: 0.0570 chunk 37 optimal weight: 0.8980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 HIS ** E 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN G 59 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.116977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.091523 restraints weight = 49198.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.091420 restraints weight = 46276.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.092496 restraints weight = 43085.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.093066 restraints weight = 28526.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.094243 restraints weight = 25502.868| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22709 Z= 0.118 Angle : 0.587 11.387 30722 Z= 0.291 Chirality : 0.047 0.317 3415 Planarity : 0.004 0.081 3898 Dihedral : 8.491 140.612 3165 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.08 % Allowed : 1.87 % Favored : 98.05 % 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: 0.53 (0.17), residues: 2673 helix: 1.71 (0.15), residues: 1245 sheet: -0.16 (0.37), residues: 224 loop : -1.02 (0.18), residues: 1204 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 0.024 0.001 PHE E 912 TRP 0.006 0.001 TRP B 322 HIS 0.008 0.001 HIS E 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (22701) covalent geometry : angle 0.58709 / 0.29 (30716) hydrogen bonds : bond 0.03560 / 2.39 ( 979) hydrogen bonds : angle 4.19184 / 2.97 ( 2832) metal coordination : bond 0.00388 / 0.19 ( 8) metal coordination : angle 1.50071 / 0.74 ( 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 380 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 378 time to evaluate : 0.863 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 891 MET cc_start: 0.8795 (mtp) cc_final: 0.8512 (mtm) REVERT: A 997 MET cc_start: 0.8859 (tpp) cc_final: 0.8523 (mmt) REVERT: A 1007 MET cc_start: 0.9094 (tpp) cc_final: 0.8782 (tpp) REVERT: B 49 LEU cc_start: 0.7769 (mt) cc_final: 0.7566 (mt) REVERT: B 57 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7707 (mm-30) REVERT: B 128 LYS cc_start: 0.8039 (mptt) cc_final: 0.7687 (tptt) REVERT: B 313 MET cc_start: 0.7209 (ppp) cc_final: 0.6729 (tmm) REVERT: B 382 TRP cc_start: 0.8917 (p-90) cc_final: 0.8378 (p90) REVERT: B 663 MET cc_start: 0.8093 (ttm) cc_final: 0.7855 (ttt) REVERT: B 678 MET cc_start: 0.8507 (tpt) cc_final: 0.8297 (tpt) REVERT: C 32 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8532 (mm-40) REVERT: E 197 GLN cc_start: 0.8637 (mt0) cc_final: 0.8152 (mt0) REVERT: E 240 SER cc_start: 0.7999 (t) cc_final: 0.7441 (t) REVERT: E 406 MET cc_start: 0.8961 (mmp) cc_final: 0.8623 (mmp) REVERT: E 408 LYS cc_start: 0.9043 (ptmt) cc_final: 0.8826 (ptmm) REVERT: E 542 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8467 (mtmm) REVERT: E 584 MET cc_start: 0.8252 (tpp) cc_final: 0.7962 (tpp) REVERT: E 680 LYS cc_start: 0.7623 (tmtt) cc_final: 0.7234 (tptp) REVERT: E 713 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7884 (tp30) REVERT: E 725 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7500 (tp30) REVERT: E 772 ASP cc_start: 0.7637 (p0) cc_final: 0.6999 (p0) REVERT: E 778 ASP cc_start: 0.8830 (t0) cc_final: 0.8469 (t0) REVERT: E 878 CYS cc_start: 0.8556 (m) cc_final: 0.8191 (m) REVERT: E 987 ASP cc_start: 0.8402 (p0) cc_final: 0.8141 (p0) REVERT: E 1001 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7937 (tm-30) REVERT: F 66 GLU cc_start: 0.6826 (mp0) cc_final: 0.6321 (mp0) REVERT: F 161 ASN cc_start: 0.7904 (m-40) cc_final: 0.7610 (m-40) REVERT: F 239 MET cc_start: 0.6341 (mmm) cc_final: 0.5833 (mmm) REVERT: F 678 MET cc_start: 0.8495 (mmp) cc_final: 0.8254 (tpp) REVERT: G 31 HIS cc_start: 0.8033 (p-80) cc_final: 0.6449 (t-90) outliers start: 2 outliers final: 0 residues processed: 378 average time/residue: 0.1509 time to fit residues: 91.6681 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 : 1.042 ------------------------------------------------------------------------------- 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: 0.0060 chunk 64 optimal weight: 0.5980 chunk 189 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 242 optimal weight: 0.9990 chunk 208 optimal weight: 0.9990 chunk 240 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS ** E 112 HIS ** 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 275 HIS G 59 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.116295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.090959 restraints weight = 48760.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.090794 restraints weight = 44679.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.091551 restraints weight = 43671.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.092224 restraints weight = 29061.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.093418 restraints weight = 25551.215| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22709 Z= 0.133 Angle : 0.580 11.114 30722 Z= 0.288 Chirality : 0.046 0.295 3415 Planarity : 0.004 0.059 3898 Dihedral : 8.525 142.688 3165 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.04 % Allowed : 1.70 % Favored : 98.26 % 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: 0.56 (0.17), residues: 2673 helix: 1.72 (0.15), residues: 1249 sheet: -0.12 (0.36), residues: 224 loop : -1.00 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 50 TYR 0.019 0.001 TYR F 274 PHE 0.021 0.001 PHE E 912 TRP 0.005 0.001 TRP E 511 HIS 0.006 0.001 HIS E 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (22701) covalent geometry : angle 0.57971 / 0.29 (30716) hydrogen bonds : bond 0.03534 / 2.38 ( 979) hydrogen bonds : angle 4.17452 / 2.95 ( 2832) metal coordination : bond 0.00316 / 0.15 ( 8) metal coordination : angle 1.20691 / 0.56 ( 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 374 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 0.884 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 1007 MET cc_start: 0.9095 (tpp) cc_final: 0.8798 (tpp) REVERT: B 49 LEU cc_start: 0.7767 (mt) cc_final: 0.7559 (mt) REVERT: B 57 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7663 (mm-30) REVERT: B 313 MET cc_start: 0.7207 (ppp) cc_final: 0.6772 (tmm) REVERT: B 318 TYR cc_start: 0.8699 (t80) cc_final: 0.8495 (t80) REVERT: B 382 TRP cc_start: 0.8995 (p-90) cc_final: 0.8439 (p90) REVERT: E 197 GLN cc_start: 0.8694 (mt0) cc_final: 0.8239 (mt0) REVERT: E 240 SER cc_start: 0.8134 (t) cc_final: 0.7619 (t) REVERT: E 252 ASP cc_start: 0.8263 (t0) cc_final: 0.8051 (t0) REVERT: E 406 MET cc_start: 0.8937 (mmp) cc_final: 0.8442 (mmp) REVERT: E 508 ASP cc_start: 0.7660 (p0) cc_final: 0.6685 (p0) REVERT: E 542 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8457 (mtmm) REVERT: E 584 MET cc_start: 0.8155 (tpp) cc_final: 0.7828 (tpp) REVERT: E 725 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7697 (tp30) REVERT: E 772 ASP cc_start: 0.7632 (p0) cc_final: 0.7009 (p0) REVERT: E 778 ASP cc_start: 0.8884 (t0) cc_final: 0.8556 (t0) REVERT: E 878 CYS cc_start: 0.8576 (m) cc_final: 0.8277 (m) REVERT: E 1001 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7945 (tm-30) REVERT: F 66 GLU cc_start: 0.6924 (mp0) cc_final: 0.6681 (mp0) REVERT: F 161 ASN cc_start: 0.7917 (m-40) cc_final: 0.7616 (m-40) REVERT: F 239 MET cc_start: 0.6478 (mmm) cc_final: 0.6026 (mmm) REVERT: F 399 PHE cc_start: 0.7295 (t80) cc_final: 0.6931 (t80) REVERT: F 678 MET cc_start: 0.8391 (mmp) cc_final: 0.8133 (tpp) REVERT: G 31 HIS cc_start: 0.8050 (p-80) cc_final: 0.7807 (p-80) outliers start: 1 outliers final: 0 residues processed: 373 average time/residue: 0.1526 time to fit residues: 91.6761 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 : 0.873 ------------------------------------------------------------------------------- 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: 2.9990 chunk 116 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN A 981 HIS ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 ASN F 55 GLN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN ** F 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN G 59 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.114760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.089259 restraints weight = 49334.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.089503 restraints weight = 46999.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.090105 restraints weight = 46872.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.090969 restraints weight = 29446.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.092095 restraints weight = 25584.341| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 22709 Z= 0.198 Angle : 0.618 11.153 30722 Z= 0.309 Chirality : 0.047 0.285 3415 Planarity : 0.004 0.077 3898 Dihedral : 8.629 144.266 3165 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.04 % Allowed : 1.70 % Favored : 98.26 % 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: 1.64 (0.15), residues: 1249 sheet: -0.22 (0.36), residues: 228 loop : -1.04 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 10 TYR 0.022 0.001 TYR C 76 PHE 0.015 0.002 PHE F 673 TRP 0.012 0.001 TRP E 266 HIS 0.006 0.001 HIS E 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (22701) covalent geometry : angle 0.61820 / 0.31 (30716) hydrogen bonds : bond 0.03846 / 2.60 ( 979) hydrogen bonds : angle 4.32245 / 3.06 ( 2832) metal coordination : bond 0.00401 / 0.19 ( 8) metal coordination : angle 1.39410 / 0.56 ( 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 361 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 0.859 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: 0.8561 (tmm) cc_final: 0.8124 (tmm) REVERT: B 49 LEU cc_start: 0.7757 (mt) cc_final: 0.7531 (mt) REVERT: B 57 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7598 (mm-30) REVERT: B 313 MET cc_start: 0.7053 (ppp) cc_final: 0.6848 (tmm) REVERT: B 318 TYR cc_start: 0.8782 (t80) cc_final: 0.8512 (t80) REVERT: B 382 TRP cc_start: 0.9052 (p-90) cc_final: 0.8505 (p90) REVERT: E 197 GLN cc_start: 0.8712 (mt0) cc_final: 0.8202 (mt0) REVERT: E 237 TYR cc_start: 0.8718 (m-80) cc_final: 0.8058 (m-10) REVERT: E 240 SER cc_start: 0.8179 (t) cc_final: 0.7575 (t) REVERT: E 268 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7998 (mt-10) REVERT: E 406 MET cc_start: 0.8929 (mmp) cc_final: 0.8394 (mmp) REVERT: E 463 LEU cc_start: 0.9206 (mt) cc_final: 0.9002 (mt) REVERT: E 500 ASN cc_start: 0.8666 (t0) cc_final: 0.8411 (t0) REVERT: E 542 LYS cc_start: 0.8774 (mtmt) cc_final: 0.8508 (mtmm) REVERT: E 567 TYR cc_start: 0.9181 (m-80) cc_final: 0.8914 (m-80) REVERT: E 584 MET cc_start: 0.8368 (tpp) cc_final: 0.8023 (tpp) REVERT: E 680 LYS cc_start: 0.7772 (tmtt) cc_final: 0.7398 (tptp) REVERT: E 725 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7503 (tm-30) REVERT: E 765 GLU cc_start: 0.7681 (tp30) cc_final: 0.7435 (tp30) REVERT: E 772 ASP cc_start: 0.7656 (p0) cc_final: 0.7042 (p0) REVERT: E 778 ASP cc_start: 0.8886 (t0) cc_final: 0.8576 (t0) REVERT: E 878 CYS cc_start: 0.8552 (m) cc_final: 0.8270 (m) REVERT: E 1001 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8002 (tm-30) REVERT: F 66 GLU cc_start: 0.6874 (mp0) cc_final: 0.6257 (mp0) REVERT: F 161 ASN cc_start: 0.7933 (m-40) cc_final: 0.7625 (m-40) REVERT: F 239 MET cc_start: 0.6592 (mmm) cc_final: 0.6295 (mmm) REVERT: F 399 PHE cc_start: 0.7321 (t80) cc_final: 0.6838 (t80) REVERT: G 31 HIS cc_start: 0.8103 (p-80) cc_final: 0.7846 (p-80) outliers start: 1 outliers final: 0 residues processed: 360 average time/residue: 0.1539 time to fit residues: 88.5839 Evaluate side-chains 289 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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: 0.6980 chunk 263 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 210 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN ** F 296 GLN ** 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 = 0.3596 r_free = 0.3596 target = 0.115898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.090237 restraints weight = 49162.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.089881 restraints weight = 46524.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.090620 restraints weight = 47185.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.091494 restraints weight = 30624.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.092180 restraints weight = 26634.064| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2937 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= 0.143 Angle : 0.598 11.452 30722 Z= 0.298 Chirality : 0.046 0.290 3415 Planarity : 0.004 0.065 3898 Dihedral : 8.575 143.814 3165 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.04 % Allowed : 1.62 % Favored : 98.34 % 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: 0.49 (0.17), residues: 2673 helix: 1.63 (0.15), residues: 1249 sheet: -0.14 (0.36), residues: 228 loop : -1.01 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 999 TYR 0.025 0.001 TYR F 274 PHE 0.017 0.001 PHE E 424 TRP 0.006 0.001 TRP F 198 HIS 0.005 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (22701) covalent geometry : angle 0.59778 / 0.30 (30716) hydrogen bonds : bond 0.03627 / 2.46 ( 979) hydrogen bonds : angle 4.20512 / 2.97 ( 2832) metal coordination : bond 0.00346 / 0.16 ( 8) metal coordination : angle 1.02371 / 0.44 ( 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 364 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 0.928 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: 0.8572 (tmm) cc_final: 0.8151 (tmm) REVERT: B 49 LEU cc_start: 0.7777 (mt) cc_final: 0.7570 (mt) REVERT: B 57 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7595 (mm-30) REVERT: B 239 MET cc_start: 0.4304 (tpp) cc_final: 0.1242 (tmm) REVERT: B 313 MET cc_start: 0.7092 (ppp) cc_final: 0.6852 (tmm) REVERT: B 318 TYR cc_start: 0.8698 (t80) cc_final: 0.8481 (t80) REVERT: B 382 TRP cc_start: 0.8989 (p-90) cc_final: 0.8656 (p90) REVERT: E 197 GLN cc_start: 0.8634 (mt0) cc_final: 0.8423 (mt0) REVERT: E 240 SER cc_start: 0.8158 (t) cc_final: 0.7892 (t) REVERT: E 406 MET cc_start: 0.8909 (mmp) cc_final: 0.8523 (mmp) REVERT: E 500 ASN cc_start: 0.8620 (t0) cc_final: 0.8356 (t0) REVERT: E 542 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8492 (mtmm) REVERT: E 584 MET cc_start: 0.8201 (tpp) cc_final: 0.7792 (tpp) REVERT: E 680 LYS cc_start: 0.7729 (tmtt) cc_final: 0.7397 (tptp) REVERT: E 725 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7731 (tp30) REVERT: E 765 GLU cc_start: 0.7581 (tp30) cc_final: 0.7364 (tp30) REVERT: E 772 ASP cc_start: 0.7638 (p0) cc_final: 0.7024 (p0) REVERT: E 778 ASP cc_start: 0.8863 (t0) cc_final: 0.8535 (t0) REVERT: E 878 CYS cc_start: 0.8659 (m) cc_final: 0.8415 (m) REVERT: E 1001 GLU cc_start: 0.8283 (tm-30) cc_final: 0.8007 (tm-30) REVERT: F 66 GLU cc_start: 0.6817 (mp0) cc_final: 0.6165 (mp0) REVERT: F 161 ASN cc_start: 0.7870 (m-40) cc_final: 0.7622 (m-40) REVERT: F 239 MET cc_start: 0.6691 (mmm) cc_final: 0.6415 (mmm) REVERT: F 399 PHE cc_start: 0.7259 (t80) cc_final: 0.6884 (t80) REVERT: G 31 HIS cc_start: 0.8024 (p-80) cc_final: 0.7801 (p-80) outliers start: 1 outliers final: 0 residues processed: 363 average time/residue: 0.1555 time to fit residues: 90.0979 Evaluate side-chains 297 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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: 0.0470 chunk 157 optimal weight: 0.0970 chunk 222 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 247 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN A 810 HIS ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN F 391 GLN G 59 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.115545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.089963 restraints weight = 49094.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.090336 restraints weight = 44650.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.090619 restraints weight = 48853.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.091809 restraints weight = 29777.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.092374 restraints weight = 24921.337| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 22709 Z= 0.170 Angle : 0.612 11.354 30722 Z= 0.305 Chirality : 0.046 0.285 3415 Planarity : 0.004 0.061 3898 Dihedral : 8.600 145.008 3165 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.04 % Allowed : 0.87 % Favored : 99.09 % 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: 0.45 (0.17), residues: 2673 helix: 1.62 (0.15), residues: 1249 sheet: -0.14 (0.36), residues: 228 loop : -1.05 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 54 TYR 0.020 0.001 TYR C 65 PHE 0.013 0.001 PHE A 912 TRP 0.008 0.001 TRP E 266 HIS 0.007 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (22701) covalent geometry : angle 0.61161 / 0.31 (30716) hydrogen bonds : bond 0.03720 / 2.53 ( 979) hydrogen bonds : angle 4.25728 / 3.00 ( 2832) metal coordination : bond 0.00329 / 0.16 ( 8) metal coordination : angle 0.94348 / 0.40 ( 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 351 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 350 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 935 MET cc_start: 0.8539 (tmm) cc_final: 0.8162 (tmm) REVERT: B 49 LEU cc_start: 0.7734 (mt) cc_final: 0.7530 (mt) REVERT: B 57 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7644 (mm-30) REVERT: B 239 MET cc_start: 0.4318 (tpp) cc_final: 0.1246 (tmm) REVERT: B 313 MET cc_start: 0.7128 (ppp) cc_final: 0.6821 (tmm) REVERT: B 318 TYR cc_start: 0.8772 (t80) cc_final: 0.8437 (t80) REVERT: B 359 TYR cc_start: 0.7971 (m-10) cc_final: 0.7610 (m-10) REVERT: B 382 TRP cc_start: 0.8973 (p-90) cc_final: 0.8457 (p90) REVERT: E 197 GLN cc_start: 0.8662 (mt0) cc_final: 0.8343 (mt0) REVERT: E 237 TYR cc_start: 0.8729 (m-10) cc_final: 0.8414 (m-10) REVERT: E 406 MET cc_start: 0.8928 (mmp) cc_final: 0.8532 (mmp) REVERT: E 500 ASN cc_start: 0.8612 (t0) cc_final: 0.8395 (t0) REVERT: E 542 LYS cc_start: 0.8754 (mtmt) cc_final: 0.8463 (mtmm) REVERT: E 567 TYR cc_start: 0.9176 (m-80) cc_final: 0.8919 (m-80) REVERT: E 584 MET cc_start: 0.8255 (tpp) cc_final: 0.7918 (tpp) REVERT: E 680 LYS cc_start: 0.7704 (tmtt) cc_final: 0.7382 (tptp) REVERT: E 765 GLU cc_start: 0.7605 (tp30) cc_final: 0.7389 (tp30) REVERT: E 772 ASP cc_start: 0.7628 (p0) cc_final: 0.7004 (p0) REVERT: E 778 ASP cc_start: 0.8825 (t0) cc_final: 0.8505 (t0) REVERT: E 1001 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7976 (tm-30) REVERT: F 52 ARG cc_start: 0.7428 (mmm160) cc_final: 0.6626 (mtt90) REVERT: F 55 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7580 (pp30) REVERT: F 66 GLU cc_start: 0.6782 (mp0) cc_final: 0.6042 (mp0) REVERT: F 161 ASN cc_start: 0.7881 (m-40) cc_final: 0.7587 (m-40) REVERT: F 239 MET cc_start: 0.6682 (mmm) cc_final: 0.6426 (mmm) REVERT: F 399 PHE cc_start: 0.7273 (t80) cc_final: 0.6869 (t80) REVERT: G 31 HIS cc_start: 0.8014 (p-80) cc_final: 0.6802 (t-90) outliers start: 1 outliers final: 0 residues processed: 350 average time/residue: 0.1489 time to fit residues: 83.7249 Evaluate side-chains 286 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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: 1.9990 chunk 63 optimal weight: 0.2980 chunk 226 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 202 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 199 optimal weight: 0.5980 chunk 125 optimal weight: 0.5980 chunk 221 optimal weight: 0.3980 chunk 88 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN G 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.116709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.091398 restraints weight = 49003.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.091380 restraints weight = 44041.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.091980 restraints weight = 46185.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.093006 restraints weight = 29387.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.093594 restraints weight = 25216.725| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3112 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= 0.126 Angle : 0.600 11.142 30722 Z= 0.299 Chirality : 0.046 0.312 3415 Planarity : 0.004 0.058 3898 Dihedral : 8.540 144.723 3165 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 0.38 (0.17), residues: 2673 helix: 1.53 (0.15), residues: 1261 sheet: 0.08 (0.38), residues: 206 loop : -1.12 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 697 TYR 0.024 0.001 TYR F 274 PHE 0.019 0.001 PHE E 912 TRP 0.009 0.001 TRP E 266 HIS 0.004 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (22701) covalent geometry : angle 0.59948 / 0.30 (30716) hydrogen bonds : bond 0.03535 / 2.39 ( 979) hydrogen bonds : angle 4.21968 / 2.96 ( 2832) metal coordination : bond 0.00339 / 0.15 ( 8) metal coordination : angle 1.24617 / 0.49 ( 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 365 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.892 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: 0.8562 (tmm) cc_final: 0.8176 (tmm) REVERT: B 57 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7708 (mm-30) REVERT: B 239 MET cc_start: 0.4290 (tpp) cc_final: 0.1238 (tmm) REVERT: B 318 TYR cc_start: 0.8693 (t80) cc_final: 0.8457 (t80) REVERT: B 359 TYR cc_start: 0.7998 (m-10) cc_final: 0.7633 (m-10) REVERT: B 382 TRP cc_start: 0.8936 (p-90) cc_final: 0.8645 (p90) REVERT: E 197 GLN cc_start: 0.8579 (mt0) cc_final: 0.8371 (mt0) REVERT: E 406 MET cc_start: 0.8923 (mmp) cc_final: 0.8547 (mmp) REVERT: E 500 ASN cc_start: 0.8646 (t0) cc_final: 0.8388 (t0) REVERT: E 542 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8417 (mtmm) REVERT: E 584 MET cc_start: 0.8241 (tpp) cc_final: 0.7790 (tpp) REVERT: E 680 LYS cc_start: 0.7709 (tmtt) cc_final: 0.7391 (tptp) REVERT: E 765 GLU cc_start: 0.7559 (tp30) cc_final: 0.7347 (tp30) REVERT: E 772 ASP cc_start: 0.7650 (p0) cc_final: 0.7055 (p0) REVERT: E 778 ASP cc_start: 0.8831 (t0) cc_final: 0.8515 (t0) REVERT: E 878 CYS cc_start: 0.8580 (m) cc_final: 0.8336 (m) REVERT: E 1001 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7855 (tm-30) REVERT: F 52 ARG cc_start: 0.7648 (mmm160) cc_final: 0.6448 (mtt90) REVERT: F 61 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7632 (mm-30) REVERT: F 66 GLU cc_start: 0.6846 (mp0) cc_final: 0.6510 (mp0) REVERT: F 161 ASN cc_start: 0.7827 (m-40) cc_final: 0.7525 (m-40) REVERT: F 239 MET cc_start: 0.6630 (mmm) cc_final: 0.6365 (mmm) REVERT: G 18 GLU cc_start: 0.5537 (mp0) cc_final: 0.5228 (mp0) REVERT: G 31 HIS cc_start: 0.7991 (p-80) cc_final: 0.6789 (t-90) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.1503 time to fit residues: 88.0525 Evaluate side-chains 289 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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: 0.0970 chunk 15 optimal weight: 0.5980 chunk 243 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 0.0010 chunk 39 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 200 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 ASN ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN G 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.116972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.091720 restraints weight = 49074.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.092974 restraints weight = 44655.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.092956 restraints weight = 48123.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.094271 restraints weight = 28437.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.096414 restraints weight = 23047.050| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22709 Z= 0.125 Angle : 0.607 11.397 30722 Z= 0.303 Chirality : 0.045 0.285 3415 Planarity : 0.004 0.053 3898 Dihedral : 8.520 145.742 3165 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.04 % Allowed : 0.25 % 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: 0.39 (0.17), residues: 2673 helix: 1.53 (0.15), residues: 1260 sheet: 0.03 (0.38), residues: 208 loop : -1.09 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 78 TYR 0.023 0.001 TYR E 237 PHE 0.026 0.001 PHE E 912 TRP 0.015 0.001 TRP B 322 HIS 0.007 0.001 HIS E 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (22701) covalent geometry : angle 0.60715 / 0.30 (30716) hydrogen bonds : bond 0.03472 / 2.35 ( 979) hydrogen bonds : angle 4.18565 / 2.93 ( 2832) metal coordination : bond 0.00340 / 0.16 ( 8) metal coordination : angle 1.08858 / 0.42 ( 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 352 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 351 time to evaluate : 1.090 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 935 MET cc_start: 0.8506 (tmm) cc_final: 0.8169 (tmm) REVERT: B 57 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7764 (mm-30) REVERT: B 239 MET cc_start: 0.4207 (tpp) cc_final: 0.1179 (tmm) REVERT: B 318 TYR cc_start: 0.8742 (t80) cc_final: 0.8474 (t80) REVERT: B 359 TYR cc_start: 0.7996 (m-10) cc_final: 0.7599 (m-10) REVERT: B 382 TRP cc_start: 0.8930 (p-90) cc_final: 0.8637 (p90) REVERT: E 197 GLN cc_start: 0.8612 (mt0) cc_final: 0.8355 (mt0) REVERT: E 406 MET cc_start: 0.8889 (mmp) cc_final: 0.8513 (mmp) REVERT: E 500 ASN cc_start: 0.8596 (t0) cc_final: 0.8382 (t0) REVERT: E 542 LYS cc_start: 0.8657 (mtmt) cc_final: 0.8368 (mtmm) REVERT: E 584 MET cc_start: 0.8117 (tpp) cc_final: 0.7835 (tpp) REVERT: E 680 LYS cc_start: 0.7568 (tmtt) cc_final: 0.7294 (tptp) REVERT: E 765 GLU cc_start: 0.7808 (tp30) cc_final: 0.7528 (tp30) REVERT: E 772 ASP cc_start: 0.7638 (p0) cc_final: 0.7050 (p0) REVERT: E 778 ASP cc_start: 0.8833 (t0) cc_final: 0.8526 (t0) REVERT: E 878 CYS cc_start: 0.8479 (m) cc_final: 0.8273 (m) REVERT: E 1001 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7867 (tm-30) REVERT: E 1007 MET cc_start: 0.8819 (mmm) cc_final: 0.8579 (mmm) REVERT: F 52 ARG cc_start: 0.7397 (mmm160) cc_final: 0.6599 (mtt90) REVERT: F 61 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7621 (mm-30) REVERT: F 66 GLU cc_start: 0.6948 (mp0) cc_final: 0.6590 (mp0) REVERT: F 161 ASN cc_start: 0.7808 (m-40) cc_final: 0.7479 (m-40) REVERT: F 239 MET cc_start: 0.6488 (mmm) cc_final: 0.6262 (mmm) REVERT: G 18 GLU cc_start: 0.5595 (mp0) cc_final: 0.5346 (mp0) REVERT: G 31 HIS cc_start: 0.8125 (p-80) cc_final: 0.6893 (t-90) outliers start: 1 outliers final: 1 residues processed: 351 average time/residue: 0.1478 time to fit residues: 83.8249 Evaluate side-chains 291 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 290 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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: 0.0370 chunk 175 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 ASN ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN G 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.116592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.090997 restraints weight = 49252.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.091607 restraints weight = 43959.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.091904 restraints weight = 48118.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.093239 restraints weight = 29217.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.093697 restraints weight = 24242.862| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22709 Z= 0.137 Angle : 0.602 11.012 30722 Z= 0.303 Chirality : 0.046 0.355 3415 Planarity : 0.004 0.050 3898 Dihedral : 8.510 146.552 3165 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % 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: 1.50 (0.15), residues: 1262 sheet: 0.11 (0.38), residues: 206 loop : -1.12 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 78 TYR 0.023 0.001 TYR F 274 PHE 0.022 0.001 PHE C 84 TRP 0.010 0.001 TRP B 322 HIS 0.008 0.001 HIS E 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (22701) covalent geometry : angle 0.60177 / 0.30 (30716) hydrogen bonds : bond 0.03507 / 2.36 ( 979) hydrogen bonds : angle 4.22897 / 2.95 ( 2832) metal coordination : bond 0.00357 / 0.16 ( 8) metal coordination : angle 1.10507 / 0.42 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3537.61 seconds wall clock time: 62 minutes 20.28 seconds (3740.28 seconds total)