Starting phenix.real_space_refine on Thu Mar 5 16:33:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qoo_14098/03_2026/7qoo_14098.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qoo_14098/03_2026/7qoo_14098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qoo_14098/03_2026/7qoo_14098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qoo_14098/03_2026/7qoo_14098.map" model { file = "/net/cci-nas-00/data/ceres_data/7qoo_14098/03_2026/7qoo_14098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qoo_14098/03_2026/7qoo_14098.cif" } resolution = 4.6 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= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 15411 2.51 5 N 4097 2.21 5 O 4444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24085 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "H" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1733 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 207} Chain: "I" Number of atoms: 5042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5042 Classifications: {'peptide': 618} Link IDs: {'PTRANS': 22, 'TRANS': 595} Chain breaks: 2 Chain: "K" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2100 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 242} Chain: "L" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2467 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 293} Chain breaks: 2 Chain: "M" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1350 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 167} Chain: "N" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2640 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 1 Chain: "O" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1584 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 189} Chain: "P" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1891 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "U" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1535 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 180} Chain: "Q" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1667 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "R" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "T" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 878 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 575 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "X" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 76 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 5.41, per 1000 atoms: 0.22 Number of scatterers: 24085 At special positions: 0 Unit cell: (187.6, 155.4, 168.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 133 16.00 O 4444 8.00 N 4097 7.00 C 15411 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 1.2 seconds 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5762 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 11 sheets defined 58.8% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'H' and resid 39 through 66 Processing helix chain 'H' and resid 74 through 118 removed outlier: 3.759A pdb=" N ILE H 78 " --> pdb=" O GLN H 74 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS H 118 " --> pdb=" O LYS H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 189 removed outlier: 4.457A pdb=" N ASP H 128 " --> pdb=" O SER H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 224 removed outlier: 4.509A pdb=" N ILE H 198 " --> pdb=" O ARG H 194 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS H 207 " --> pdb=" O GLN H 203 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN H 217 " --> pdb=" O GLN H 213 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN H 218 " --> pdb=" O HIS H 214 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS H 224 " --> pdb=" O ILE H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 240 Processing helix chain 'I' and resid 60 through 74 removed outlier: 3.552A pdb=" N MET I 68 " --> pdb=" O ASP I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 100 removed outlier: 3.977A pdb=" N VAL I 95 " --> pdb=" O HIS I 91 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN I 97 " --> pdb=" O LYS I 93 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL I 98 " --> pdb=" O THR I 94 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA I 99 " --> pdb=" O VAL I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 117 removed outlier: 3.660A pdb=" N ASP I 110 " --> pdb=" O SER I 106 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN I 114 " --> pdb=" O ASP I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 132 removed outlier: 3.928A pdb=" N ASN I 126 " --> pdb=" O GLY I 122 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG I 128 " --> pdb=" O ALA I 124 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE I 129 " --> pdb=" O VAL I 125 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU I 130 " --> pdb=" O ASN I 126 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS I 131 " --> pdb=" O THR I 127 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N CYS I 132 " --> pdb=" O ARG I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 152 removed outlier: 3.546A pdb=" N VAL I 148 " --> pdb=" O VAL I 144 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER I 149 " --> pdb=" O VAL I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 171 removed outlier: 3.887A pdb=" N LYS I 161 " --> pdb=" O SER I 157 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL I 162 " --> pdb=" O GLY I 158 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 183 No H-bonds generated for 'chain 'I' and resid 181 through 183' Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 197 through 207 removed outlier: 3.505A pdb=" N CYS I 202 " --> pdb=" O CYS I 198 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS I 203 " --> pdb=" O PRO I 199 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU I 204 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU I 207 " --> pdb=" O HIS I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 230 removed outlier: 3.718A pdb=" N LEU I 222 " --> pdb=" O ARG I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 246 removed outlier: 3.548A pdb=" N LEU I 238 " --> pdb=" O HIS I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 250 removed outlier: 3.680A pdb=" N ILE I 250 " --> pdb=" O PRO I 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 247 through 250' Processing helix chain 'I' and resid 267 through 274 Processing helix chain 'I' and resid 340 through 344 removed outlier: 3.518A pdb=" N GLN I 343 " --> pdb=" O PRO I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 347 through 353 removed outlier: 3.687A pdb=" N LEU I 351 " --> pdb=" O PHE I 347 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN I 352 " --> pdb=" O PRO I 348 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN I 353 " --> pdb=" O GLN I 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 347 through 353' Processing helix chain 'I' and resid 372 through 377 removed outlier: 3.567A pdb=" N ILE I 376 " --> pdb=" O LEU I 372 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN I 377 " --> pdb=" O LEU I 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 372 through 377' Processing helix chain 'I' and resid 382 through 399 removed outlier: 3.502A pdb=" N ARG I 387 " --> pdb=" O PRO I 383 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE I 388 " --> pdb=" O VAL I 384 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU I 392 " --> pdb=" O PHE I 388 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN I 394 " --> pdb=" O TYR I 390 " (cutoff:3.500A) Processing helix chain 'I' and resid 407 through 429 removed outlier: 3.608A pdb=" N THR I 420 " --> pdb=" O ASN I 416 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG I 423 " --> pdb=" O ASP I 419 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS I 426 " --> pdb=" O ILE I 422 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 443 removed outlier: 3.500A pdb=" N GLU I 436 " --> pdb=" O PHE I 432 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA I 437 " --> pdb=" O TYR I 433 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS I 441 " --> pdb=" O ALA I 437 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU I 443 " --> pdb=" O LEU I 439 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 456 Processing helix chain 'I' and resid 466 through 474 removed outlier: 3.679A pdb=" N VAL I 470 " --> pdb=" O SER I 466 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS I 471 " --> pdb=" O PHE I 467 " (cutoff:3.500A) Proline residue: I 472 - end of helix No H-bonds generated for 'chain 'I' and resid 466 through 474' Processing helix chain 'I' and resid 474 through 483 removed outlier: 3.966A pdb=" N LEU I 481 " --> pdb=" O HIS I 477 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE I 483 " --> pdb=" O ALA I 479 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 511 removed outlier: 3.871A pdb=" N LEU I 494 " --> pdb=" O LYS I 490 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU I 499 " --> pdb=" O GLN I 495 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU I 505 " --> pdb=" O LEU I 501 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP I 507 " --> pdb=" O ASN I 503 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET I 510 " --> pdb=" O LEU I 506 " (cutoff:3.500A) Processing helix chain 'I' and resid 522 through 529 Processing helix chain 'I' and resid 529 through 552 removed outlier: 3.706A pdb=" N VAL I 533 " --> pdb=" O SER I 529 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU I 536 " --> pdb=" O SER I 532 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR I 546 " --> pdb=" O TRP I 542 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG I 549 " --> pdb=" O THR I 545 " (cutoff:3.500A) Processing helix chain 'I' and resid 554 through 563 removed outlier: 3.613A pdb=" N LEU I 558 " --> pdb=" O ASN I 554 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE I 560 " --> pdb=" O PHE I 556 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU I 562 " --> pdb=" O LEU I 558 " (cutoff:3.500A) Processing helix chain 'I' and resid 563 through 569 removed outlier: 3.926A pdb=" N LYS I 567 " --> pdb=" O ASP I 563 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL I 568 " --> pdb=" O PHE I 564 " (cutoff:3.500A) Processing helix chain 'I' and resid 587 through 593 Processing helix chain 'I' and resid 596 through 624 removed outlier: 3.536A pdb=" N LEU I 600 " --> pdb=" O ASP I 596 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA I 616 " --> pdb=" O LYS I 612 " (cutoff:3.500A) Processing helix chain 'I' and resid 634 through 650 removed outlier: 3.667A pdb=" N GLN I 638 " --> pdb=" O SER I 634 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER I 646 " --> pdb=" O HIS I 642 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS I 650 " --> pdb=" O SER I 646 " (cutoff:3.500A) Processing helix chain 'I' and resid 688 through 700 removed outlier: 3.716A pdb=" N LEU I 696 " --> pdb=" O ALA I 692 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER I 700 " --> pdb=" O LEU I 696 " (cutoff:3.500A) Processing helix chain 'I' and resid 713 through 726 removed outlier: 3.687A pdb=" N GLN I 726 " --> pdb=" O TYR I 722 " (cutoff:3.500A) Processing helix chain 'I' and resid 728 through 736 removed outlier: 3.623A pdb=" N ARG I 736 " --> pdb=" O LYS I 732 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 31 through 43 Processing helix chain 'K' and resid 56 through 70 removed outlier: 3.885A pdb=" N LEU K 60 " --> pdb=" O GLN K 56 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE K 61 " --> pdb=" O LEU K 57 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N MET K 62 " --> pdb=" O SER K 58 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN K 63 " --> pdb=" O LEU K 59 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL K 64 " --> pdb=" O LEU K 60 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA K 69 " --> pdb=" O LYS K 65 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU K 70 " --> pdb=" O CYS K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 77 Processing helix chain 'K' and resid 88 through 148 removed outlier: 3.540A pdb=" N LEU K 108 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU K 120 " --> pdb=" O GLU K 116 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU K 123 " --> pdb=" O LYS K 119 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU K 125 " --> pdb=" O ASP K 121 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN K 126 " --> pdb=" O LEU K 122 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL K 141 " --> pdb=" O GLU K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 188 removed outlier: 3.632A pdb=" N ILE K 158 " --> pdb=" O SER K 154 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN K 160 " --> pdb=" O SER K 156 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET K 166 " --> pdb=" O LEU K 162 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS K 170 " --> pdb=" O MET K 166 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU K 171 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU K 184 " --> pdb=" O LEU K 180 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU K 185 " --> pdb=" O GLY K 181 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS K 187 " --> pdb=" O PHE K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 226 removed outlier: 3.603A pdb=" N ILE K 218 " --> pdb=" O GLU K 214 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU K 223 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE K 224 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP K 225 " --> pdb=" O ASN K 221 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL K 226 " --> pdb=" O ARG K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 249 removed outlier: 3.673A pdb=" N LEU K 246 " --> pdb=" O TYR K 242 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN K 249 " --> pdb=" O LEU K 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 39 removed outlier: 3.661A pdb=" N VAL L 34 " --> pdb=" O ARG L 30 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS L 36 " --> pdb=" O GLU L 32 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN L 37 " --> pdb=" O SER L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 68 removed outlier: 3.625A pdb=" N VAL L 64 " --> pdb=" O ASP L 60 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA L 65 " --> pdb=" O PRO L 61 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE L 66 " --> pdb=" O GLN L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 106 removed outlier: 3.606A pdb=" N ARG L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL L 100 " --> pdb=" O ASN L 96 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA L 101 " --> pdb=" O ALA L 97 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS L 103 " --> pdb=" O ILE L 99 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 204 removed outlier: 3.502A pdb=" N ILE L 195 " --> pdb=" O SER L 191 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE L 196 " --> pdb=" O ASN L 192 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TRP L 199 " --> pdb=" O ILE L 195 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN L 201 " --> pdb=" O GLY L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 216 through 226 removed outlier: 4.008A pdb=" N TRP L 220 " --> pdb=" O PHE L 216 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET L 221 " --> pdb=" O ASN L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 257 through 269 removed outlier: 4.180A pdb=" N SER L 267 " --> pdb=" O ALA L 263 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL L 268 " --> pdb=" O LEU L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 296 removed outlier: 3.842A pdb=" N VAL L 280 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP L 281 " --> pdb=" O GLN L 277 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG L 293 " --> pdb=" O SER L 289 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N HIS L 294 " --> pdb=" O HIS L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 327 through 344 removed outlier: 3.951A pdb=" N VAL L 331 " --> pdb=" O TYR L 327 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR L 334 " --> pdb=" O GLY L 330 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE L 340 " --> pdb=" O THR L 336 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE L 341 " --> pdb=" O GLU L 337 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE L 343 " --> pdb=" O ALA L 339 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 35 removed outlier: 3.768A pdb=" N GLN M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU M 31 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET M 35 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 85 removed outlier: 3.615A pdb=" N THR M 81 " --> pdb=" O SER M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 94 removed outlier: 3.971A pdb=" N LEU M 94 " --> pdb=" O SER M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 123 removed outlier: 3.989A pdb=" N VAL M 117 " --> pdb=" O HIS M 113 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL M 118 " --> pdb=" O ARG M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 154 removed outlier: 3.775A pdb=" N THR M 141 " --> pdb=" O GLY M 137 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL M 147 " --> pdb=" O ALA M 143 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG M 148 " --> pdb=" O GLN M 144 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL M 149 " --> pdb=" O ARG M 145 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE M 152 " --> pdb=" O ARG M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 169 removed outlier: 3.618A pdb=" N LEU M 166 " --> pdb=" O ALA M 162 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER M 167 " --> pdb=" O LEU M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 15 removed outlier: 3.973A pdb=" N PHE N 8 " --> pdb=" O THR N 4 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE N 9 " --> pdb=" O VAL N 5 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE N 13 " --> pdb=" O ILE N 9 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU N 14 " --> pdb=" O LYS N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 29 removed outlier: 3.597A pdb=" N ILE N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU N 25 " --> pdb=" O LEU N 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS N 26 " --> pdb=" O THR N 22 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA N 27 " --> pdb=" O THR N 23 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP N 29 " --> pdb=" O LEU N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 37 removed outlier: 3.672A pdb=" N LEU N 36 " --> pdb=" O SER N 32 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN N 37 " --> pdb=" O GLU N 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 32 through 37' Processing helix chain 'N' and resid 44 through 59 removed outlier: 3.869A pdb=" N HIS N 54 " --> pdb=" O GLN N 50 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU N 55 " --> pdb=" O HIS N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 77 removed outlier: 3.544A pdb=" N ASP N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE N 71 " --> pdb=" O ALA N 67 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE N 72 " --> pdb=" O LEU N 68 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE N 76 " --> pdb=" O ILE N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 108 removed outlier: 3.746A pdb=" N ASN N 106 " --> pdb=" O LYS N 102 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER N 107 " --> pdb=" O GLN N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 114 removed outlier: 3.608A pdb=" N ARG N 114 " --> pdb=" O LYS N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 170 No H-bonds generated for 'chain 'N' and resid 168 through 170' Processing helix chain 'N' and resid 171 through 183 removed outlier: 3.509A pdb=" N GLY N 176 " --> pdb=" O THR N 172 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA N 178 " --> pdb=" O LEU N 174 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU N 179 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA N 182 " --> pdb=" O ALA N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 197 through 205 removed outlier: 3.714A pdb=" N ALA N 203 " --> pdb=" O ASP N 199 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL N 205 " --> pdb=" O LEU N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 241 through 246 removed outlier: 4.425A pdb=" N GLU N 246 " --> pdb=" O ILE N 242 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 256 Processing helix chain 'N' and resid 305 through 309 removed outlier: 3.839A pdb=" N SER N 308 " --> pdb=" O ALA N 305 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU N 309 " --> pdb=" O LEU N 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 305 through 309' Processing helix chain 'N' and resid 325 through 330 removed outlier: 3.793A pdb=" N ARG N 330 " --> pdb=" O ILE N 326 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 111 removed outlier: 3.525A pdb=" N ILE O 104 " --> pdb=" O ASN O 100 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS O 109 " --> pdb=" O LEU O 105 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE O 110 " --> pdb=" O GLN O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 161 through 166 Processing helix chain 'O' and resid 167 through 172 removed outlier: 4.326A pdb=" N THR O 171 " --> pdb=" O LYS O 167 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN O 172 " --> pdb=" O TYR O 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 167 through 172' Processing helix chain 'O' and resid 173 through 198 removed outlier: 3.678A pdb=" N GLN O 193 " --> pdb=" O GLY O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 262 through 274 removed outlier: 3.585A pdb=" N THR O 273 " --> pdb=" O ALA O 269 " (cutoff:3.500A) Processing helix chain 'O' and resid 279 through 288 removed outlier: 3.521A pdb=" N PHE O 284 " --> pdb=" O LEU O 280 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA O 285 " --> pdb=" O HIS O 281 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR O 288 " --> pdb=" O PHE O 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 62 Processing helix chain 'P' and resid 62 through 74 removed outlier: 3.658A pdb=" N THR P 72 " --> pdb=" O SER P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 150 through 161 removed outlier: 3.716A pdb=" N VAL P 154 " --> pdb=" O LEU P 150 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER P 155 " --> pdb=" O SER P 151 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU P 159 " --> pdb=" O SER P 155 " (cutoff:3.500A) Processing helix chain 'P' and resid 162 through 191 removed outlier: 3.607A pdb=" N PHE P 166 " --> pdb=" O ASP P 162 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU P 170 " --> pdb=" O PHE P 166 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS P 171 " --> pdb=" O PHE P 167 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR P 179 " --> pdb=" O GLU P 175 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG P 182 " --> pdb=" O GLU P 178 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS P 185 " --> pdb=" O LYS P 181 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS P 186 " --> pdb=" O ARG P 182 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR P 191 " --> pdb=" O LEU P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 199 through 203 removed outlier: 4.202A pdb=" N SER P 202 " --> pdb=" O GLU P 199 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER P 203 " --> pdb=" O GLY P 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 199 through 203' Processing helix chain 'P' and resid 243 through 247 removed outlier: 3.502A pdb=" N ALA P 246 " --> pdb=" O PRO P 243 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU P 247 " --> pdb=" O GLN P 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 243 through 247' Processing helix chain 'P' and resid 257 through 270 removed outlier: 3.688A pdb=" N THR P 264 " --> pdb=" O LEU P 260 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU P 265 " --> pdb=" O SER P 261 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL P 266 " --> pdb=" O PHE P 262 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 281 removed outlier: 3.599A pdb=" N LEU P 278 " --> pdb=" O ALA P 274 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE P 279 " --> pdb=" O LEU P 275 " (cutoff:3.500A) Processing helix chain 'U' and resid 250 through 261 removed outlier: 4.049A pdb=" N VAL U 254 " --> pdb=" O GLU U 250 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU U 255 " --> pdb=" O LEU U 251 " (cutoff:3.500A) Proline residue: U 256 - end of helix removed outlier: 3.622A pdb=" N GLU U 259 " --> pdb=" O LEU U 255 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR U 261 " --> pdb=" O GLU U 257 " (cutoff:3.500A) Processing helix chain 'U' and resid 262 through 267 removed outlier: 3.584A pdb=" N GLN U 266 " --> pdb=" O HIS U 262 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN U 267 " --> pdb=" O LEU U 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 262 through 267' Processing helix chain 'U' and resid 271 through 331 removed outlier: 3.649A pdb=" N ALA U 277 " --> pdb=" O VAL U 273 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL U 285 " --> pdb=" O PHE U 281 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS U 286 " --> pdb=" O TYR U 282 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET U 298 " --> pdb=" O LYS U 294 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE U 310 " --> pdb=" O ASN U 306 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER U 311 " --> pdb=" O ALA U 307 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP U 312 " --> pdb=" O LYS U 308 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS U 315 " --> pdb=" O SER U 311 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS U 316 " --> pdb=" O ASP U 312 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU U 322 " --> pdb=" O GLN U 318 " (cutoff:3.500A) Processing helix chain 'U' and resid 331 through 370 removed outlier: 3.502A pdb=" N ASN U 353 " --> pdb=" O SER U 349 " (cutoff:3.500A) Processing helix chain 'U' and resid 386 through 394 Processing helix chain 'U' and resid 394 through 399 Processing helix chain 'U' and resid 399 through 418 removed outlier: 3.829A pdb=" N ARG U 405 " --> pdb=" O GLU U 401 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN U 410 " --> pdb=" O ASN U 406 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 99 removed outlier: 3.601A pdb=" N ARG Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS Q 83 " --> pdb=" O SER Q 79 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET Q 93 " --> pdb=" O GLU Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 124 removed outlier: 3.590A pdb=" N GLU Q 122 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 157 Processing helix chain 'Q' and resid 158 through 174 removed outlier: 3.709A pdb=" N GLU Q 167 " --> pdb=" O ASP Q 163 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU Q 171 " --> pdb=" O GLU Q 167 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N MET Q 172 " --> pdb=" O THR Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 182 removed outlier: 3.523A pdb=" N LYS Q 182 " --> pdb=" O SER Q 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 202 removed outlier: 3.516A pdb=" N GLU Q 192 " --> pdb=" O SER Q 188 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU Q 195 " --> pdb=" O GLU Q 191 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL Q 197 " --> pdb=" O GLU Q 193 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET Q 200 " --> pdb=" O ARG Q 196 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 230 removed outlier: 3.778A pdb=" N ALA Q 230 " --> pdb=" O LYS Q 226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 235 through 237 No H-bonds generated for 'chain 'Q' and resid 235 through 237' Processing helix chain 'Q' and resid 238 through 247 removed outlier: 3.654A pdb=" N LEU Q 245 " --> pdb=" O ASP Q 241 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 268 Processing helix chain 'R' and resid 87 through 96 Processing helix chain 'R' and resid 96 through 104 removed outlier: 3.693A pdb=" N ILE R 103 " --> pdb=" O GLU R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 114 Processing helix chain 'R' and resid 118 through 123 removed outlier: 4.018A pdb=" N LEU R 122 " --> pdb=" O GLU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 149 removed outlier: 3.663A pdb=" N GLN R 137 " --> pdb=" O LYS R 133 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET R 143 " --> pdb=" O THR R 139 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN R 147 " --> pdb=" O MET R 143 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN R 149 " --> pdb=" O LYS R 145 " (cutoff:3.500A) Processing helix chain 'T' and resid 455 through 472 removed outlier: 3.959A pdb=" N HIS T 462 " --> pdb=" O ALA T 458 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR T 463 " --> pdb=" O GLY T 459 " (cutoff:3.500A) Processing helix chain 'T' and resid 476 through 504 removed outlier: 3.564A pdb=" N VAL T 500 " --> pdb=" O ASP T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 511 through 522 removed outlier: 4.044A pdb=" N LEU T 515 " --> pdb=" O LYS T 511 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET T 519 " --> pdb=" O LEU T 515 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG T 520 " --> pdb=" O GLU T 516 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 539 removed outlier: 4.037A pdb=" N LEU T 534 " --> pdb=" O SER T 530 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL T 535 " --> pdb=" O LEU T 531 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU T 536 " --> pdb=" O HIS T 532 " (cutoff:3.500A) Processing helix chain 'T' and resid 540 through 548 removed outlier: 3.694A pdb=" N LEU T 546 " --> pdb=" O GLU T 542 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU T 547 " --> pdb=" O TYR T 543 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 29 removed outlier: 3.710A pdb=" N LYS W 23 " --> pdb=" O ARG W 19 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG W 24 " --> pdb=" O GLY W 20 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS W 27 " --> pdb=" O LYS W 23 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG W 28 " --> pdb=" O ARG W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 65 removed outlier: 3.504A pdb=" N LEU W 49 " --> pdb=" O LEU W 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL W 51 " --> pdb=" O CYS W 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS W 52 " --> pdb=" O LEU W 48 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU W 57 " --> pdb=" O ARG W 53 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER W 65 " --> pdb=" O ASN W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 80 removed outlier: 3.607A pdb=" N VAL W 75 " --> pdb=" O ASN W 71 " (cutoff:3.500A) Processing helix chain 'W' and resid 81 through 87 removed outlier: 3.786A pdb=" N ARG W 87 " --> pdb=" O LEU W 83 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 15 removed outlier: 3.684A pdb=" N UNK X 13 " --> pdb=" O UNK X 9 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N UNK X 14 " --> pdb=" O UNK X 10 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 232 through 233 Processing sheet with id=AA2, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain 'L' and resid 117 through 123 removed outlier: 3.535A pdb=" N PHE L 162 " --> pdb=" O PHE L 137 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP L 158 " --> pdb=" O ILE L 141 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N SER L 143 " --> pdb=" O VAL L 156 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL L 156 " --> pdb=" O SER L 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 117 through 123 removed outlier: 3.535A pdb=" N PHE L 162 " --> pdb=" O PHE L 137 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP L 158 " --> pdb=" O ILE L 141 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N SER L 143 " --> pdb=" O VAL L 156 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL L 156 " --> pdb=" O SER L 143 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS L 319 " --> pdb=" O HIS L 315 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU L 304 " --> pdb=" O SER L 242 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER L 242 " --> pdb=" O LEU L 304 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG L 306 " --> pdb=" O LEU L 240 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP L 241 " --> pdb=" O ILE L 252 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP L 251 " --> pdb=" O SER N 298 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER N 298 " --> pdb=" O ASP L 251 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU N 294 " --> pdb=" O ALA L 255 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA N 267 " --> pdb=" O PHE N 297 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 43 through 49 removed outlier: 7.052A pdb=" N ALA M 16 " --> pdb=" O LYS M 45 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N HIS M 47 " --> pdb=" O ALA M 16 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE M 18 " --> pdb=" O HIS M 47 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA M 49 " --> pdb=" O ILE M 18 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU M 20 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N VAL M 67 " --> pdb=" O THR M 17 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU M 19 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL M 69 " --> pdb=" O LEU M 19 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL M 21 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASN M 71 " --> pdb=" O VAL M 21 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU M 129 " --> pdb=" O PHE M 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 119 through 122 removed outlier: 3.521A pdb=" N SER N 122 " --> pdb=" O ARG N 134 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N TYR N 151 " --> pdb=" O SER N 164 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TRP N 83 " --> pdb=" O LEU N 193 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU N 193 " --> pdb=" O TRP N 83 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL N 85 " --> pdb=" O MET N 191 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLN N 187 " --> pdb=" O SER N 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 113 through 117 removed outlier: 3.854A pdb=" N LYS O 116 " --> pdb=" O CYS O 123 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS O 123 " --> pdb=" O LYS O 116 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N HIS O 152 " --> pdb=" O ASP O 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 217 through 224 removed outlier: 3.564A pdb=" N LEU O 224 " --> pdb=" O PHE O 231 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 77 through 87 removed outlier: 5.385A pdb=" N ILE P 78 " --> pdb=" O ASN P 110 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN P 110 " --> pdb=" O ILE P 78 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER P 82 " --> pdb=" O ARG P 106 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG P 106 " --> pdb=" O SER P 82 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE P 120 " --> pdb=" O HIS P 105 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY P 109 " --> pdb=" O PHE P 116 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLN P 121 " --> pdb=" O THR P 136 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER P 132 " --> pdb=" O ILE P 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 195 through 196 removed outlier: 3.564A pdb=" N TYR P 196 " --> pdb=" O GLY P 207 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY P 207 " --> pdb=" O TYR P 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 509 through 510 1143 hydrogen bonds defined for protein. 3360 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: 4.34 Time building geometry restraints manager: 2.49 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: 7627 1.34 - 1.47: 5498 1.47 - 1.59: 11208 1.59 - 1.71: 0 1.71 - 1.84: 209 Bond restraints: 24542 Sorted by residual: bond pdb=" C LYS I 471 " pdb=" N PRO I 472 " ideal model delta sigma weight residual 1.337 1.398 -0.061 1.24e-02 6.50e+03 2.44e+01 bond pdb=" N ASP N 29 " pdb=" CA ASP N 29 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.50e+00 bond pdb=" C PHE I 347 " pdb=" N PRO I 348 " ideal model delta sigma weight residual 1.335 1.363 -0.028 9.40e-03 1.13e+04 8.81e+00 bond pdb=" C THR N 158 " pdb=" N PRO N 159 " ideal model delta sigma weight residual 1.331 1.354 -0.022 7.90e-03 1.60e+04 8.04e+00 bond pdb=" C GLU I 382 " pdb=" N PRO I 383 " ideal model delta sigma weight residual 1.337 1.364 -0.027 1.06e-02 8.90e+03 6.63e+00 ... (remaining 24537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 32311 2.78 - 5.55: 647 5.55 - 8.33: 100 8.33 - 11.11: 34 11.11 - 13.88: 4 Bond angle restraints: 33096 Sorted by residual: angle pdb=" C GLN I 278 " pdb=" N ARG I 279 " pdb=" CA ARG I 279 " ideal model delta sigma weight residual 122.08 130.76 -8.68 1.47e+00 4.63e-01 3.49e+01 angle pdb=" C ILE I 260 " pdb=" N TYR I 261 " pdb=" CA TYR I 261 " ideal model delta sigma weight residual 121.54 132.79 -11.25 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C TRP N 28 " pdb=" N ASP N 29 " pdb=" CA ASP N 29 " ideal model delta sigma weight residual 121.54 132.21 -10.67 1.91e+00 2.74e-01 3.12e+01 angle pdb=" CA CYS I 451 " pdb=" CB CYS I 451 " pdb=" SG CYS I 451 " ideal model delta sigma weight residual 114.40 127.08 -12.68 2.30e+00 1.89e-01 3.04e+01 angle pdb=" C TYR L 81 " pdb=" N LYS L 82 " pdb=" CA LYS L 82 " ideal model delta sigma weight residual 122.07 129.88 -7.81 1.43e+00 4.89e-01 2.98e+01 ... (remaining 33091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 14253 16.59 - 33.19: 610 33.19 - 49.78: 197 49.78 - 66.37: 6 66.37 - 82.96: 26 Dihedral angle restraints: 15092 sinusoidal: 6297 harmonic: 8795 Sorted by residual: dihedral pdb=" CA PHE T 558 " pdb=" C PHE T 558 " pdb=" N PRO T 559 " pdb=" CA PRO T 559 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ALA N 317 " pdb=" C ALA N 317 " pdb=" N PRO N 318 " pdb=" CA PRO N 318 " ideal model delta harmonic sigma weight residual 180.00 157.81 22.19 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA LYS N 143 " pdb=" C LYS N 143 " pdb=" N PRO N 144 " pdb=" CA PRO N 144 " ideal model delta harmonic sigma weight residual 180.00 -158.95 -21.05 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 15089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3331 0.077 - 0.155: 380 0.155 - 0.232: 36 0.232 - 0.310: 15 0.310 - 0.387: 4 Chirality restraints: 3766 Sorted by residual: chirality pdb=" CB ILE L 41 " pdb=" CA ILE L 41 " pdb=" CG1 ILE L 41 " pdb=" CG2 ILE L 41 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CB ILE N 188 " pdb=" CA ILE N 188 " pdb=" CG1 ILE N 188 " pdb=" CG2 ILE N 188 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CG LEU M 146 " pdb=" CB LEU M 146 " pdb=" CD1 LEU M 146 " pdb=" CD2 LEU M 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 3763 not shown) Planarity restraints: 4177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 240 " -0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO K 241 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO K 241 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO K 241 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 443 " 0.046 5.00e-02 4.00e+02 6.90e-02 7.63e+00 pdb=" N PRO I 444 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO I 444 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO I 444 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE T 558 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.83e+00 pdb=" N PRO T 559 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO T 559 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO T 559 " -0.039 5.00e-02 4.00e+02 ... (remaining 4174 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 7595 2.87 - 3.38: 19883 3.38 - 3.89: 37250 3.89 - 4.39: 41221 4.39 - 4.90: 70856 Nonbonded interactions: 176805 Sorted by model distance: nonbonded pdb=" OD1 ASN L 217 " pdb=" OH TYR L 334 " model vdw 2.363 3.040 nonbonded pdb=" OG SER N 32 " pdb=" OD1 ASN N 34 " model vdw 2.367 3.040 nonbonded pdb=" OG SER L 76 " pdb=" OG SER L 209 " model vdw 2.372 3.040 nonbonded pdb=" O LEU I 205 " pdb=" OG1 THR I 209 " model vdw 2.374 3.040 nonbonded pdb=" O VAL L 165 " pdb=" OG1 THR L 336 " model vdw 2.381 3.040 ... (remaining 176800 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 21.680 Find NCS groups from input model: 0.160 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 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 : 0.005 0.061 24542 Z= 0.270 Angle : 0.994 13.882 33096 Z= 0.533 Chirality : 0.053 0.387 3766 Planarity : 0.008 0.084 4177 Dihedral : 11.191 82.963 9330 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.15 % Allowed : 2.99 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % 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: -5.80 (0.10), residues: 2920 helix: -4.95 (0.03), residues: 1604 sheet: -0.88 (0.30), residues: 254 loop : -2.35 (0.14), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 124 TYR 0.030 0.002 TYR O 183 PHE 0.030 0.002 PHE I 583 TRP 0.032 0.002 TRP K 239 HIS 0.011 0.002 HIS O 271 Details of bonding type rmsd covalent geometry : bond 0.00543 (24542) covalent geometry : angle 0.99441 (33096) hydrogen bonds : bond 0.30796 ( 1123) hydrogen bonds : angle 10.52781 ( 3360) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 811 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: C 304 ILE cc_start: 0.5401 (OUTLIER) cc_final: 0.4622 (tp) REVERT: C 305 ILE cc_start: 0.6406 (mp) cc_final: 0.6156 (mp) REVERT: H 89 ILE cc_start: 0.8426 (tp) cc_final: 0.8161 (tp) REVERT: H 98 ILE cc_start: 0.8029 (mm) cc_final: 0.7798 (mm) REVERT: H 130 MET cc_start: 0.7999 (mmp) cc_final: 0.6994 (ptm) REVERT: H 137 ASN cc_start: 0.8161 (m-40) cc_final: 0.6437 (m-40) REVERT: I 88 LEU cc_start: 0.6904 (pp) cc_final: 0.5598 (pp) REVERT: I 334 ASN cc_start: 0.6712 (m-40) cc_final: 0.6086 (p0) REVERT: I 355 HIS cc_start: 0.7257 (p-80) cc_final: 0.6836 (p-80) REVERT: I 357 LEU cc_start: 0.7798 (tt) cc_final: 0.7447 (tt) REVERT: I 416 ASN cc_start: 0.7452 (t0) cc_final: 0.7200 (p0) REVERT: I 461 TRP cc_start: 0.6090 (m-90) cc_final: 0.5871 (m-90) REVERT: I 599 ILE cc_start: 0.8438 (mt) cc_final: 0.7912 (tp) REVERT: I 600 LEU cc_start: 0.9192 (mt) cc_final: 0.8728 (mt) REVERT: I 607 MET cc_start: 0.7129 (mmm) cc_final: 0.6710 (mmm) REVERT: I 620 ASN cc_start: 0.6532 (t0) cc_final: 0.5872 (t0) REVERT: I 683 VAL cc_start: 0.8354 (p) cc_final: 0.8138 (t) REVERT: K 31 MET cc_start: 0.8566 (ptp) cc_final: 0.8298 (ptp) REVERT: K 65 LYS cc_start: 0.8589 (mtmm) cc_final: 0.7827 (ttpt) REVERT: K 80 GLU cc_start: 0.5531 (mt-10) cc_final: 0.5306 (tp30) REVERT: K 82 ILE cc_start: 0.7286 (mt) cc_final: 0.7042 (mp) REVERT: K 103 ASP cc_start: 0.8550 (m-30) cc_final: 0.8127 (t0) REVERT: K 106 MET cc_start: 0.7514 (mtt) cc_final: 0.6887 (mtm) REVERT: K 122 LEU cc_start: 0.8189 (tp) cc_final: 0.7931 (tp) REVERT: K 135 ILE cc_start: 0.8383 (mm) cc_final: 0.8081 (mm) REVERT: K 215 MET cc_start: 0.5010 (mtt) cc_final: 0.4665 (mtt) REVERT: K 261 ARG cc_start: 0.9298 (mpt180) cc_final: 0.9078 (mmt90) REVERT: L 47 ARG cc_start: 0.7615 (mtp85) cc_final: 0.7235 (mtp-110) REVERT: L 52 CYS cc_start: 0.4096 (t) cc_final: 0.3865 (p) REVERT: L 93 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.7690 (mmm-85) REVERT: L 116 ASN cc_start: 0.7530 (p0) cc_final: 0.6768 (p0) REVERT: L 144 LYS cc_start: 0.2420 (mttt) cc_final: 0.1956 (tttp) REVERT: L 221 MET cc_start: 0.7990 (ptm) cc_final: 0.7660 (ptm) REVERT: L 226 THR cc_start: 0.8734 (p) cc_final: 0.8422 (p) REVERT: L 288 TYR cc_start: 0.7643 (m-10) cc_final: 0.7234 (m-80) REVERT: M 64 ASP cc_start: 0.7056 (m-30) cc_final: 0.6229 (m-30) REVERT: M 68 PHE cc_start: 0.7765 (m-80) cc_final: 0.7528 (m-80) REVERT: M 71 ASN cc_start: 0.7456 (t0) cc_final: 0.7103 (m110) REVERT: M 94 LEU cc_start: 0.7413 (mt) cc_final: 0.7147 (pp) REVERT: M 131 CYS cc_start: 0.7654 (t) cc_final: 0.7229 (t) REVERT: M 146 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7709 (mm) REVERT: M 166 LEU cc_start: 0.8201 (tp) cc_final: 0.7904 (pp) REVERT: N 18 MET cc_start: 0.7296 (pmm) cc_final: 0.6024 (tpt) REVERT: N 19 ASN cc_start: 0.8560 (p0) cc_final: 0.8224 (p0) REVERT: N 106 ASN cc_start: 0.7758 (p0) cc_final: 0.6897 (m-40) REVERT: N 145 ASN cc_start: 0.5944 (t0) cc_final: 0.5430 (t0) REVERT: N 151 TYR cc_start: 0.7658 (m-80) cc_final: 0.7401 (m-80) REVERT: N 271 LEU cc_start: 0.8606 (mp) cc_final: 0.8387 (mp) REVERT: O 128 THR cc_start: 0.7752 (p) cc_final: 0.6639 (p) REVERT: O 174 GLN cc_start: 0.7907 (pt0) cc_final: 0.7464 (tt0) REVERT: O 176 PHE cc_start: 0.7750 (t80) cc_final: 0.7411 (t80) REVERT: O 198 GLN cc_start: 0.7545 (pt0) cc_final: 0.6384 (tp40) REVERT: O 205 LEU cc_start: 0.7788 (pp) cc_final: 0.7521 (tt) REVERT: O 222 TYR cc_start: 0.7202 (p90) cc_final: 0.6730 (p90) REVERT: O 281 HIS cc_start: 0.7033 (p-80) cc_final: 0.6510 (p-80) REVERT: P 69 PHE cc_start: 0.7076 (t80) cc_final: 0.6515 (t80) REVERT: P 136 THR cc_start: 0.6681 (p) cc_final: 0.6149 (p) REVERT: P 162 ASP cc_start: 0.7635 (t0) cc_final: 0.7117 (m-30) REVERT: P 174 VAL cc_start: 0.8700 (t) cc_final: 0.8453 (t) REVERT: U 334 LEU cc_start: 0.7242 (pp) cc_final: 0.7026 (pt) REVERT: U 396 THR cc_start: 0.8454 (p) cc_final: 0.7826 (t) REVERT: Q 165 MET cc_start: 0.7658 (mtp) cc_final: 0.7281 (mmp) REVERT: W 72 LYS cc_start: 0.7409 (mptp) cc_final: 0.6866 (pttm) outliers start: 4 outliers final: 0 residues processed: 813 average time/residue: 0.1780 time to fit residues: 217.5532 Evaluate side-chains 457 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 455 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 20.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 71 GLN ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN I 213 ASN I 410 HIS I 559 HIS I 642 HIS I 685 HIS K 39 GLN K 63 GLN K 168 ASN ** L 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 277 GLN M 73 HIS M 115 HIS ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 185 HIS O 153 HIS O 175 HIS ** O 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 246 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.110973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.100225 restraints weight = 153977.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.100780 restraints weight = 126396.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.101254 restraints weight = 107060.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.101414 restraints weight = 89919.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.101502 restraints weight = 86320.146| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24542 Z= 0.159 Angle : 0.653 10.749 33096 Z= 0.346 Chirality : 0.042 0.171 3766 Planarity : 0.006 0.105 4177 Dihedral : 5.005 84.339 3174 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % 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: -3.08 (0.13), residues: 2920 helix: -2.39 (0.10), residues: 1613 sheet: 0.01 (0.31), residues: 259 loop : -1.68 (0.16), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 5 TYR 0.021 0.002 TYR N 141 PHE 0.019 0.002 PHE L 254 TRP 0.029 0.002 TRP I 167 HIS 0.007 0.001 HIS N 239 Details of bonding type rmsd covalent geometry : bond 0.00341 (24542) covalent geometry : angle 0.65338 (33096) hydrogen bonds : bond 0.04839 ( 1123) hydrogen bonds : angle 4.88282 ( 3360) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 571 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 GLU cc_start: 0.8526 (mp0) cc_final: 0.8313 (mp0) REVERT: H 98 ILE cc_start: 0.8247 (mm) cc_final: 0.7989 (mm) REVERT: H 105 ARG cc_start: 0.8575 (mmt-90) cc_final: 0.8363 (tpp80) REVERT: H 130 MET cc_start: 0.8319 (mmp) cc_final: 0.7075 (ptm) REVERT: H 137 ASN cc_start: 0.8005 (m-40) cc_final: 0.7711 (m-40) REVERT: H 141 MET cc_start: 0.8567 (mpp) cc_final: 0.8321 (mpp) REVERT: H 164 LEU cc_start: 0.7668 (tt) cc_final: 0.6904 (tp) REVERT: I 334 ASN cc_start: 0.6383 (m-40) cc_final: 0.5953 (p0) REVERT: I 339 PHE cc_start: 0.7233 (t80) cc_final: 0.6920 (t80) REVERT: I 355 HIS cc_start: 0.6972 (p-80) cc_final: 0.6480 (p-80) REVERT: I 369 ASN cc_start: 0.7733 (t0) cc_final: 0.7259 (t0) REVERT: I 372 LEU cc_start: 0.8778 (mt) cc_final: 0.8097 (mt) REVERT: I 425 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8583 (mm-30) REVERT: I 456 LEU cc_start: 0.7562 (mt) cc_final: 0.7309 (mt) REVERT: I 552 SER cc_start: 0.7604 (p) cc_final: 0.7367 (m) REVERT: I 575 TYR cc_start: 0.7730 (m-10) cc_final: 0.7150 (m-10) REVERT: I 600 LEU cc_start: 0.9285 (mt) cc_final: 0.9037 (mt) REVERT: I 641 ASN cc_start: 0.9002 (t0) cc_final: 0.8705 (m110) REVERT: I 646 SER cc_start: 0.8126 (t) cc_final: 0.7860 (p) REVERT: K 65 LYS cc_start: 0.8553 (mtmm) cc_final: 0.8060 (ttpt) REVERT: K 80 GLU cc_start: 0.5927 (mt-10) cc_final: 0.5276 (tp30) REVERT: K 103 ASP cc_start: 0.8636 (m-30) cc_final: 0.8254 (t0) REVERT: L 116 ASN cc_start: 0.7275 (p0) cc_final: 0.6398 (p0) REVERT: L 144 LYS cc_start: 0.2294 (mttt) cc_final: 0.1609 (tttp) REVERT: L 158 TRP cc_start: 0.7448 (t60) cc_final: 0.7039 (t60) REVERT: L 163 CYS cc_start: 0.8148 (p) cc_final: 0.7668 (t) REVERT: L 165 VAL cc_start: 0.8127 (t) cc_final: 0.7519 (m) REVERT: L 253 SER cc_start: 0.8223 (m) cc_final: 0.7957 (m) REVERT: L 313 SER cc_start: 0.6170 (p) cc_final: 0.5929 (p) REVERT: M 30 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7699 (mm-40) REVERT: M 33 ASP cc_start: 0.8165 (m-30) cc_final: 0.7751 (m-30) REVERT: M 38 GLU cc_start: 0.6690 (mt-10) cc_final: 0.6119 (pt0) REVERT: M 45 LYS cc_start: 0.6260 (tttt) cc_final: 0.5896 (tttp) REVERT: M 64 ASP cc_start: 0.7297 (m-30) cc_final: 0.6807 (m-30) REVERT: M 94 LEU cc_start: 0.7693 (mt) cc_final: 0.7131 (pp) REVERT: M 102 THR cc_start: 0.7689 (p) cc_final: 0.7363 (t) REVERT: N 18 MET cc_start: 0.8107 (pmm) cc_final: 0.6482 (tpt) REVERT: N 19 ASN cc_start: 0.8868 (p0) cc_final: 0.8543 (p0) REVERT: N 197 TYR cc_start: 0.8135 (m-80) cc_final: 0.7896 (m-80) REVERT: N 334 PHE cc_start: 0.8236 (m-10) cc_final: 0.7933 (m-10) REVERT: O 174 GLN cc_start: 0.8062 (pt0) cc_final: 0.7746 (pm20) REVERT: O 178 PHE cc_start: 0.8532 (m-10) cc_final: 0.7983 (m-80) REVERT: O 180 LEU cc_start: 0.8896 (mt) cc_final: 0.8695 (mt) REVERT: O 182 GLU cc_start: 0.7317 (mm-30) cc_final: 0.5984 (mm-30) REVERT: O 185 ASN cc_start: 0.8578 (m110) cc_final: 0.8124 (m110) REVERT: O 211 ARG cc_start: 0.8196 (mmt-90) cc_final: 0.7553 (mmt180) REVERT: O 214 LEU cc_start: 0.7772 (tp) cc_final: 0.7371 (tt) REVERT: O 222 TYR cc_start: 0.8295 (p90) cc_final: 0.7509 (p90) REVERT: O 281 HIS cc_start: 0.7618 (p-80) cc_final: 0.7305 (p-80) REVERT: O 284 PHE cc_start: 0.8189 (m-10) cc_final: 0.7879 (m-80) REVERT: P 162 ASP cc_start: 0.8217 (t0) cc_final: 0.7541 (m-30) REVERT: P 206 MET cc_start: 0.7512 (ppp) cc_final: 0.7248 (ppp) REVERT: P 244 GLN cc_start: 0.7845 (mt0) cc_final: 0.7100 (mm-40) REVERT: P 253 ARG cc_start: 0.8115 (mmp80) cc_final: 0.7542 (mmp80) REVERT: U 325 ASP cc_start: 0.9011 (t70) cc_final: 0.8554 (t0) REVERT: U 346 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8040 (tm-30) REVERT: U 383 ASP cc_start: 0.6552 (m-30) cc_final: 0.6262 (m-30) REVERT: U 396 THR cc_start: 0.8709 (p) cc_final: 0.8326 (t) REVERT: Q 165 MET cc_start: 0.8108 (mtp) cc_final: 0.7477 (mmm) REVERT: Q 192 GLU cc_start: 0.8605 (tp30) cc_final: 0.8129 (tp30) REVERT: Q 201 HIS cc_start: 0.6983 (m90) cc_final: 0.6287 (m90) REVERT: Q 246 HIS cc_start: 0.8067 (m-70) cc_final: 0.7202 (t70) REVERT: R 122 LEU cc_start: 0.7737 (pp) cc_final: 0.7508 (pp) REVERT: R 143 MET cc_start: 0.7008 (ppp) cc_final: 0.6804 (mmt) REVERT: W 73 GLU cc_start: 0.8802 (tp30) cc_final: 0.7901 (mp0) REVERT: W 74 HIS cc_start: 0.7304 (m90) cc_final: 0.6971 (m170) outliers start: 2 outliers final: 1 residues processed: 573 average time/residue: 0.1671 time to fit residues: 149.0127 Evaluate side-chains 410 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 409 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 12 optimal weight: 6.9990 chunk 41 optimal weight: 0.0060 chunk 203 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 278 optimal weight: 0.0070 chunk 152 optimal weight: 1.9990 chunk 246 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 229 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 503 ASN L 71 GLN L 201 GLN ** L 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 342 GLN M 29 GLN M 71 ASN M 164 ASN ** N 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 HIS O 185 ASN ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.110287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.099476 restraints weight = 154832.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.099953 restraints weight = 133435.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.100604 restraints weight = 112372.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.100447 restraints weight = 97490.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.100625 restraints weight = 94385.240| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24542 Z= 0.108 Angle : 0.568 10.429 33096 Z= 0.288 Chirality : 0.041 0.166 3766 Planarity : 0.004 0.057 4177 Dihedral : 4.630 83.948 3174 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.15 % Allowed : 3.21 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % 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: -1.35 (0.14), residues: 2920 helix: -0.67 (0.12), residues: 1615 sheet: 0.35 (0.32), residues: 255 loop : -1.37 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 147 TYR 0.021 0.001 TYR Q 262 PHE 0.017 0.001 PHE I 245 TRP 0.029 0.002 TRP L 265 HIS 0.007 0.001 HIS N 239 Details of bonding type rmsd covalent geometry : bond 0.00225 (24542) covalent geometry : angle 0.56760 (33096) hydrogen bonds : bond 0.03765 ( 1123) hydrogen bonds : angle 4.24618 ( 3360) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 543 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 93 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8309 (ttmt) REVERT: H 98 ILE cc_start: 0.8282 (mm) cc_final: 0.8053 (mm) REVERT: H 105 ARG cc_start: 0.8561 (mmt-90) cc_final: 0.8314 (tpp80) REVERT: H 130 MET cc_start: 0.8252 (mmp) cc_final: 0.7118 (ptm) REVERT: H 137 ASN cc_start: 0.8194 (m-40) cc_final: 0.7171 (m-40) REVERT: H 141 MET cc_start: 0.8633 (mpp) cc_final: 0.7991 (mpp) REVERT: I 334 ASN cc_start: 0.6329 (m-40) cc_final: 0.5934 (p0) REVERT: I 339 PHE cc_start: 0.7190 (t80) cc_final: 0.6899 (t80) REVERT: I 355 HIS cc_start: 0.7037 (p-80) cc_final: 0.6588 (p-80) REVERT: I 369 ASN cc_start: 0.7847 (t0) cc_final: 0.7455 (t0) REVERT: I 372 LEU cc_start: 0.8809 (mt) cc_final: 0.8182 (mt) REVERT: I 399 GLU cc_start: 0.8652 (pp20) cc_final: 0.7665 (pp20) REVERT: I 575 TYR cc_start: 0.7627 (m-10) cc_final: 0.7206 (m-10) REVERT: I 588 PHE cc_start: 0.7883 (t80) cc_final: 0.7328 (t80) REVERT: I 607 MET cc_start: 0.8130 (mmm) cc_final: 0.7853 (mmm) REVERT: I 613 ASN cc_start: 0.9100 (m-40) cc_final: 0.8797 (m-40) REVERT: I 696 LEU cc_start: 0.7871 (mp) cc_final: 0.7637 (mt) REVERT: K 31 MET cc_start: 0.8689 (ptp) cc_final: 0.8425 (ptp) REVERT: K 35 MET cc_start: 0.8638 (ptm) cc_final: 0.7992 (ttp) REVERT: K 62 MET cc_start: 0.7501 (ppp) cc_final: 0.7190 (tmm) REVERT: K 65 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8012 (ttpt) REVERT: K 80 GLU cc_start: 0.5915 (mt-10) cc_final: 0.5185 (tp30) REVERT: K 103 ASP cc_start: 0.8556 (m-30) cc_final: 0.8072 (t0) REVERT: K 135 ILE cc_start: 0.8382 (mm) cc_final: 0.8139 (mm) REVERT: L 48 LYS cc_start: 0.7837 (mtpt) cc_final: 0.7453 (mtpp) REVERT: L 116 ASN cc_start: 0.7309 (p0) cc_final: 0.6404 (p0) REVERT: L 144 LYS cc_start: 0.2268 (mttt) cc_final: 0.1631 (tttp) REVERT: L 158 TRP cc_start: 0.7493 (t60) cc_final: 0.6857 (t60) REVERT: L 163 CYS cc_start: 0.8081 (p) cc_final: 0.7834 (t) REVERT: L 165 VAL cc_start: 0.8179 (t) cc_final: 0.7568 (m) REVERT: L 221 MET cc_start: 0.8664 (ptm) cc_final: 0.8253 (ptm) REVERT: L 225 TRP cc_start: 0.7885 (m-10) cc_final: 0.7648 (m100) REVERT: L 253 SER cc_start: 0.8168 (m) cc_final: 0.7932 (m) REVERT: L 336 THR cc_start: 0.8385 (p) cc_final: 0.8136 (p) REVERT: L 342 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7971 (tp-100) REVERT: M 30 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7660 (mm-40) REVERT: M 33 ASP cc_start: 0.8155 (m-30) cc_final: 0.7807 (m-30) REVERT: M 45 LYS cc_start: 0.6264 (tttt) cc_final: 0.5930 (tttp) REVERT: M 64 ASP cc_start: 0.7277 (m-30) cc_final: 0.6592 (m-30) REVERT: M 94 LEU cc_start: 0.7624 (mt) cc_final: 0.7105 (pp) REVERT: M 102 THR cc_start: 0.7890 (p) cc_final: 0.7514 (t) REVERT: N 7 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7545 (tm-30) REVERT: N 18 MET cc_start: 0.8065 (pmm) cc_final: 0.6499 (tpt) REVERT: N 19 ASN cc_start: 0.8841 (p0) cc_final: 0.8575 (p0) REVERT: N 211 GLN cc_start: 0.6336 (mp10) cc_final: 0.5480 (tp-100) REVERT: N 264 LEU cc_start: 0.8822 (mt) cc_final: 0.8619 (mp) REVERT: N 334 PHE cc_start: 0.8301 (m-10) cc_final: 0.8055 (m-10) REVERT: O 174 GLN cc_start: 0.8000 (pt0) cc_final: 0.7665 (pm20) REVERT: O 182 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6372 (mm-30) REVERT: O 214 LEU cc_start: 0.7680 (tp) cc_final: 0.7424 (tt) REVERT: O 222 TYR cc_start: 0.8192 (p90) cc_final: 0.7479 (p90) REVERT: P 69 PHE cc_start: 0.7438 (t80) cc_final: 0.7013 (t80) REVERT: P 162 ASP cc_start: 0.8289 (t0) cc_final: 0.7589 (m-30) REVERT: P 168 ARG cc_start: 0.7409 (ptm160) cc_final: 0.6949 (ptm160) REVERT: P 244 GLN cc_start: 0.7839 (mt0) cc_final: 0.7318 (mm-40) REVERT: P 253 ARG cc_start: 0.8141 (mmp80) cc_final: 0.7719 (mmm160) REVERT: U 325 ASP cc_start: 0.8864 (t70) cc_final: 0.8607 (t0) REVERT: U 396 THR cc_start: 0.8667 (p) cc_final: 0.8261 (t) REVERT: Q 180 LYS cc_start: 0.6305 (tptt) cc_final: 0.6009 (tptt) REVERT: Q 184 GLN cc_start: 0.7730 (pp30) cc_final: 0.7488 (pp30) REVERT: Q 192 GLU cc_start: 0.8544 (tp30) cc_final: 0.8122 (tp30) REVERT: Q 201 HIS cc_start: 0.6947 (m90) cc_final: 0.6472 (m90) REVERT: Q 246 HIS cc_start: 0.7604 (m-70) cc_final: 0.7272 (t70) REVERT: W 72 LYS cc_start: 0.7902 (mptt) cc_final: 0.7175 (mmtt) REVERT: W 73 GLU cc_start: 0.8843 (tp30) cc_final: 0.7955 (mp0) REVERT: W 74 HIS cc_start: 0.7338 (m90) cc_final: 0.6664 (m90) outliers start: 4 outliers final: 0 residues processed: 545 average time/residue: 0.1642 time to fit residues: 140.8600 Evaluate side-chains 398 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 397 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 90 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 204 optimal weight: 0.6980 chunk 240 optimal weight: 3.9990 chunk 96 optimal weight: 0.0370 chunk 249 optimal weight: 40.0000 chunk 239 optimal weight: 2.9990 chunk 279 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 GLN I 67 GLN I 502 GLN I 503 ASN I 642 HIS K 213 HIS ** L 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 ASN M 115 HIS M 144 GLN M 164 ASN ** N 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 249 GLN ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 GLN O 153 HIS O 175 HIS ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 417 GLN ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Q 246 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.109425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.098983 restraints weight = 154352.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.099030 restraints weight = 135501.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.099608 restraints weight = 114812.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.099746 restraints weight = 99115.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.099916 restraints weight = 94063.954| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 24542 Z= 0.102 Angle : 0.541 9.610 33096 Z= 0.273 Chirality : 0.040 0.162 3766 Planarity : 0.004 0.042 4177 Dihedral : 4.364 69.600 3174 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.07 % Allowed : 1.92 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % 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 (0.15), residues: 2920 helix: 0.23 (0.13), residues: 1629 sheet: 0.50 (0.31), residues: 263 loop : -1.13 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 177 TYR 0.019 0.001 TYR K 172 PHE 0.014 0.001 PHE I 245 TRP 0.023 0.001 TRP I 461 HIS 0.008 0.001 HIS P 171 Details of bonding type rmsd covalent geometry : bond 0.00219 (24542) covalent geometry : angle 0.54108 (33096) hydrogen bonds : bond 0.03369 ( 1123) hydrogen bonds : angle 3.98920 ( 3360) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 544 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: H 98 ILE cc_start: 0.8263 (mm) cc_final: 0.8051 (mm) REVERT: H 130 MET cc_start: 0.8238 (mmp) cc_final: 0.7062 (ptm) REVERT: H 137 ASN cc_start: 0.8252 (m-40) cc_final: 0.7548 (m-40) REVERT: H 141 MET cc_start: 0.8546 (mpp) cc_final: 0.7917 (mpp) REVERT: I 334 ASN cc_start: 0.6309 (m-40) cc_final: 0.5936 (p0) REVERT: I 339 PHE cc_start: 0.7238 (t80) cc_final: 0.6943 (t80) REVERT: I 355 HIS cc_start: 0.7049 (p-80) cc_final: 0.6608 (p-80) REVERT: I 369 ASN cc_start: 0.7997 (t0) cc_final: 0.7515 (t0) REVERT: I 372 LEU cc_start: 0.8880 (mt) cc_final: 0.8196 (mt) REVERT: I 399 GLU cc_start: 0.8300 (pp20) cc_final: 0.7202 (pp20) REVERT: I 575 TYR cc_start: 0.7695 (m-10) cc_final: 0.7191 (m-10) REVERT: I 588 PHE cc_start: 0.8110 (t80) cc_final: 0.7859 (t80) REVERT: I 613 ASN cc_start: 0.9117 (m-40) cc_final: 0.8828 (m-40) REVERT: I 643 TYR cc_start: 0.7508 (m-80) cc_final: 0.6649 (m-80) REVERT: K 65 LYS cc_start: 0.8699 (mtmm) cc_final: 0.8032 (ttpt) REVERT: K 80 GLU cc_start: 0.5968 (mt-10) cc_final: 0.5152 (tp30) REVERT: K 103 ASP cc_start: 0.8569 (m-30) cc_final: 0.8081 (t0) REVERT: L 48 LYS cc_start: 0.7749 (mtpt) cc_final: 0.7457 (mtpp) REVERT: L 116 ASN cc_start: 0.7283 (p0) cc_final: 0.6377 (p0) REVERT: L 144 LYS cc_start: 0.2317 (mttt) cc_final: 0.1633 (tttm) REVERT: L 163 CYS cc_start: 0.8157 (p) cc_final: 0.7805 (t) REVERT: L 165 VAL cc_start: 0.8118 (t) cc_final: 0.7634 (m) REVERT: L 183 LEU cc_start: 0.7904 (tp) cc_final: 0.7692 (tp) REVERT: L 221 MET cc_start: 0.8634 (ptm) cc_final: 0.8286 (ptm) REVERT: L 225 TRP cc_start: 0.7995 (m-10) cc_final: 0.7693 (m100) REVERT: L 253 SER cc_start: 0.8195 (m) cc_final: 0.7954 (m) REVERT: L 281 ASP cc_start: 0.7808 (t0) cc_final: 0.7147 (p0) REVERT: L 288 TYR cc_start: 0.7786 (m-10) cc_final: 0.7325 (m-80) REVERT: L 299 LEU cc_start: 0.8261 (mt) cc_final: 0.7831 (mt) REVERT: M 30 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7728 (mm-40) REVERT: M 33 ASP cc_start: 0.8230 (m-30) cc_final: 0.7837 (m-30) REVERT: M 38 GLU cc_start: 0.7268 (pt0) cc_final: 0.6886 (pt0) REVERT: M 45 LYS cc_start: 0.6385 (tttt) cc_final: 0.5954 (tttp) REVERT: M 56 SER cc_start: 0.7952 (p) cc_final: 0.7749 (m) REVERT: M 64 ASP cc_start: 0.7650 (m-30) cc_final: 0.6963 (m-30) REVERT: M 94 LEU cc_start: 0.7891 (mt) cc_final: 0.7265 (pp) REVERT: M 102 THR cc_start: 0.7728 (p) cc_final: 0.7455 (t) REVERT: M 164 ASN cc_start: 0.6791 (OUTLIER) cc_final: 0.6479 (m-40) REVERT: N 18 MET cc_start: 0.8060 (pmm) cc_final: 0.6337 (tpp) REVERT: N 19 ASN cc_start: 0.8880 (p0) cc_final: 0.8550 (p0) REVERT: N 211 GLN cc_start: 0.6513 (mp10) cc_final: 0.5550 (tp-100) REVERT: N 314 ILE cc_start: 0.4765 (pt) cc_final: 0.4458 (pt) REVERT: N 334 PHE cc_start: 0.8265 (m-10) cc_final: 0.8050 (m-10) REVERT: O 174 GLN cc_start: 0.8085 (pt0) cc_final: 0.7523 (tt0) REVERT: O 182 GLU cc_start: 0.7373 (tp30) cc_final: 0.6839 (mm-30) REVERT: O 214 LEU cc_start: 0.7828 (tp) cc_final: 0.7528 (tt) REVERT: O 222 TYR cc_start: 0.8099 (p90) cc_final: 0.7247 (p90) REVERT: O 284 PHE cc_start: 0.8228 (m-10) cc_final: 0.7896 (m-80) REVERT: P 69 PHE cc_start: 0.7464 (t80) cc_final: 0.7044 (t80) REVERT: P 162 ASP cc_start: 0.8372 (t0) cc_final: 0.7582 (m-30) REVERT: P 168 ARG cc_start: 0.7503 (ptm160) cc_final: 0.7095 (ptm160) REVERT: P 253 ARG cc_start: 0.8183 (mmp80) cc_final: 0.7743 (mmm160) REVERT: U 239 CYS cc_start: 0.5034 (p) cc_final: 0.4755 (t) REVERT: U 243 MET cc_start: 0.6835 (ttp) cc_final: 0.6032 (ttp) REVERT: U 329 ARG cc_start: 0.8468 (mmm160) cc_final: 0.7003 (tmm-80) REVERT: U 383 ASP cc_start: 0.6921 (m-30) cc_final: 0.6128 (m-30) REVERT: U 396 THR cc_start: 0.8568 (p) cc_final: 0.8152 (t) REVERT: Q 180 LYS cc_start: 0.6235 (tptt) cc_final: 0.5964 (tptt) REVERT: Q 192 GLU cc_start: 0.8594 (tp30) cc_final: 0.8150 (tp30) REVERT: Q 201 HIS cc_start: 0.7045 (m90) cc_final: 0.6462 (m90) REVERT: Q 252 LYS cc_start: 0.7748 (pttm) cc_final: 0.6929 (tptm) REVERT: T 473 MET cc_start: -0.1042 (ttt) cc_final: -0.1497 (mtp) outliers start: 2 outliers final: 0 residues processed: 546 average time/residue: 0.1664 time to fit residues: 141.8564 Evaluate side-chains 397 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 396 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 265 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 230 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 266 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 GLN H 213 GLN ** I 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 502 GLN ** I 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 GLN K 160 ASN L 325 HIS M 71 ASN M 115 HIS M 144 GLN ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 GLN ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN O 100 ASN O 133 ASN O 152 HIS ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 284 ASN U 409 HIS ** U 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.102220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.093102 restraints weight = 142724.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.092953 restraints weight = 141424.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.093469 restraints weight = 121909.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.093332 restraints weight = 100604.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.093463 restraints weight = 96267.169| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 24542 Z= 0.248 Angle : 0.796 12.932 33096 Z= 0.409 Chirality : 0.047 0.219 3766 Planarity : 0.005 0.074 4177 Dihedral : 5.011 31.993 3174 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % 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: -0.33 (0.15), residues: 2920 helix: 0.29 (0.12), residues: 1663 sheet: 0.24 (0.31), residues: 263 loop : -1.05 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG M 62 TYR 0.021 0.002 TYR I 488 PHE 0.029 0.003 PHE L 162 TRP 0.033 0.003 TRP P 222 HIS 0.019 0.002 HIS P 171 Details of bonding type rmsd covalent geometry : bond 0.00540 (24542) covalent geometry : angle 0.79588 (33096) hydrogen bonds : bond 0.04335 ( 1123) hydrogen bonds : angle 4.50715 ( 3360) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 472 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7433 (mt-10) REVERT: H 98 ILE cc_start: 0.8466 (mm) cc_final: 0.8244 (mm) REVERT: H 127 MET cc_start: 0.7905 (mtp) cc_final: 0.7365 (mtp) REVERT: H 130 MET cc_start: 0.8565 (mmp) cc_final: 0.7342 (ptm) REVERT: H 141 MET cc_start: 0.8563 (mpp) cc_final: 0.8090 (mpp) REVERT: I 334 ASN cc_start: 0.6495 (m-40) cc_final: 0.5921 (p0) REVERT: I 339 PHE cc_start: 0.7182 (t80) cc_final: 0.6817 (t80) REVERT: I 355 HIS cc_start: 0.7264 (p-80) cc_final: 0.6800 (p-80) REVERT: I 369 ASN cc_start: 0.8126 (t0) cc_final: 0.7505 (t0) REVERT: I 372 LEU cc_start: 0.9138 (mt) cc_final: 0.8375 (mt) REVERT: I 399 GLU cc_start: 0.8446 (pp20) cc_final: 0.7614 (pp20) REVERT: I 452 ARG cc_start: 0.8030 (ttp-170) cc_final: 0.7803 (ttp80) REVERT: I 505 LEU cc_start: 0.8535 (mt) cc_final: 0.8322 (mt) REVERT: I 572 TYR cc_start: 0.7948 (t80) cc_final: 0.7708 (t80) REVERT: I 575 TYR cc_start: 0.8186 (m-10) cc_final: 0.7649 (m-80) REVERT: I 603 LEU cc_start: 0.8190 (tp) cc_final: 0.7956 (tp) REVERT: I 610 TYR cc_start: 0.8949 (m-10) cc_final: 0.8748 (m-10) REVERT: I 613 ASN cc_start: 0.9100 (m-40) cc_final: 0.8845 (m-40) REVERT: I 729 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7976 (mm110) REVERT: K 103 ASP cc_start: 0.8582 (m-30) cc_final: 0.8027 (t0) REVERT: L 48 LYS cc_start: 0.7903 (mtpt) cc_final: 0.7608 (mtpp) REVERT: L 116 ASN cc_start: 0.6988 (p0) cc_final: 0.6062 (p0) REVERT: L 144 LYS cc_start: 0.2575 (mttt) cc_final: 0.1557 (tttm) REVERT: L 281 ASP cc_start: 0.8089 (t0) cc_final: 0.7412 (p0) REVERT: L 288 TYR cc_start: 0.7974 (m-10) cc_final: 0.7276 (m-80) REVERT: L 299 LEU cc_start: 0.8462 (mt) cc_final: 0.7946 (mt) REVERT: L 300 SER cc_start: 0.8451 (p) cc_final: 0.7896 (p) REVERT: M 30 GLN cc_start: 0.8339 (mm-40) cc_final: 0.8101 (mm-40) REVERT: M 33 ASP cc_start: 0.8422 (m-30) cc_final: 0.7966 (m-30) REVERT: M 38 GLU cc_start: 0.7143 (pt0) cc_final: 0.6742 (pt0) REVERT: M 45 LYS cc_start: 0.6708 (tttt) cc_final: 0.6240 (tttp) REVERT: M 50 LYS cc_start: 0.7158 (mmmt) cc_final: 0.6929 (mmmm) REVERT: M 63 ILE cc_start: 0.6996 (tp) cc_final: 0.6760 (mm) REVERT: M 64 ASP cc_start: 0.7334 (m-30) cc_final: 0.7120 (m-30) REVERT: M 94 LEU cc_start: 0.7781 (mt) cc_final: 0.7248 (tp) REVERT: M 107 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8035 (mp0) REVERT: N 307 LYS cc_start: 0.8740 (ptmt) cc_final: 0.8530 (ptmt) REVERT: O 174 GLN cc_start: 0.8105 (pt0) cc_final: 0.7795 (pm20) REVERT: O 180 LEU cc_start: 0.8854 (mt) cc_final: 0.8582 (mm) REVERT: O 182 GLU cc_start: 0.7638 (tp30) cc_final: 0.7129 (mm-30) REVERT: O 214 LEU cc_start: 0.8811 (tp) cc_final: 0.8456 (tt) REVERT: O 222 TYR cc_start: 0.8458 (p90) cc_final: 0.8037 (p90) REVERT: O 278 LYS cc_start: 0.6743 (tppt) cc_final: 0.6533 (tptt) REVERT: O 284 PHE cc_start: 0.8469 (m-10) cc_final: 0.8248 (m-80) REVERT: P 112 HIS cc_start: 0.5970 (t-170) cc_final: 0.5671 (t-170) REVERT: P 113 MET cc_start: 0.8154 (mmt) cc_final: 0.7773 (mmt) REVERT: P 142 MET cc_start: 0.7776 (tpt) cc_final: 0.6948 (tpp) REVERT: P 161 LYS cc_start: 0.8512 (mttt) cc_final: 0.8214 (mmtt) REVERT: P 162 ASP cc_start: 0.8606 (t0) cc_final: 0.7805 (m-30) REVERT: P 168 ARG cc_start: 0.7873 (ptm160) cc_final: 0.7599 (ptm160) REVERT: P 206 MET cc_start: 0.7420 (ppp) cc_final: 0.7140 (ppp) REVERT: P 244 GLN cc_start: 0.8049 (mt0) cc_final: 0.7778 (mt0) REVERT: P 253 ARG cc_start: 0.8307 (mmp80) cc_final: 0.7714 (mmm160) REVERT: P 275 LEU cc_start: 0.8758 (mt) cc_final: 0.8545 (mp) REVERT: P 280 LYS cc_start: 0.5710 (tttm) cc_final: 0.4961 (tmtt) REVERT: U 329 ARG cc_start: 0.8730 (mmm160) cc_final: 0.8363 (tpp-160) REVERT: U 342 ASP cc_start: 0.8627 (t0) cc_final: 0.7906 (m-30) REVERT: U 383 ASP cc_start: 0.7087 (m-30) cc_final: 0.6873 (m-30) REVERT: U 396 THR cc_start: 0.8684 (p) cc_final: 0.8336 (t) REVERT: Q 180 LYS cc_start: 0.6550 (tptt) cc_final: 0.6156 (tptt) REVERT: Q 184 GLN cc_start: 0.7832 (pp30) cc_final: 0.7627 (pp30) REVERT: Q 192 GLU cc_start: 0.8678 (tp30) cc_final: 0.8264 (tp30) REVERT: Q 226 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8448 (mttt) REVERT: R 121 ASN cc_start: 0.8264 (t0) cc_final: 0.7880 (t0) REVERT: T 473 MET cc_start: -0.1137 (ttt) cc_final: -0.1410 (mtp) outliers start: 1 outliers final: 0 residues processed: 473 average time/residue: 0.1598 time to fit residues: 119.1252 Evaluate side-chains 355 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 170 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 287 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 271 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 239 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 234 HIS ** I 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 503 ASN K 168 ASN L 257 HIS M 71 ASN M 115 HIS M 144 GLN ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 GLN ** N 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 406 ASN U 410 GLN U 417 GLN ** Q 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.104124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.095096 restraints weight = 152637.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.095237 restraints weight = 126017.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.095438 restraints weight = 120007.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.095390 restraints weight = 105110.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.095553 restraints weight = 94235.050| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24542 Z= 0.130 Angle : 0.605 9.664 33096 Z= 0.306 Chirality : 0.043 0.188 3766 Planarity : 0.004 0.041 4177 Dihedral : 4.567 34.074 3174 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % 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: 0.25 (0.15), residues: 2920 helix: 0.80 (0.13), residues: 1664 sheet: 0.36 (0.31), residues: 263 loop : -0.87 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 62 TYR 0.023 0.001 TYR N 141 PHE 0.024 0.001 PHE L 98 TRP 0.018 0.002 TRP P 222 HIS 0.012 0.001 HIS P 171 Details of bonding type rmsd covalent geometry : bond 0.00278 (24542) covalent geometry : angle 0.60463 (33096) hydrogen bonds : bond 0.03546 ( 1123) hydrogen bonds : angle 4.05665 ( 3360) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 477 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 ASP cc_start: 0.7814 (m-30) cc_final: 0.7438 (m-30) REVERT: H 86 GLU cc_start: 0.9020 (pt0) cc_final: 0.8734 (pt0) REVERT: H 98 ILE cc_start: 0.8445 (mm) cc_final: 0.8233 (mm) REVERT: H 105 ARG cc_start: 0.8660 (tpp-160) cc_final: 0.8098 (tpp80) REVERT: H 127 MET cc_start: 0.8029 (mtp) cc_final: 0.7401 (mtp) REVERT: H 130 MET cc_start: 0.8412 (mmp) cc_final: 0.7236 (ptm) REVERT: H 141 MET cc_start: 0.8430 (mpp) cc_final: 0.8150 (mpp) REVERT: I 229 MET cc_start: 0.6770 (ppp) cc_final: 0.6294 (ppp) REVERT: I 334 ASN cc_start: 0.6451 (m-40) cc_final: 0.5843 (p0) REVERT: I 339 PHE cc_start: 0.7105 (t80) cc_final: 0.6770 (t80) REVERT: I 355 HIS cc_start: 0.7198 (p-80) cc_final: 0.6762 (p-80) REVERT: I 369 ASN cc_start: 0.8104 (t0) cc_final: 0.7529 (t0) REVERT: I 372 LEU cc_start: 0.8997 (mt) cc_final: 0.8301 (mt) REVERT: I 399 GLU cc_start: 0.8606 (pp20) cc_final: 0.7466 (pp20) REVERT: I 414 PHE cc_start: 0.8480 (t80) cc_final: 0.8054 (t80) REVERT: I 454 GLN cc_start: 0.7307 (mp10) cc_final: 0.7038 (mp10) REVERT: I 499 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7877 (mt-10) REVERT: I 503 ASN cc_start: 0.8306 (m-40) cc_final: 0.7991 (m110) REVERT: I 575 TYR cc_start: 0.8068 (m-10) cc_final: 0.7696 (m-80) REVERT: I 588 PHE cc_start: 0.7671 (t80) cc_final: 0.7376 (t80) REVERT: I 603 LEU cc_start: 0.8215 (tp) cc_final: 0.7929 (tp) REVERT: I 613 ASN cc_start: 0.9092 (m-40) cc_final: 0.8800 (m-40) REVERT: K 103 ASP cc_start: 0.8599 (m-30) cc_final: 0.8039 (t0) REVERT: L 48 LYS cc_start: 0.7879 (mtpt) cc_final: 0.7611 (mtpp) REVERT: L 116 ASN cc_start: 0.7117 (p0) cc_final: 0.6203 (p0) REVERT: L 144 LYS cc_start: 0.2525 (mttt) cc_final: 0.1549 (tttp) REVERT: L 281 ASP cc_start: 0.7962 (t0) cc_final: 0.7398 (p0) REVERT: L 288 TYR cc_start: 0.7981 (m-10) cc_final: 0.7232 (m-80) REVERT: L 299 LEU cc_start: 0.8463 (mt) cc_final: 0.7975 (mt) REVERT: L 300 SER cc_start: 0.8433 (p) cc_final: 0.7955 (m) REVERT: M 30 GLN cc_start: 0.8271 (mm-40) cc_final: 0.8063 (mm-40) REVERT: M 33 ASP cc_start: 0.8411 (m-30) cc_final: 0.8001 (m-30) REVERT: M 38 GLU cc_start: 0.7243 (pt0) cc_final: 0.6999 (pt0) REVERT: M 45 LYS cc_start: 0.6590 (tttt) cc_final: 0.6100 (tttp) REVERT: M 50 LYS cc_start: 0.7152 (mmmt) cc_final: 0.6884 (mmmm) REVERT: M 64 ASP cc_start: 0.7364 (m-30) cc_final: 0.6968 (m-30) REVERT: M 94 LEU cc_start: 0.7955 (mt) cc_final: 0.7571 (pp) REVERT: M 107 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8031 (mp0) REVERT: N 7 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7968 (tm-30) REVERT: O 117 LEU cc_start: 0.7218 (mp) cc_final: 0.6835 (pp) REVERT: O 174 GLN cc_start: 0.8075 (pt0) cc_final: 0.7646 (pm20) REVERT: O 182 GLU cc_start: 0.7471 (tp30) cc_final: 0.6762 (tp30) REVERT: O 214 LEU cc_start: 0.8754 (tp) cc_final: 0.8456 (tt) REVERT: O 222 TYR cc_start: 0.8129 (p90) cc_final: 0.7837 (p90) REVERT: P 112 HIS cc_start: 0.6102 (t-170) cc_final: 0.5816 (t70) REVERT: P 113 MET cc_start: 0.8235 (mmt) cc_final: 0.7823 (mmt) REVERT: P 161 LYS cc_start: 0.8385 (mttt) cc_final: 0.8163 (mmtt) REVERT: P 162 ASP cc_start: 0.8535 (t0) cc_final: 0.7688 (m-30) REVERT: P 206 MET cc_start: 0.7441 (ppp) cc_final: 0.7240 (ppp) REVERT: P 244 GLN cc_start: 0.8010 (mt0) cc_final: 0.7759 (mt0) REVERT: P 253 ARG cc_start: 0.8318 (mmp80) cc_final: 0.7872 (mmm160) REVERT: P 280 LYS cc_start: 0.5691 (tttm) cc_final: 0.5135 (tmtt) REVERT: U 329 ARG cc_start: 0.8697 (mmm160) cc_final: 0.8478 (tpp-160) REVERT: U 342 ASP cc_start: 0.8617 (t0) cc_final: 0.7883 (m-30) REVERT: U 383 ASP cc_start: 0.6928 (m-30) cc_final: 0.6524 (m-30) REVERT: U 396 THR cc_start: 0.8661 (p) cc_final: 0.8283 (t) REVERT: Q 180 LYS cc_start: 0.6545 (tptt) cc_final: 0.6166 (tptt) REVERT: Q 192 GLU cc_start: 0.8671 (tp30) cc_final: 0.8304 (tp30) REVERT: Q 226 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8352 (ttmt) REVERT: T 473 MET cc_start: -0.1330 (ttt) cc_final: -0.1556 (mtp) outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 0.1615 time to fit residues: 120.0889 Evaluate side-chains 376 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 162 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 278 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 163 optimal weight: 8.9990 chunk 249 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN ** I 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 GLN L 232 HIS M 71 ASN M 115 HIS M 144 GLN N 35 GLN ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 GLN P 186 HIS ** U 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 366 GLN U 410 GLN ** Q 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.097847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.090551 restraints weight = 136688.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.089902 restraints weight = 139029.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.089861 restraints weight = 122658.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.090015 restraints weight = 94518.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.090093 restraints weight = 89398.220| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.7025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 24542 Z= 0.254 Angle : 0.807 12.524 33096 Z= 0.414 Chirality : 0.048 0.205 3766 Planarity : 0.005 0.067 4177 Dihedral : 5.274 37.857 3174 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.07 % Allowed : 1.81 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % 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: -0.23 (0.15), residues: 2920 helix: 0.45 (0.12), residues: 1649 sheet: -0.07 (0.30), residues: 269 loop : -1.04 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 196 TYR 0.027 0.003 TYR N 141 PHE 0.029 0.003 PHE M 92 TRP 0.042 0.003 TRP U 238 HIS 0.009 0.002 HIS U 403 Details of bonding type rmsd covalent geometry : bond 0.00554 (24542) covalent geometry : angle 0.80654 (33096) hydrogen bonds : bond 0.04545 ( 1123) hydrogen bonds : angle 4.60753 ( 3360) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 452 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 MET cc_start: 0.8965 (tpp) cc_final: 0.8622 (tpp) REVERT: H 62 ASP cc_start: 0.7846 (m-30) cc_final: 0.7557 (m-30) REVERT: H 98 ILE cc_start: 0.8549 (mm) cc_final: 0.8322 (mm) REVERT: H 127 MET cc_start: 0.8075 (mtp) cc_final: 0.7598 (mtp) REVERT: H 130 MET cc_start: 0.8618 (mmp) cc_final: 0.7477 (ptm) REVERT: I 221 LYS cc_start: 0.5700 (tttt) cc_final: 0.5282 (tttt) REVERT: I 229 MET cc_start: 0.6558 (ppp) cc_final: 0.6089 (ppp) REVERT: I 334 ASN cc_start: 0.6781 (m-40) cc_final: 0.5854 (p0) REVERT: I 339 PHE cc_start: 0.6965 (t80) cc_final: 0.6699 (t80) REVERT: I 355 HIS cc_start: 0.7457 (p-80) cc_final: 0.7011 (p-80) REVERT: I 369 ASN cc_start: 0.8182 (t0) cc_final: 0.7612 (t0) REVERT: I 399 GLU cc_start: 0.8403 (pp20) cc_final: 0.7087 (pp20) REVERT: I 414 PHE cc_start: 0.8428 (t80) cc_final: 0.7897 (t80) REVERT: I 416 ASN cc_start: 0.7610 (t0) cc_final: 0.7255 (p0) REVERT: I 452 ARG cc_start: 0.7885 (ttp-170) cc_final: 0.7659 (ttp80) REVERT: I 454 GLN cc_start: 0.7515 (mp10) cc_final: 0.7223 (mp10) REVERT: I 499 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7916 (mt-10) REVERT: I 503 ASN cc_start: 0.8223 (m-40) cc_final: 0.7964 (m110) REVERT: I 603 LEU cc_start: 0.8226 (tp) cc_final: 0.8024 (tp) REVERT: I 613 ASN cc_start: 0.9081 (m-40) cc_final: 0.8773 (m-40) REVERT: I 721 ASP cc_start: 0.8237 (m-30) cc_final: 0.8027 (t0) REVERT: K 38 CYS cc_start: 0.8519 (m) cc_final: 0.8042 (t) REVERT: K 59 LEU cc_start: 0.9149 (mt) cc_final: 0.8826 (mm) REVERT: K 63 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7785 (mm-40) REVERT: K 103 ASP cc_start: 0.8613 (m-30) cc_final: 0.7971 (t0) REVERT: L 46 ARG cc_start: 0.7202 (mtm180) cc_final: 0.6891 (mtm-85) REVERT: L 116 ASN cc_start: 0.7126 (p0) cc_final: 0.6245 (p0) REVERT: L 288 TYR cc_start: 0.8185 (m-10) cc_final: 0.7393 (m-80) REVERT: L 299 LEU cc_start: 0.8432 (mt) cc_final: 0.7924 (mt) REVERT: L 300 SER cc_start: 0.8523 (p) cc_final: 0.7880 (t) REVERT: M 33 ASP cc_start: 0.8470 (m-30) cc_final: 0.7960 (m-30) REVERT: M 38 GLU cc_start: 0.7024 (pt0) cc_final: 0.6613 (pt0) REVERT: M 45 LYS cc_start: 0.6527 (tttt) cc_final: 0.6078 (tttp) REVERT: M 50 LYS cc_start: 0.7176 (mmmt) cc_final: 0.6967 (mmmm) REVERT: M 64 ASP cc_start: 0.7407 (m-30) cc_final: 0.6930 (m-30) REVERT: M 94 LEU cc_start: 0.7869 (mt) cc_final: 0.7338 (tp) REVERT: M 107 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8235 (mp0) REVERT: N 100 ASP cc_start: 0.8854 (t0) cc_final: 0.8624 (t70) REVERT: N 154 TYR cc_start: 0.8777 (t80) cc_final: 0.8252 (t80) REVERT: N 331 MET cc_start: 0.8702 (pmm) cc_final: 0.8203 (pmm) REVERT: O 178 PHE cc_start: 0.8557 (m-10) cc_final: 0.8157 (m-80) REVERT: O 180 LEU cc_start: 0.8802 (mt) cc_final: 0.8563 (mm) REVERT: O 182 GLU cc_start: 0.7779 (tp30) cc_final: 0.7404 (mm-30) REVERT: O 278 LYS cc_start: 0.6821 (tppt) cc_final: 0.6580 (tptt) REVERT: O 284 PHE cc_start: 0.8295 (m-80) cc_final: 0.7698 (m-80) REVERT: P 112 HIS cc_start: 0.6625 (t-170) cc_final: 0.6370 (t70) REVERT: P 113 MET cc_start: 0.8211 (mmt) cc_final: 0.7829 (mmt) REVERT: P 142 MET cc_start: 0.7785 (tpt) cc_final: 0.7055 (tpp) REVERT: P 162 ASP cc_start: 0.8509 (t0) cc_final: 0.7980 (m-30) REVERT: P 244 GLN cc_start: 0.8105 (mt0) cc_final: 0.7878 (mt0) REVERT: P 253 ARG cc_start: 0.8358 (mmp80) cc_final: 0.8027 (mmm160) REVERT: U 239 CYS cc_start: 0.7562 (p) cc_final: 0.7279 (p) REVERT: U 309 MET cc_start: 0.8211 (ttt) cc_final: 0.7981 (ttt) REVERT: U 396 THR cc_start: 0.8673 (p) cc_final: 0.8371 (t) REVERT: Q 226 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8595 (mttt) REVERT: T 473 MET cc_start: -0.1092 (ttt) cc_final: -0.1599 (mtp) outliers start: 2 outliers final: 0 residues processed: 454 average time/residue: 0.1602 time to fit residues: 115.7808 Evaluate side-chains 356 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 355 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 198 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 238 optimal weight: 4.9990 chunk 285 optimal weight: 20.0000 chunk 163 optimal weight: 0.0570 chunk 286 optimal weight: 5.9990 chunk 131 optimal weight: 0.0670 chunk 232 optimal weight: 5.9990 chunk 250 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 overall best weight: 2.1840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN ** I 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 HIS ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 GLN ** N 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 HIS O 175 HIS ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 171 HIS T 545 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.100508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.092752 restraints weight = 136082.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.092717 restraints weight = 123094.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.092588 restraints weight = 126378.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.092622 restraints weight = 97586.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.092762 restraints weight = 87707.612| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.6972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24542 Z= 0.134 Angle : 0.639 10.569 33096 Z= 0.323 Chirality : 0.044 0.168 3766 Planarity : 0.004 0.050 4177 Dihedral : 4.831 41.915 3174 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % 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: 0.23 (0.15), residues: 2920 helix: 0.85 (0.13), residues: 1661 sheet: -0.03 (0.31), residues: 263 loop : -0.89 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 161 TYR 0.023 0.002 TYR U 365 PHE 0.022 0.002 PHE I 640 TRP 0.028 0.002 TRP I 504 HIS 0.010 0.001 HIS P 171 Details of bonding type rmsd covalent geometry : bond 0.00297 (24542) covalent geometry : angle 0.63924 (33096) hydrogen bonds : bond 0.03803 ( 1123) hydrogen bonds : angle 4.17973 ( 3360) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 ASP cc_start: 0.7862 (m-30) cc_final: 0.7584 (m-30) REVERT: H 98 ILE cc_start: 0.8494 (mm) cc_final: 0.8256 (mm) REVERT: H 127 MET cc_start: 0.8126 (mtp) cc_final: 0.7577 (mtp) REVERT: H 130 MET cc_start: 0.8445 (mmp) cc_final: 0.7398 (ptm) REVERT: H 141 MET cc_start: 0.8428 (mpp) cc_final: 0.7847 (mpp) REVERT: I 221 LYS cc_start: 0.5568 (tttt) cc_final: 0.5238 (tmtt) REVERT: I 229 MET cc_start: 0.6581 (ppp) cc_final: 0.6184 (ppp) REVERT: I 339 PHE cc_start: 0.7052 (t80) cc_final: 0.6751 (t80) REVERT: I 355 HIS cc_start: 0.7405 (p-80) cc_final: 0.7024 (p-80) REVERT: I 369 ASN cc_start: 0.8121 (t0) cc_final: 0.7580 (t0) REVERT: I 399 GLU cc_start: 0.8472 (pp20) cc_final: 0.7166 (pp20) REVERT: I 414 PHE cc_start: 0.8433 (t80) cc_final: 0.7767 (t80) REVERT: I 416 ASN cc_start: 0.7530 (t0) cc_final: 0.7200 (p0) REVERT: I 452 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7674 (ttp80) REVERT: I 499 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7924 (mt-10) REVERT: I 503 ASN cc_start: 0.8180 (m-40) cc_final: 0.7920 (m110) REVERT: I 613 ASN cc_start: 0.9069 (m-40) cc_final: 0.8789 (m-40) REVERT: I 721 ASP cc_start: 0.8125 (m-30) cc_final: 0.7910 (t0) REVERT: K 103 ASP cc_start: 0.8641 (m-30) cc_final: 0.8030 (t0) REVERT: L 46 ARG cc_start: 0.7103 (mtm180) cc_final: 0.6687 (ttm-80) REVERT: L 116 ASN cc_start: 0.7164 (p0) cc_final: 0.6305 (p0) REVERT: L 230 MET cc_start: 0.7226 (tmm) cc_final: 0.6940 (tmm) REVERT: L 288 TYR cc_start: 0.8135 (m-10) cc_final: 0.7371 (m-80) REVERT: L 299 LEU cc_start: 0.8427 (mt) cc_final: 0.7816 (mt) REVERT: L 300 SER cc_start: 0.8508 (p) cc_final: 0.7917 (p) REVERT: M 33 ASP cc_start: 0.8349 (m-30) cc_final: 0.7995 (m-30) REVERT: M 38 GLU cc_start: 0.7068 (pt0) cc_final: 0.6782 (pt0) REVERT: M 45 LYS cc_start: 0.6588 (tttt) cc_final: 0.6045 (tttp) REVERT: M 64 ASP cc_start: 0.7212 (m-30) cc_final: 0.6855 (m-30) REVERT: M 94 LEU cc_start: 0.8201 (mt) cc_final: 0.7715 (pp) REVERT: M 107 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8192 (mp0) REVERT: N 100 ASP cc_start: 0.8628 (t0) cc_final: 0.8408 (t70) REVERT: N 154 TYR cc_start: 0.8712 (t80) cc_final: 0.8232 (t80) REVERT: N 211 GLN cc_start: 0.7211 (mp10) cc_final: 0.6875 (tp-100) REVERT: O 178 PHE cc_start: 0.8637 (m-10) cc_final: 0.8203 (m-80) REVERT: O 182 GLU cc_start: 0.7674 (tp30) cc_final: 0.6831 (tp30) REVERT: O 222 TYR cc_start: 0.8243 (p90) cc_final: 0.7831 (p90) REVERT: O 284 PHE cc_start: 0.8268 (m-80) cc_final: 0.7816 (m-80) REVERT: P 112 HIS cc_start: 0.6682 (t-170) cc_final: 0.6369 (t70) REVERT: P 113 MET cc_start: 0.8229 (mmt) cc_final: 0.7815 (mmt) REVERT: P 142 MET cc_start: 0.7824 (tpt) cc_final: 0.7117 (tpp) REVERT: P 161 LYS cc_start: 0.8496 (mttt) cc_final: 0.8028 (mmtt) REVERT: P 162 ASP cc_start: 0.8412 (t0) cc_final: 0.7641 (m-30) REVERT: P 197 LEU cc_start: 0.7584 (mp) cc_final: 0.7155 (mp) REVERT: P 244 GLN cc_start: 0.8056 (mt0) cc_final: 0.7806 (mt0) REVERT: P 253 ARG cc_start: 0.8372 (mmp80) cc_final: 0.7896 (mmm160) REVERT: U 239 CYS cc_start: 0.7573 (p) cc_final: 0.7247 (p) REVERT: U 319 ARG cc_start: 0.7685 (tpp80) cc_final: 0.7407 (tpp80) REVERT: U 382 TYR cc_start: 0.7502 (m-10) cc_final: 0.7236 (m-10) REVERT: U 396 THR cc_start: 0.8611 (p) cc_final: 0.8331 (t) REVERT: U 397 LEU cc_start: 0.8977 (mt) cc_final: 0.8774 (mt) REVERT: Q 143 MET cc_start: 0.7512 (ptm) cc_final: 0.7235 (ppp) REVERT: Q 184 GLN cc_start: 0.8009 (pp30) cc_final: 0.7780 (pp30) REVERT: Q 201 HIS cc_start: 0.7223 (m90) cc_final: 0.6945 (m-70) REVERT: Q 226 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8468 (mttt) REVERT: Q 252 LYS cc_start: 0.7681 (pttm) cc_final: 0.6913 (tptm) REVERT: T 473 MET cc_start: -0.1303 (ttt) cc_final: -0.1627 (mtp) REVERT: T 475 MET cc_start: 0.4051 (tpp) cc_final: 0.3283 (tmm) outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 0.1619 time to fit residues: 120.2266 Evaluate side-chains 361 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 236 optimal weight: 1.9990 chunk 210 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 219 optimal weight: 0.8980 chunk 198 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 213 GLN ** I 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 ASN ** M 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 GLN M 156 HIS ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 GLN O 193 GLN ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 417 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.100167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.092258 restraints weight = 140772.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.092129 restraints weight = 127825.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.092327 restraints weight = 116560.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.092306 restraints weight = 95044.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.092454 restraints weight = 88933.119| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.7083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24542 Z= 0.137 Angle : 0.635 9.976 33096 Z= 0.322 Chirality : 0.043 0.160 3766 Planarity : 0.004 0.045 4177 Dihedral : 4.690 43.048 3174 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % 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 (0.15), residues: 2920 helix: 0.98 (0.13), residues: 1666 sheet: 0.01 (0.31), residues: 268 loop : -0.81 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 177 TYR 0.024 0.002 TYR U 365 PHE 0.016 0.002 PHE I 482 TRP 0.032 0.002 TRP I 504 HIS 0.017 0.001 HIS P 171 Details of bonding type rmsd covalent geometry : bond 0.00303 (24542) covalent geometry : angle 0.63524 (33096) hydrogen bonds : bond 0.03739 ( 1123) hydrogen bonds : angle 4.13313 ( 3360) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 MET cc_start: 0.8989 (tpp) cc_final: 0.8750 (tpp) REVERT: H 97 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7422 (mm-30) REVERT: H 98 ILE cc_start: 0.8524 (mm) cc_final: 0.8311 (mm) REVERT: H 104 ASP cc_start: 0.8810 (t0) cc_final: 0.8529 (t0) REVERT: H 127 MET cc_start: 0.8110 (mtp) cc_final: 0.7580 (mtp) REVERT: H 130 MET cc_start: 0.8457 (mmp) cc_final: 0.7413 (ptm) REVERT: H 141 MET cc_start: 0.8291 (mpp) cc_final: 0.7967 (mpp) REVERT: I 221 LYS cc_start: 0.5695 (tttt) cc_final: 0.5322 (tmtt) REVERT: I 229 MET cc_start: 0.6619 (ppp) cc_final: 0.6227 (ppp) REVERT: I 339 PHE cc_start: 0.7069 (t80) cc_final: 0.6781 (t80) REVERT: I 355 HIS cc_start: 0.7377 (p-80) cc_final: 0.6978 (p-80) REVERT: I 369 ASN cc_start: 0.8146 (t0) cc_final: 0.7607 (t0) REVERT: I 399 GLU cc_start: 0.8582 (pp20) cc_final: 0.7302 (pp20) REVERT: I 414 PHE cc_start: 0.8488 (t80) cc_final: 0.7940 (t80) REVERT: I 452 ARG cc_start: 0.8003 (ttp-170) cc_final: 0.7797 (ttp80) REVERT: I 499 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7946 (mt-10) REVERT: I 503 ASN cc_start: 0.8143 (m-40) cc_final: 0.7925 (m110) REVERT: I 613 ASN cc_start: 0.9033 (m-40) cc_final: 0.8711 (m-40) REVERT: I 643 TYR cc_start: 0.7934 (m-80) cc_final: 0.6540 (m-80) REVERT: I 714 LYS cc_start: 0.7756 (mptt) cc_final: 0.7343 (pttt) REVERT: I 721 ASP cc_start: 0.8122 (m-30) cc_final: 0.7898 (t0) REVERT: K 103 ASP cc_start: 0.8615 (m-30) cc_final: 0.8025 (t0) REVERT: K 127 ARG cc_start: 0.8304 (tmm-80) cc_final: 0.8003 (tmm-80) REVERT: K 215 MET cc_start: 0.5797 (mtt) cc_final: 0.5585 (mtt) REVERT: L 99 ILE cc_start: 0.9132 (pt) cc_final: 0.8772 (pt) REVERT: L 116 ASN cc_start: 0.7273 (p0) cc_final: 0.6416 (p0) REVERT: L 224 MET cc_start: 0.8452 (ttm) cc_final: 0.8182 (mmt) REVERT: L 230 MET cc_start: 0.7124 (tmm) cc_final: 0.6756 (tmm) REVERT: L 300 SER cc_start: 0.8496 (p) cc_final: 0.8273 (p) REVERT: M 24 GLU cc_start: 0.7949 (pm20) cc_final: 0.7744 (pm20) REVERT: M 33 ASP cc_start: 0.8378 (m-30) cc_final: 0.7945 (m-30) REVERT: M 38 GLU cc_start: 0.7240 (pt0) cc_final: 0.7020 (pt0) REVERT: M 45 LYS cc_start: 0.6551 (tttt) cc_final: 0.6011 (tttp) REVERT: M 64 ASP cc_start: 0.7271 (m-30) cc_final: 0.6904 (m-30) REVERT: M 94 LEU cc_start: 0.8124 (mt) cc_final: 0.7637 (pp) REVERT: M 107 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8194 (mp0) REVERT: M 160 VAL cc_start: 0.8780 (t) cc_final: 0.8542 (p) REVERT: N 154 TYR cc_start: 0.8763 (t80) cc_final: 0.8298 (t80) REVERT: N 211 GLN cc_start: 0.7199 (mp10) cc_final: 0.6876 (tp-100) REVERT: N 331 MET cc_start: 0.8577 (pmm) cc_final: 0.8034 (pmm) REVERT: O 174 GLN cc_start: 0.8090 (pm20) cc_final: 0.7597 (tt0) REVERT: O 175 HIS cc_start: 0.7909 (t70) cc_final: 0.7355 (t70) REVERT: O 176 PHE cc_start: 0.8687 (t80) cc_final: 0.8356 (t80) REVERT: O 178 PHE cc_start: 0.8634 (m-10) cc_final: 0.8420 (m-80) REVERT: O 180 LEU cc_start: 0.8723 (mt) cc_final: 0.8394 (mt) REVERT: O 182 GLU cc_start: 0.7596 (tp30) cc_final: 0.7277 (mm-30) REVERT: O 222 TYR cc_start: 0.8219 (p90) cc_final: 0.7824 (p90) REVERT: O 278 LYS cc_start: 0.7850 (tptt) cc_final: 0.7119 (tptp) REVERT: O 284 PHE cc_start: 0.8205 (m-80) cc_final: 0.7822 (m-80) REVERT: P 112 HIS cc_start: 0.6781 (t-170) cc_final: 0.6481 (t70) REVERT: P 113 MET cc_start: 0.8230 (mmt) cc_final: 0.7676 (mmt) REVERT: P 142 MET cc_start: 0.7715 (tpt) cc_final: 0.6980 (tpp) REVERT: P 161 LYS cc_start: 0.8406 (mttt) cc_final: 0.7997 (mmtt) REVERT: P 162 ASP cc_start: 0.8336 (t0) cc_final: 0.7612 (m-30) REVERT: P 206 MET cc_start: 0.7400 (ppp) cc_final: 0.7196 (ppp) REVERT: P 222 TRP cc_start: 0.7936 (t-100) cc_final: 0.7637 (t-100) REVERT: P 244 GLN cc_start: 0.8033 (mt0) cc_final: 0.7766 (mt0) REVERT: P 253 ARG cc_start: 0.8423 (mmp80) cc_final: 0.7941 (mmm160) REVERT: U 239 CYS cc_start: 0.7438 (p) cc_final: 0.7061 (p) REVERT: U 319 ARG cc_start: 0.7710 (tpp80) cc_final: 0.7432 (tpp80) REVERT: U 396 THR cc_start: 0.8658 (p) cc_final: 0.8351 (t) REVERT: U 397 LEU cc_start: 0.9009 (mt) cc_final: 0.8783 (mt) REVERT: U 415 LEU cc_start: 0.4565 (mt) cc_final: 0.4356 (mt) REVERT: Q 131 MET cc_start: -0.2491 (mtm) cc_final: -0.2755 (mtt) REVERT: Q 143 MET cc_start: 0.7502 (ptm) cc_final: 0.7238 (ppp) REVERT: Q 167 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7797 (tm-30) REVERT: Q 171 LEU cc_start: 0.8255 (pt) cc_final: 0.7995 (mp) REVERT: Q 201 HIS cc_start: 0.7196 (m90) cc_final: 0.6959 (m-70) REVERT: Q 226 LYS cc_start: 0.8807 (mtmt) cc_final: 0.8461 (mttt) REVERT: T 473 MET cc_start: -0.1534 (ttt) cc_final: -0.1903 (mtp) REVERT: T 475 MET cc_start: 0.3887 (tpp) cc_final: 0.3204 (tmm) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.1615 time to fit residues: 116.4306 Evaluate side-chains 357 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 86 optimal weight: 9.9990 chunk 146 optimal weight: 0.0570 chunk 244 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 100 optimal weight: 0.2980 chunk 242 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.6704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 ASN M 115 HIS M 144 GLN ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 GLN ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 GLN O 153 HIS ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.100882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.093263 restraints weight = 136168.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.093161 restraints weight = 124937.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.093093 restraints weight = 114754.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.093081 restraints weight = 91254.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.093173 restraints weight = 84529.959| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.7142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24542 Z= 0.120 Angle : 0.622 9.917 33096 Z= 0.314 Chirality : 0.043 0.209 3766 Planarity : 0.004 0.049 4177 Dihedral : 4.589 42.911 3174 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % 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: 0.60 (0.16), residues: 2920 helix: 1.14 (0.13), residues: 1666 sheet: 0.05 (0.31), residues: 269 loop : -0.67 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 177 TYR 0.022 0.001 TYR N 141 PHE 0.033 0.001 PHE N 266 TRP 0.048 0.002 TRP K 239 HIS 0.012 0.001 HIS P 171 Details of bonding type rmsd covalent geometry : bond 0.00267 (24542) covalent geometry : angle 0.62229 (33096) hydrogen bonds : bond 0.03661 ( 1123) hydrogen bonds : angle 4.03052 ( 3360) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 MET cc_start: 0.8973 (tpp) cc_final: 0.8753 (tpp) REVERT: H 62 ASP cc_start: 0.7761 (m-30) cc_final: 0.7466 (m-30) REVERT: H 98 ILE cc_start: 0.8441 (mm) cc_final: 0.8218 (mm) REVERT: H 104 ASP cc_start: 0.8860 (t0) cc_final: 0.8570 (t0) REVERT: H 127 MET cc_start: 0.8139 (mtp) cc_final: 0.7624 (mtp) REVERT: H 130 MET cc_start: 0.8459 (mmp) cc_final: 0.7400 (ptm) REVERT: H 141 MET cc_start: 0.8272 (mpp) cc_final: 0.7971 (mpp) REVERT: I 221 LYS cc_start: 0.5724 (tttt) cc_final: 0.5375 (tmtt) REVERT: I 229 MET cc_start: 0.6677 (ppp) cc_final: 0.6328 (ppp) REVERT: I 339 PHE cc_start: 0.7116 (t80) cc_final: 0.6773 (t80) REVERT: I 355 HIS cc_start: 0.7445 (p-80) cc_final: 0.7071 (p-80) REVERT: I 369 ASN cc_start: 0.8118 (t0) cc_final: 0.7456 (t0) REVERT: I 372 LEU cc_start: 0.8936 (mt) cc_final: 0.8204 (mt) REVERT: I 399 GLU cc_start: 0.8571 (pp20) cc_final: 0.7356 (pp20) REVERT: I 414 PHE cc_start: 0.8381 (t80) cc_final: 0.7880 (t80) REVERT: I 452 ARG cc_start: 0.7905 (ttp-170) cc_final: 0.7686 (ttp80) REVERT: I 607 MET cc_start: 0.8602 (mmm) cc_final: 0.8358 (mmm) REVERT: I 613 ASN cc_start: 0.8995 (m-40) cc_final: 0.8706 (m-40) REVERT: I 714 LYS cc_start: 0.7712 (mptt) cc_final: 0.7283 (pttt) REVERT: I 721 ASP cc_start: 0.8077 (m-30) cc_final: 0.7855 (t70) REVERT: K 103 ASP cc_start: 0.8629 (m-30) cc_final: 0.8012 (t0) REVERT: K 127 ARG cc_start: 0.8303 (tmm-80) cc_final: 0.8000 (tmm-80) REVERT: K 215 MET cc_start: 0.5773 (mtt) cc_final: 0.5571 (mtt) REVERT: L 116 ASN cc_start: 0.7269 (p0) cc_final: 0.6385 (p0) REVERT: L 224 MET cc_start: 0.8449 (ttm) cc_final: 0.8193 (mmt) REVERT: L 230 MET cc_start: 0.6934 (tmm) cc_final: 0.6648 (tmm) REVERT: L 281 ASP cc_start: 0.7935 (t0) cc_final: 0.7720 (m-30) REVERT: L 300 SER cc_start: 0.8509 (p) cc_final: 0.8128 (p) REVERT: M 33 ASP cc_start: 0.8365 (m-30) cc_final: 0.7972 (m-30) REVERT: M 38 GLU cc_start: 0.7185 (pt0) cc_final: 0.6945 (pt0) REVERT: M 45 LYS cc_start: 0.6521 (tttt) cc_final: 0.5955 (tttp) REVERT: M 64 ASP cc_start: 0.7264 (m-30) cc_final: 0.6947 (m-30) REVERT: M 94 LEU cc_start: 0.8061 (mt) cc_final: 0.7570 (pp) REVERT: M 107 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8219 (mp0) REVERT: N 106 ASN cc_start: 0.8328 (p0) cc_final: 0.8074 (m-40) REVERT: N 154 TYR cc_start: 0.8728 (t80) cc_final: 0.8364 (t80) REVERT: N 211 GLN cc_start: 0.7223 (mp10) cc_final: 0.6857 (tp40) REVERT: O 174 GLN cc_start: 0.8124 (pm20) cc_final: 0.7560 (tt0) REVERT: O 175 HIS cc_start: 0.7952 (t70) cc_final: 0.7287 (t70) REVERT: O 176 PHE cc_start: 0.8660 (t80) cc_final: 0.8319 (t80) REVERT: O 178 PHE cc_start: 0.8562 (m-10) cc_final: 0.8353 (m-80) REVERT: O 180 LEU cc_start: 0.8690 (mt) cc_final: 0.8388 (mt) REVERT: O 182 GLU cc_start: 0.7666 (tp30) cc_final: 0.7354 (mm-30) REVERT: O 278 LYS cc_start: 0.7827 (tptt) cc_final: 0.7125 (tptp) REVERT: O 284 PHE cc_start: 0.8252 (m-80) cc_final: 0.7886 (m-80) REVERT: P 112 HIS cc_start: 0.6813 (t-170) cc_final: 0.6554 (t70) REVERT: P 113 MET cc_start: 0.8227 (mmt) cc_final: 0.7703 (mmt) REVERT: P 142 MET cc_start: 0.7750 (tpt) cc_final: 0.7046 (tpp) REVERT: P 153 PHE cc_start: 0.8215 (t80) cc_final: 0.7941 (t80) REVERT: P 170 LEU cc_start: 0.8417 (mt) cc_final: 0.8191 (mt) REVERT: P 222 TRP cc_start: 0.7932 (t-100) cc_final: 0.7621 (t-100) REVERT: P 244 GLN cc_start: 0.8090 (mt0) cc_final: 0.7864 (mt0) REVERT: P 253 ARG cc_start: 0.8422 (mmp80) cc_final: 0.7951 (mmm160) REVERT: U 319 ARG cc_start: 0.7668 (tpp80) cc_final: 0.7391 (tpp80) REVERT: U 335 LYS cc_start: 0.8837 (mppt) cc_final: 0.8533 (tptm) REVERT: U 396 THR cc_start: 0.8664 (p) cc_final: 0.8377 (t) REVERT: U 397 LEU cc_start: 0.9006 (mt) cc_final: 0.8770 (mt) REVERT: Q 131 MET cc_start: -0.2588 (mtm) cc_final: -0.2872 (mtt) REVERT: Q 143 MET cc_start: 0.7433 (ptm) cc_final: 0.7181 (ppp) REVERT: Q 184 GLN cc_start: 0.8068 (pp30) cc_final: 0.7868 (pp30) REVERT: Q 201 HIS cc_start: 0.7191 (m90) cc_final: 0.6963 (m-70) REVERT: Q 226 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8401 (mttt) REVERT: Q 242 LEU cc_start: 0.8668 (tp) cc_final: 0.8454 (mm) REVERT: Q 252 LYS cc_start: 0.7765 (pttm) cc_final: 0.7026 (tmtt) REVERT: R 101 MET cc_start: 0.7824 (mmm) cc_final: 0.7369 (mtt) REVERT: R 104 MET cc_start: 0.8229 (mtm) cc_final: 0.7996 (mtp) REVERT: T 473 MET cc_start: -0.1445 (ttt) cc_final: -0.1789 (mtp) REVERT: T 475 MET cc_start: 0.3952 (tpp) cc_final: 0.3274 (tmm) REVERT: W 73 GLU cc_start: 0.8488 (tp30) cc_final: 0.8254 (tp30) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.1521 time to fit residues: 110.1688 Evaluate side-chains 354 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 215 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 287 optimal weight: 0.9990 chunk 40 optimal weight: 0.0570 chunk 48 optimal weight: 7.9990 chunk 251 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 ASN M 115 HIS M 144 GLN ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 GLN O 153 HIS ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.101043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.093031 restraints weight = 139952.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.092537 restraints weight = 128596.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.092703 restraints weight = 121228.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.093327 restraints weight = 94492.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.093358 restraints weight = 78977.952| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.7239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24542 Z= 0.117 Angle : 0.618 9.865 33096 Z= 0.311 Chirality : 0.043 0.201 3766 Planarity : 0.004 0.045 4177 Dihedral : 4.511 43.500 3174 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % 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: 0.70 (0.16), residues: 2920 helix: 1.24 (0.13), residues: 1667 sheet: 0.04 (0.31), residues: 269 loop : -0.67 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 47 TYR 0.021 0.001 TYR N 141 PHE 0.026 0.001 PHE N 266 TRP 0.043 0.002 TRP K 239 HIS 0.012 0.001 HIS P 171 Details of bonding type rmsd covalent geometry : bond 0.00260 (24542) covalent geometry : angle 0.61833 (33096) hydrogen bonds : bond 0.03561 ( 1123) hydrogen bonds : angle 3.97627 ( 3360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4572.18 seconds wall clock time: 79 minutes 57.47 seconds (4797.47 seconds total)