Starting phenix.real_space_refine on Fri Jun 20 14:58:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qoo_14098/06_2025/7qoo_14098.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qoo_14098/06_2025/7qoo_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_14098/06_2025/7qoo_14098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qoo_14098/06_2025/7qoo_14098.map" model { file = "/net/cci-nas-00/data/ceres_data/7qoo_14098/06_2025/7qoo_14098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qoo_14098/06_2025/7qoo_14098.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.32, per 1000 atoms: 0.59 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: 5.75 Conformation dependent library (CDL) restraints added in 3.0 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: 2.36 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: 7.05 Time building geometry restraints manager: 6.81 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.170 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 51.600 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.950 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.032 0.002 TRP K 239 HIS 0.011 0.002 HIS O 271 PHE 0.030 0.002 PHE I 583 TYR 0.030 0.002 TYR O 183 ARG 0.009 0.001 ARG N 124 Details of bonding type rmsd hydrogen bonds : bond 0.30796 ( 1123) hydrogen bonds : angle 10.52781 ( 3360) covalent geometry : bond 0.00543 (24542) covalent geometry : angle 0.99441 (33096) *********************** 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 : 3.108 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: 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: 0.7799 (mm) REVERT: H 130 MET cc_start: 0.7999 (mmp) cc_final: 0.6993 (ptm) REVERT: H 137 ASN cc_start: 0.8161 (m-40) cc_final: 0.6436 (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: 0.6088 (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: 0.7446 (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: 0.5873 (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: 0.7041 (mp) REVERT: K 103 ASP cc_start: 0.8549 (m-30) cc_final: 0.8127 (t0) REVERT: K 106 MET cc_start: 0.7515 (mtt) cc_final: 0.6887 (mtm) REVERT: K 122 LEU cc_start: 0.8189 (tp) cc_final: 0.7929 (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: 0.4664 (mtt) REVERT: K 261 ARG cc_start: 0.9298 (mpt180) cc_final: 0.9079 (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: 0.3866 (p) REVERT: L 93 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.7692 (mmm-85) REVERT: L 116 ASN cc_start: 0.7530 (p0) cc_final: 0.6766 (p0) REVERT: L 144 LYS cc_start: 0.2420 (mttt) cc_final: 0.1959 (tttp) REVERT: L 221 MET cc_start: 0.7990 (ptm) cc_final: 0.7662 (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: 0.7236 (m-80) REVERT: M 64 ASP cc_start: 0.7056 (m-30) cc_final: 0.6230 (m-30) REVERT: M 68 PHE cc_start: 0.7765 (m-80) cc_final: 0.7524 (m-80) REVERT: M 71 ASN cc_start: 0.7456 (t0) cc_final: 0.7102 (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: 0.7706 (mm) REVERT: M 166 LEU cc_start: 0.8201 (tp) cc_final: 0.7903 (pp) REVERT: N 18 MET cc_start: 0.7296 (pmm) cc_final: 0.6032 (tpt) REVERT: N 19 ASN cc_start: 0.8560 (p0) cc_final: 0.8226 (p0) REVERT: N 106 ASN cc_start: 0.7757 (p0) cc_final: 0.6896 (m-40) REVERT: N 145 ASN cc_start: 0.5944 (t0) cc_final: 0.5433 (t0) REVERT: N 151 TYR cc_start: 0.7658 (m-80) cc_final: 0.7400 (m-80) REVERT: N 271 LEU cc_start: 0.8606 (mp) cc_final: 0.8388 (mp) REVERT: O 128 THR cc_start: 0.7752 (p) cc_final: 0.6637 (p) REVERT: O 174 GLN cc_start: 0.7907 (pt0) cc_final: 0.7469 (tt0) REVERT: O 176 PHE cc_start: 0.7750 (t80) cc_final: 0.7413 (t80) REVERT: O 198 GLN cc_start: 0.7545 (pt0) cc_final: 0.6383 (tp40) REVERT: O 222 TYR cc_start: 0.7202 (p90) cc_final: 0.6726 (p90) REVERT: O 281 HIS cc_start: 0.7033 (p-80) cc_final: 0.6508 (p-80) REVERT: P 69 PHE cc_start: 0.7076 (t80) cc_final: 0.6516 (t80) REVERT: P 136 THR cc_start: 0.6681 (p) cc_final: 0.6179 (p) REVERT: P 162 ASP cc_start: 0.7635 (t0) cc_final: 0.7194 (m-30) REVERT: P 174 VAL cc_start: 0.8700 (t) cc_final: 0.8455 (t) REVERT: U 334 LEU cc_start: 0.7242 (pp) cc_final: 0.7027 (pt) REVERT: U 396 THR cc_start: 0.8454 (p) cc_final: 0.7878 (t) REVERT: Q 165 MET cc_start: 0.7658 (mtp) cc_final: 0.7282 (mmp) REVERT: W 72 LYS cc_start: 0.7409 (mptp) cc_final: 0.6867 (pttm) outliers start: 4 outliers final: 0 residues processed: 813 average time/residue: 0.3988 time to fit residues: 481.2109 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 : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 0.9990 chunk 220 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 264 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 168 ASN M 73 HIS M 115 HIS ** M 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** O 100 ASN O 175 HIS ** O 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 403 HIS U 409 HIS Q 246 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.109856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.099373 restraints weight = 153190.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.099532 restraints weight = 136895.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.100257 restraints weight = 113259.138| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 24542 Z= 0.179 Angle : 0.678 9.839 33096 Z= 0.360 Chirality : 0.042 0.169 3766 Planarity : 0.006 0.103 4177 Dihedral : 5.016 85.235 3174 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.13), residues: 2920 helix: -2.38 (0.10), residues: 1625 sheet: -0.06 (0.31), residues: 265 loop : -1.66 (0.16), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 167 HIS 0.009 0.001 HIS N 239 PHE 0.019 0.002 PHE I 640 TYR 0.018 0.002 TYR N 141 ARG 0.009 0.001 ARG N 11 Details of bonding type rmsd hydrogen bonds : bond 0.04602 ( 1123) hydrogen bonds : angle 4.80237 ( 3360) covalent geometry : bond 0.00384 (24542) covalent geometry : angle 0.67775 (33096) *********************** 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 583 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 582 time to evaluate : 2.852 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 79 GLU cc_start: 0.8526 (mp0) cc_final: 0.8324 (mp0) REVERT: H 98 ILE cc_start: 0.8241 (mm) cc_final: 0.7994 (mm) REVERT: H 105 ARG cc_start: 0.8574 (mmt-90) cc_final: 0.8358 (tpp80) REVERT: H 130 MET cc_start: 0.8331 (mmp) cc_final: 0.7118 (ptm) REVERT: H 137 ASN cc_start: 0.8078 (m-40) cc_final: 0.7791 (m-40) REVERT: H 141 MET cc_start: 0.8563 (mpp) cc_final: 0.8223 (mpp) REVERT: H 164 LEU cc_start: 0.7832 (tt) cc_final: 0.7374 (tt) REVERT: I 334 ASN cc_start: 0.6280 (m-40) cc_final: 0.5956 (p0) REVERT: I 339 PHE cc_start: 0.7166 (t80) cc_final: 0.6892 (t80) REVERT: I 355 HIS cc_start: 0.6961 (p-80) cc_final: 0.6470 (p-80) REVERT: I 369 ASN cc_start: 0.7854 (t0) cc_final: 0.7468 (t0) REVERT: I 372 LEU cc_start: 0.8923 (mt) cc_final: 0.8283 (mt) REVERT: I 425 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8585 (mm-30) REVERT: I 456 LEU cc_start: 0.7550 (mt) cc_final: 0.7304 (mt) REVERT: I 575 TYR cc_start: 0.7748 (m-10) cc_final: 0.7442 (m-10) REVERT: I 646 SER cc_start: 0.8058 (t) cc_final: 0.7764 (p) REVERT: I 696 LEU cc_start: 0.7839 (mp) cc_final: 0.7597 (mt) REVERT: K 65 LYS cc_start: 0.8566 (mtmm) cc_final: 0.8069 (ttpt) REVERT: K 80 GLU cc_start: 0.5995 (mt-10) cc_final: 0.5278 (tp30) REVERT: K 103 ASP cc_start: 0.8633 (m-30) cc_final: 0.8237 (t0) REVERT: K 127 ARG cc_start: 0.8215 (tmm-80) cc_final: 0.7970 (tmm-80) REVERT: L 116 ASN cc_start: 0.7320 (p0) cc_final: 0.6422 (p0) REVERT: L 144 LYS cc_start: 0.2475 (mttt) cc_final: 0.1664 (tttp) REVERT: L 158 TRP cc_start: 0.7505 (t60) cc_final: 0.6819 (t60) REVERT: L 163 CYS cc_start: 0.8239 (p) cc_final: 0.7811 (t) REVERT: L 165 VAL cc_start: 0.8134 (t) cc_final: 0.7297 (m) REVERT: L 214 ASN cc_start: 0.8194 (m-40) cc_final: 0.7967 (p0) REVERT: L 238 GLU cc_start: 0.6804 (tp30) cc_final: 0.6463 (tp30) REVERT: L 253 SER cc_start: 0.8109 (m) cc_final: 0.7857 (m) REVERT: M 30 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7741 (mm-40) REVERT: M 33 ASP cc_start: 0.8145 (m-30) cc_final: 0.7757 (m-30) REVERT: M 45 LYS cc_start: 0.6303 (tttt) cc_final: 0.5901 (tttp) REVERT: M 56 SER cc_start: 0.7924 (p) cc_final: 0.7718 (m) REVERT: M 64 ASP cc_start: 0.7236 (m-30) cc_final: 0.6672 (m-30) REVERT: M 94 LEU cc_start: 0.7768 (mt) cc_final: 0.7135 (pp) REVERT: M 102 THR cc_start: 0.7674 (p) cc_final: 0.7301 (t) REVERT: N 18 MET cc_start: 0.8208 (pmm) cc_final: 0.6547 (tpt) REVERT: N 19 ASN cc_start: 0.8881 (p0) cc_final: 0.8558 (p0) REVERT: N 51 HIS cc_start: 0.6257 (m90) cc_final: 0.6013 (m90) REVERT: N 206 PHE cc_start: 0.8318 (m-10) cc_final: 0.8063 (m-10) REVERT: N 211 GLN cc_start: 0.6237 (mp10) cc_final: 0.5330 (tp-100) REVERT: N 334 PHE cc_start: 0.8271 (m-10) cc_final: 0.7986 (m-10) REVERT: O 174 GLN cc_start: 0.8089 (pt0) cc_final: 0.7719 (pm20) REVERT: O 178 PHE cc_start: 0.8587 (m-10) cc_final: 0.8056 (m-80) REVERT: O 182 GLU cc_start: 0.7337 (mm-30) cc_final: 0.5963 (mm-30) REVERT: O 185 ASN cc_start: 0.8497 (m110) cc_final: 0.8146 (m110) REVERT: O 205 LEU cc_start: 0.8052 (tt) cc_final: 0.7384 (pp) REVERT: O 211 ARG cc_start: 0.8341 (mmt-90) cc_final: 0.7564 (mmt180) REVERT: O 214 LEU cc_start: 0.7967 (tp) cc_final: 0.7628 (tt) REVERT: O 222 TYR cc_start: 0.8138 (p90) cc_final: 0.7361 (p90) REVERT: O 284 PHE cc_start: 0.8237 (m-10) cc_final: 0.7931 (m-80) REVERT: P 162 ASP cc_start: 0.8229 (t0) cc_final: 0.7624 (m-30) REVERT: P 165 MET cc_start: 0.8901 (mmp) cc_final: 0.8506 (mmp) REVERT: P 206 MET cc_start: 0.7471 (ppp) cc_final: 0.7264 (ppp) REVERT: P 244 GLN cc_start: 0.7927 (mt0) cc_final: 0.7245 (mm-40) REVERT: P 253 ARG cc_start: 0.8188 (mmp80) cc_final: 0.7862 (mmm160) REVERT: U 325 ASP cc_start: 0.8993 (t70) cc_final: 0.8541 (t0) REVERT: U 346 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8097 (tm-30) REVERT: U 383 ASP cc_start: 0.6649 (m-30) cc_final: 0.6377 (m-30) REVERT: U 396 THR cc_start: 0.8603 (p) cc_final: 0.8164 (t) REVERT: Q 165 MET cc_start: 0.8132 (mtp) cc_final: 0.7512 (mmm) REVERT: Q 180 LYS cc_start: 0.6169 (tptt) cc_final: 0.5947 (tptt) REVERT: Q 184 GLN cc_start: 0.7667 (pp30) cc_final: 0.7437 (pp30) REVERT: Q 192 GLU cc_start: 0.8590 (tp30) cc_final: 0.8119 (tp30) REVERT: Q 201 HIS cc_start: 0.6980 (m90) cc_final: 0.6284 (m90) REVERT: Q 246 HIS cc_start: 0.8058 (m-70) cc_final: 0.7185 (t70) REVERT: Q 262 TYR cc_start: 0.5970 (m-80) cc_final: 0.5758 (m-80) REVERT: R 90 LEU cc_start: 0.7814 (mt) cc_final: 0.7478 (mt) REVERT: R 122 LEU cc_start: 0.7723 (pp) cc_final: 0.7479 (pp) REVERT: W 72 LYS cc_start: 0.7675 (mptt) cc_final: 0.7237 (mptt) REVERT: W 73 GLU cc_start: 0.8748 (tp30) cc_final: 0.7803 (mp0) REVERT: W 74 HIS cc_start: 0.7073 (m90) cc_final: 0.6334 (m90) outliers start: 1 outliers final: 1 residues processed: 583 average time/residue: 0.3627 time to fit residues: 326.2706 Evaluate side-chains 405 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 404 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 198 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 225 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 157 optimal weight: 0.0070 chunk 120 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 chunk 231 optimal weight: 8.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 GLN ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 213 HIS L 201 GLN ** L 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 342 GLN M 29 GLN M 71 ASN M 115 HIS M 125 GLN M 164 ASN ** 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** O 185 ASN ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 GLN U 403 HIS Q 151 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.109265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.098887 restraints weight = 153920.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.098988 restraints weight = 135118.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.099860 restraints weight = 114439.065| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24542 Z= 0.109 Angle : 0.558 9.791 33096 Z= 0.284 Chirality : 0.041 0.164 3766 Planarity : 0.004 0.050 4177 Dihedral : 4.623 84.983 3174 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.11 % Allowed : 2.92 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.14), residues: 2920 helix: -0.64 (0.12), residues: 1608 sheet: 0.23 (0.31), residues: 263 loop : -1.31 (0.17), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 265 HIS 0.007 0.001 HIS P 171 PHE 0.017 0.001 PHE I 245 TYR 0.013 0.001 TYR I 261 ARG 0.005 0.000 ARG L 303 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 1123) hydrogen bonds : angle 4.20793 ( 3360) covalent geometry : bond 0.00228 (24542) covalent geometry : angle 0.55823 (33096) *********************** 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 542 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 539 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8529 (ttmt) cc_final: 0.8267 (ttmt) REVERT: H 105 ARG cc_start: 0.8564 (mmt-90) cc_final: 0.8282 (tpp80) REVERT: H 130 MET cc_start: 0.8239 (mmp) cc_final: 0.7102 (ptm) REVERT: H 137 ASN cc_start: 0.8291 (m-40) cc_final: 0.7280 (m-40) REVERT: H 141 MET cc_start: 0.8392 (mpp) cc_final: 0.7928 (mpp) REVERT: I 334 ASN cc_start: 0.6268 (m-40) cc_final: 0.5929 (p0) REVERT: I 339 PHE cc_start: 0.7132 (t80) cc_final: 0.6863 (t80) REVERT: I 355 HIS cc_start: 0.7047 (p-80) cc_final: 0.6581 (p-80) REVERT: I 369 ASN cc_start: 0.7987 (t0) cc_final: 0.7499 (t0) REVERT: I 372 LEU cc_start: 0.8865 (mt) cc_final: 0.8232 (mt) REVERT: I 399 GLU cc_start: 0.8316 (pp20) cc_final: 0.7126 (pp20) REVERT: I 575 TYR cc_start: 0.7729 (m-10) cc_final: 0.7219 (m-80) REVERT: I 588 PHE cc_start: 0.7884 (t80) cc_final: 0.7274 (t80) REVERT: I 607 MET cc_start: 0.8150 (mmm) cc_final: 0.7943 (mmm) REVERT: I 613 ASN cc_start: 0.9092 (m-40) cc_final: 0.8774 (m-40) REVERT: I 646 SER cc_start: 0.8075 (t) cc_final: 0.7854 (p) REVERT: K 31 MET cc_start: 0.8723 (ptp) cc_final: 0.8455 (ptp) REVERT: K 35 MET cc_start: 0.8693 (ptm) cc_final: 0.8069 (ttp) REVERT: K 62 MET cc_start: 0.7502 (ppp) cc_final: 0.7248 (tmm) REVERT: K 65 LYS cc_start: 0.8686 (mtmm) cc_final: 0.8044 (ttpt) REVERT: K 80 GLU cc_start: 0.6002 (mt-10) cc_final: 0.5193 (tp30) REVERT: K 103 ASP cc_start: 0.8567 (m-30) cc_final: 0.8092 (t0) REVERT: K 127 ARG cc_start: 0.8206 (tmm-80) cc_final: 0.7979 (tmm-80) REVERT: K 135 ILE cc_start: 0.8377 (mm) cc_final: 0.8102 (mm) REVERT: L 48 LYS cc_start: 0.7843 (mtpt) cc_final: 0.7476 (mtpp) REVERT: L 116 ASN cc_start: 0.7157 (p0) cc_final: 0.6363 (p0) REVERT: L 144 LYS cc_start: 0.2403 (mttt) cc_final: 0.1531 (tttp) REVERT: L 158 TRP cc_start: 0.7504 (t60) cc_final: 0.6806 (t60) REVERT: L 165 VAL cc_start: 0.8149 (t) cc_final: 0.7328 (m) REVERT: L 214 ASN cc_start: 0.8213 (m-40) cc_final: 0.7724 (p0) REVERT: L 221 MET cc_start: 0.8676 (ptm) cc_final: 0.8213 (ptm) REVERT: L 225 TRP cc_start: 0.7820 (m-10) cc_final: 0.7588 (m100) REVERT: L 253 SER cc_start: 0.8006 (m) cc_final: 0.7727 (m) REVERT: L 281 ASP cc_start: 0.7701 (t0) cc_final: 0.7127 (p0) REVERT: L 336 THR cc_start: 0.8383 (p) cc_final: 0.8167 (p) REVERT: L 342 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8015 (tp-100) REVERT: M 30 GLN cc_start: 0.7967 (mm-40) cc_final: 0.7697 (mm-40) REVERT: M 33 ASP cc_start: 0.8219 (m-30) cc_final: 0.7834 (m-30) REVERT: M 45 LYS cc_start: 0.6302 (tttt) cc_final: 0.5944 (tttp) REVERT: M 50 LYS cc_start: 0.7120 (mmtm) cc_final: 0.6918 (mmmm) REVERT: M 64 ASP cc_start: 0.7619 (m-30) cc_final: 0.7076 (m-30) REVERT: M 94 LEU cc_start: 0.7706 (mt) cc_final: 0.7128 (pp) REVERT: M 102 THR cc_start: 0.7776 (p) cc_final: 0.7439 (t) REVERT: M 135 VAL cc_start: 0.8800 (t) cc_final: 0.8544 (p) REVERT: N 18 MET cc_start: 0.8124 (pmm) cc_final: 0.6433 (tpp) REVERT: N 19 ASN cc_start: 0.8855 (p0) cc_final: 0.8583 (p0) REVERT: N 211 GLN cc_start: 0.6515 (mp10) cc_final: 0.5610 (tp-100) REVERT: N 334 PHE cc_start: 0.8351 (m-10) cc_final: 0.8128 (m-10) REVERT: O 130 PHE cc_start: 0.6351 (t80) cc_final: 0.5706 (t80) REVERT: O 174 GLN cc_start: 0.8003 (pt0) cc_final: 0.7627 (pm20) REVERT: O 182 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6478 (mm-30) REVERT: O 214 LEU cc_start: 0.7991 (tp) cc_final: 0.7727 (tt) REVERT: O 222 TYR cc_start: 0.7959 (p90) cc_final: 0.7467 (p90) REVERT: O 281 HIS cc_start: 0.7646 (p-80) cc_final: 0.7250 (p-80) REVERT: P 69 PHE cc_start: 0.7501 (t80) cc_final: 0.7072 (t80) REVERT: P 162 ASP cc_start: 0.8299 (t0) cc_final: 0.7555 (m-30) REVERT: P 168 ARG cc_start: 0.7472 (ptm160) cc_final: 0.7093 (ptm160) REVERT: P 253 ARG cc_start: 0.8229 (mmp80) cc_final: 0.7870 (mmm160) REVERT: U 329 ARG cc_start: 0.8616 (mmm160) cc_final: 0.8201 (tpp-160) REVERT: U 396 THR cc_start: 0.8553 (p) cc_final: 0.8159 (t) REVERT: Q 192 GLU cc_start: 0.8578 (tp30) cc_final: 0.8151 (tp30) REVERT: Q 201 HIS cc_start: 0.6937 (m90) cc_final: 0.6483 (m-70) REVERT: Q 246 HIS cc_start: 0.7604 (m-70) cc_final: 0.7218 (t70) REVERT: W 72 LYS cc_start: 0.7820 (mptt) cc_final: 0.7473 (mmtm) REVERT: W 73 GLU cc_start: 0.8773 (tp30) cc_final: 0.7904 (mp0) REVERT: W 74 HIS cc_start: 0.6931 (m90) cc_final: 0.6616 (m90) outliers start: 3 outliers final: 0 residues processed: 541 average time/residue: 0.3456 time to fit residues: 292.6789 Evaluate side-chains 402 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 401 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 204 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 271 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 195 optimal weight: 0.7980 chunk 268 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 503 ASN K 63 GLN K 160 ASN K 213 HIS ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 217 ASN L 257 HIS L 325 HIS M 71 ASN M 115 HIS M 164 ASN ** 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 268 GLN N 280 ASN O 175 HIS ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 287 ASN Q 151 ASN Q 246 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.104935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.095009 restraints weight = 152035.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.094748 restraints weight = 134592.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.095288 restraints weight = 118608.876| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 24542 Z= 0.176 Angle : 0.639 10.351 33096 Z= 0.328 Chirality : 0.043 0.177 3766 Planarity : 0.004 0.048 4177 Dihedral : 4.653 75.699 3174 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.15 % Allowed : 2.55 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 2920 helix: 0.34 (0.13), residues: 1606 sheet: 0.27 (0.31), residues: 263 loop : -0.99 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP U 238 HIS 0.013 0.001 HIS P 171 PHE 0.027 0.002 PHE O 284 TYR 0.020 0.002 TYR Q 262 ARG 0.016 0.001 ARG M 145 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 1123) hydrogen bonds : angle 4.15363 ( 3360) covalent geometry : bond 0.00388 (24542) covalent geometry : angle 0.63902 (33096) *********************** 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 510 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 506 time to evaluate : 2.788 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: H 65 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7382 (mt-10) REVERT: H 98 ILE cc_start: 0.8412 (mm) cc_final: 0.8192 (mm) REVERT: H 130 MET cc_start: 0.8427 (mmp) cc_final: 0.7177 (ptm) REVERT: H 141 MET cc_start: 0.8393 (mpp) cc_final: 0.8063 (mpp) REVERT: I 171 MET cc_start: 0.6556 (tpp) cc_final: 0.6313 (tpp) REVERT: I 334 ASN cc_start: 0.6417 (m-40) cc_final: 0.6010 (p0) REVERT: I 339 PHE cc_start: 0.7135 (t80) cc_final: 0.6808 (t80) REVERT: I 355 HIS cc_start: 0.7264 (p-80) cc_final: 0.6821 (p-80) REVERT: I 369 ASN cc_start: 0.8083 (t0) cc_final: 0.7455 (t0) REVERT: I 372 LEU cc_start: 0.9108 (mt) cc_final: 0.8391 (mt) REVERT: I 399 GLU cc_start: 0.8366 (pp20) cc_final: 0.7401 (pp20) REVERT: I 575 TYR cc_start: 0.8090 (m-10) cc_final: 0.7688 (m-10) REVERT: I 613 ASN cc_start: 0.9116 (m-40) cc_final: 0.8835 (m-40) REVERT: I 643 TYR cc_start: 0.7627 (m-80) cc_final: 0.6649 (m-80) REVERT: I 646 SER cc_start: 0.8258 (t) cc_final: 0.7998 (p) REVERT: K 62 MET cc_start: 0.7244 (ppp) cc_final: 0.6762 (tmm) REVERT: K 65 LYS cc_start: 0.8848 (mtmm) cc_final: 0.8554 (mttm) REVERT: K 103 ASP cc_start: 0.8644 (m-30) cc_final: 0.8100 (t0) REVERT: K 145 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6335 (mp0) REVERT: K 215 MET cc_start: 0.5548 (mtt) cc_final: 0.5338 (mtt) REVERT: L 48 LYS cc_start: 0.7982 (mtpt) cc_final: 0.7579 (mtpp) REVERT: L 116 ASN cc_start: 0.7242 (p0) cc_final: 0.6287 (p0) REVERT: L 144 LYS cc_start: 0.2477 (mttt) cc_final: 0.1550 (tttm) REVERT: L 199 TRP cc_start: 0.7489 (t60) cc_final: 0.7260 (t60) REVERT: L 225 TRP cc_start: 0.8400 (m-10) cc_final: 0.7960 (m-10) REVERT: L 253 SER cc_start: 0.8411 (m) cc_final: 0.7893 (p) REVERT: L 281 ASP cc_start: 0.7966 (t0) cc_final: 0.7336 (p0) REVERT: L 288 TYR cc_start: 0.7913 (m-10) cc_final: 0.7313 (m-80) REVERT: L 299 LEU cc_start: 0.8505 (mt) cc_final: 0.8007 (mt) REVERT: L 300 SER cc_start: 0.8287 (p) cc_final: 0.7857 (p) REVERT: L 334 TYR cc_start: 0.7795 (t80) cc_final: 0.7510 (t80) REVERT: M 1 MET cc_start: 0.5596 (ttt) cc_final: 0.5344 (ttt) REVERT: M 30 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7971 (mm-40) REVERT: M 33 ASP cc_start: 0.8378 (m-30) cc_final: 0.7936 (m-30) REVERT: M 35 MET cc_start: 0.7968 (mmm) cc_final: 0.7719 (mtt) REVERT: M 45 LYS cc_start: 0.6532 (tttt) cc_final: 0.6209 (tttp) REVERT: M 64 ASP cc_start: 0.7535 (m-30) cc_final: 0.7011 (m-30) REVERT: M 94 LEU cc_start: 0.7910 (mt) cc_final: 0.7195 (pp) REVERT: M 164 ASN cc_start: 0.6797 (OUTLIER) cc_final: 0.6517 (m-40) REVERT: N 211 GLN cc_start: 0.6798 (mp10) cc_final: 0.5861 (tp-100) REVERT: O 174 GLN cc_start: 0.8074 (pt0) cc_final: 0.7427 (tt0) REVERT: O 182 GLU cc_start: 0.7505 (tp30) cc_final: 0.7068 (mm-30) REVERT: O 198 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8394 (pt0) REVERT: O 205 LEU cc_start: 0.8236 (tt) cc_final: 0.7487 (pp) REVERT: O 214 LEU cc_start: 0.8485 (tp) cc_final: 0.8223 (tt) REVERT: O 222 TYR cc_start: 0.8076 (p90) cc_final: 0.7496 (p90) REVERT: O 284 PHE cc_start: 0.8070 (m-80) cc_final: 0.7587 (m-80) REVERT: P 161 LYS cc_start: 0.8486 (mttt) cc_final: 0.8111 (mmtt) REVERT: P 162 ASP cc_start: 0.8433 (t0) cc_final: 0.7617 (m-30) REVERT: P 168 ARG cc_start: 0.7774 (ptm160) cc_final: 0.7446 (ptm160) REVERT: P 206 MET cc_start: 0.7408 (ppp) cc_final: 0.7196 (ppp) REVERT: P 253 ARG cc_start: 0.8334 (mmp80) cc_final: 0.7696 (mmp80) REVERT: P 275 LEU cc_start: 0.8704 (mt) cc_final: 0.8437 (mp) REVERT: U 329 ARG cc_start: 0.8753 (mmm160) cc_final: 0.8518 (tpp-160) REVERT: U 342 ASP cc_start: 0.8568 (t0) cc_final: 0.7837 (m-30) REVERT: U 396 THR cc_start: 0.8676 (p) cc_final: 0.8299 (t) REVERT: Q 192 GLU cc_start: 0.8668 (tp30) cc_final: 0.8272 (tp30) REVERT: Q 201 HIS cc_start: 0.7129 (m90) cc_final: 0.6594 (m-70) REVERT: R 126 SER cc_start: 0.6564 (m) cc_final: 0.6361 (t) REVERT: T 473 MET cc_start: -0.1731 (mtp) cc_final: -0.1981 (mtp) REVERT: W 72 LYS cc_start: 0.7825 (mptt) cc_final: 0.7108 (mmtt) REVERT: W 73 GLU cc_start: 0.8723 (tp30) cc_final: 0.7805 (mp0) REVERT: W 74 HIS cc_start: 0.6855 (m90) cc_final: 0.6459 (m90) outliers start: 4 outliers final: 0 residues processed: 509 average time/residue: 0.3683 time to fit residues: 288.8558 Evaluate side-chains 377 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 375 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 24 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 192 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 264 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 232 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 234 HIS ** I 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 503 ASN K 63 GLN ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 217 ASN M 71 ASN M 115 HIS ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 152 HIS ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 GLN P 186 HIS U 284 ASN U 417 GLN Q 151 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.100855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.092373 restraints weight = 134554.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.091897 restraints weight = 123101.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.092260 restraints weight = 113422.961| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 24542 Z= 0.231 Angle : 0.749 12.725 33096 Z= 0.390 Chirality : 0.046 0.195 3766 Planarity : 0.005 0.060 4177 Dihedral : 5.052 40.513 3174 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.04 % Allowed : 2.99 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 2920 helix: 0.30 (0.12), residues: 1649 sheet: 0.07 (0.30), residues: 269 loop : -1.06 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP P 222 HIS 0.020 0.002 HIS P 171 PHE 0.020 0.002 PHE L 162 TYR 0.022 0.002 TYR N 269 ARG 0.012 0.001 ARG M 106 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 1123) hydrogen bonds : angle 4.46392 ( 3360) covalent geometry : bond 0.00486 (24542) covalent geometry : angle 0.74936 (33096) *********************** 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 456 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 455 time to evaluate : 2.899 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: H 65 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7878 (mt-10) REVERT: H 130 MET cc_start: 0.8582 (mmp) cc_final: 0.7360 (ptm) REVERT: H 141 MET cc_start: 0.8394 (mpp) cc_final: 0.8082 (mpp) REVERT: I 229 MET cc_start: 0.6681 (ppp) cc_final: 0.6370 (ppp) REVERT: I 334 ASN cc_start: 0.6594 (m-40) cc_final: 0.5795 (p0) REVERT: I 339 PHE cc_start: 0.6982 (t80) cc_final: 0.6702 (t80) REVERT: I 355 HIS cc_start: 0.7325 (p-80) cc_final: 0.6889 (p-80) REVERT: I 369 ASN cc_start: 0.8181 (t0) cc_final: 0.7648 (t0) REVERT: I 382 GLU cc_start: 0.7737 (pm20) cc_final: 0.7449 (tp30) REVERT: I 399 GLU cc_start: 0.8490 (pp20) cc_final: 0.7729 (pp20) REVERT: I 452 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7742 (ttp80) REVERT: I 454 GLN cc_start: 0.7315 (mp10) cc_final: 0.7093 (mp10) REVERT: I 499 GLU cc_start: 0.7555 (mp0) cc_final: 0.7061 (mp0) REVERT: I 575 TYR cc_start: 0.8295 (m-10) cc_final: 0.7922 (m-80) REVERT: I 588 PHE cc_start: 0.8364 (t80) cc_final: 0.7792 (t80) REVERT: I 607 MET cc_start: 0.8332 (mmm) cc_final: 0.8107 (mmm) REVERT: I 613 ASN cc_start: 0.9128 (m-40) cc_final: 0.8843 (m-40) REVERT: K 36 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8242 (mt-10) REVERT: K 62 MET cc_start: 0.7398 (ppp) cc_final: 0.7094 (tmm) REVERT: K 65 LYS cc_start: 0.8911 (mtmm) cc_final: 0.8622 (mttm) REVERT: K 103 ASP cc_start: 0.8640 (m-30) cc_final: 0.8041 (t0) REVERT: K 127 ARG cc_start: 0.8384 (tmm-80) cc_final: 0.8055 (tmm-80) REVERT: L 48 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7862 (mtpp) REVERT: L 116 ASN cc_start: 0.6996 (p0) cc_final: 0.6098 (p0) REVERT: L 144 LYS cc_start: 0.2530 (mttt) cc_final: 0.1476 (tttp) REVERT: L 253 SER cc_start: 0.8501 (m) cc_final: 0.8188 (p) REVERT: L 281 ASP cc_start: 0.8195 (t0) cc_final: 0.7472 (p0) REVERT: L 288 TYR cc_start: 0.8103 (m-10) cc_final: 0.7354 (m-80) REVERT: L 299 LEU cc_start: 0.8450 (mt) cc_final: 0.7956 (mt) REVERT: L 300 SER cc_start: 0.8406 (p) cc_final: 0.7897 (p) REVERT: L 334 TYR cc_start: 0.7968 (t80) cc_final: 0.7525 (t80) REVERT: M 30 GLN cc_start: 0.8338 (mm-40) cc_final: 0.8130 (mm-40) REVERT: M 33 ASP cc_start: 0.8497 (m-30) cc_final: 0.8028 (m-30) REVERT: M 45 LYS cc_start: 0.6622 (tttt) cc_final: 0.6217 (tttp) REVERT: M 64 ASP cc_start: 0.7652 (m-30) cc_final: 0.7153 (m-30) REVERT: M 94 LEU cc_start: 0.7943 (mt) cc_final: 0.7373 (pp) REVERT: N 154 TYR cc_start: 0.8809 (t80) cc_final: 0.8440 (t80) REVERT: O 174 GLN cc_start: 0.8115 (pt0) cc_final: 0.7555 (tt0) REVERT: O 175 HIS cc_start: 0.7761 (t70) cc_final: 0.7531 (t70) REVERT: O 182 GLU cc_start: 0.7628 (tp30) cc_final: 0.7277 (mm-30) REVERT: O 222 TYR cc_start: 0.8141 (p90) cc_final: 0.7837 (p90) REVERT: O 284 PHE cc_start: 0.8275 (m-80) cc_final: 0.7969 (m-80) REVERT: P 161 LYS cc_start: 0.8635 (mttt) cc_final: 0.8196 (mmtt) REVERT: P 162 ASP cc_start: 0.8536 (t0) cc_final: 0.7736 (m-30) REVERT: P 206 MET cc_start: 0.7469 (ppp) cc_final: 0.7221 (ppp) REVERT: P 253 ARG cc_start: 0.8322 (mmp80) cc_final: 0.7833 (mmm160) REVERT: U 329 ARG cc_start: 0.8920 (mmm160) cc_final: 0.8650 (tpp-160) REVERT: U 396 THR cc_start: 0.8620 (p) cc_final: 0.8296 (t) REVERT: Q 201 HIS cc_start: 0.7084 (m90) cc_final: 0.6537 (m-70) REVERT: Q 252 LYS cc_start: 0.8110 (pttt) cc_final: 0.7518 (tptm) REVERT: T 473 MET cc_start: -0.1612 (mtp) cc_final: -0.1844 (mtp) REVERT: T 475 MET cc_start: 0.3737 (tpp) cc_final: 0.3171 (tmm) outliers start: 1 outliers final: 0 residues processed: 456 average time/residue: 0.3445 time to fit residues: 245.8970 Evaluate side-chains 352 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 209 optimal weight: 20.0000 chunk 260 optimal weight: 8.9990 chunk 221 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 406 ASN I 503 ASN K 63 GLN ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 ASN M 115 HIS ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 GLN ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN T 545 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.102773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.093812 restraints weight = 141822.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.093478 restraints weight = 125949.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.093809 restraints weight = 112191.798| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.6343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24542 Z= 0.119 Angle : 0.590 9.527 33096 Z= 0.299 Chirality : 0.043 0.188 3766 Planarity : 0.004 0.041 4177 Dihedral : 4.649 37.856 3174 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.07 % Allowed : 1.55 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 2920 helix: 0.86 (0.13), residues: 1658 sheet: 0.18 (0.30), residues: 269 loop : -0.80 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 461 HIS 0.012 0.001 HIS P 171 PHE 0.022 0.001 PHE L 98 TYR 0.019 0.001 TYR K 172 ARG 0.007 0.000 ARG N 134 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 1123) hydrogen bonds : angle 4.03821 ( 3360) covalent geometry : bond 0.00263 (24542) covalent geometry : angle 0.59048 (33096) *********************** 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 464 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 462 time to evaluate : 3.068 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 65 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7916 (mt-10) REVERT: H 105 ARG cc_start: 0.8642 (tpp-160) cc_final: 0.8141 (tpp80) REVERT: H 130 MET cc_start: 0.8554 (mmp) cc_final: 0.7329 (ptm) REVERT: H 141 MET cc_start: 0.8417 (mpp) cc_final: 0.8072 (mpp) REVERT: I 229 MET cc_start: 0.6786 (ppp) cc_final: 0.6330 (ppp) REVERT: I 334 ASN cc_start: 0.6710 (m-40) cc_final: 0.5793 (p0) REVERT: I 339 PHE cc_start: 0.7062 (t80) cc_final: 0.6720 (t80) REVERT: I 355 HIS cc_start: 0.7354 (p-80) cc_final: 0.6968 (p-80) REVERT: I 369 ASN cc_start: 0.8213 (t0) cc_final: 0.7590 (t0) REVERT: I 372 LEU cc_start: 0.9097 (mt) cc_final: 0.8371 (mt) REVERT: I 382 GLU cc_start: 0.7592 (pm20) cc_final: 0.7303 (tp30) REVERT: I 399 GLU cc_start: 0.8529 (pp20) cc_final: 0.7790 (pp20) REVERT: I 454 GLN cc_start: 0.7182 (mp10) cc_final: 0.6968 (mp10) REVERT: I 503 ASN cc_start: 0.8279 (m-40) cc_final: 0.7948 (m110) REVERT: I 530 MET cc_start: 0.7612 (ptt) cc_final: 0.7411 (ptt) REVERT: I 607 MET cc_start: 0.8408 (mmm) cc_final: 0.8200 (mmm) REVERT: I 613 ASN cc_start: 0.9074 (m-40) cc_final: 0.8800 (m-40) REVERT: K 103 ASP cc_start: 0.8676 (m-30) cc_final: 0.8032 (t0) REVERT: K 127 ARG cc_start: 0.8354 (tmm-80) cc_final: 0.8006 (tmm-80) REVERT: L 48 LYS cc_start: 0.8079 (mtpt) cc_final: 0.7777 (mtpp) REVERT: L 116 ASN cc_start: 0.7062 (p0) cc_final: 0.6217 (p0) REVERT: L 144 LYS cc_start: 0.2512 (mttt) cc_final: 0.1390 (tttp) REVERT: L 288 TYR cc_start: 0.8029 (m-10) cc_final: 0.7296 (m-80) REVERT: L 299 LEU cc_start: 0.8421 (mt) cc_final: 0.7836 (mt) REVERT: L 300 SER cc_start: 0.8479 (p) cc_final: 0.7890 (m) REVERT: L 334 TYR cc_start: 0.7951 (t80) cc_final: 0.7529 (t80) REVERT: M 30 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8089 (mm-40) REVERT: M 33 ASP cc_start: 0.8410 (m-30) cc_final: 0.7995 (m-30) REVERT: M 45 LYS cc_start: 0.6588 (tttt) cc_final: 0.6150 (tttp) REVERT: M 64 ASP cc_start: 0.7542 (m-30) cc_final: 0.7104 (m-30) REVERT: M 94 LEU cc_start: 0.7838 (mt) cc_final: 0.6967 (pp) REVERT: M 107 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7827 (mp0) REVERT: N 154 TYR cc_start: 0.8736 (t80) cc_final: 0.8439 (t80) REVERT: N 211 GLN cc_start: 0.7209 (mp10) cc_final: 0.6686 (tp-100) REVERT: O 174 GLN cc_start: 0.8059 (pt0) cc_final: 0.7532 (tt0) REVERT: O 175 HIS cc_start: 0.7750 (t70) cc_final: 0.7380 (t70) REVERT: O 176 PHE cc_start: 0.8668 (t80) cc_final: 0.8376 (t80) REVERT: O 180 LEU cc_start: 0.8775 (mt) cc_final: 0.8360 (mt) REVERT: O 182 GLU cc_start: 0.7551 (tp30) cc_final: 0.6806 (tp30) REVERT: O 222 TYR cc_start: 0.7892 (p90) cc_final: 0.7521 (p90) REVERT: O 277 THR cc_start: 0.9086 (t) cc_final: 0.8828 (p) REVERT: O 281 HIS cc_start: 0.7632 (p-80) cc_final: 0.7353 (p90) REVERT: O 284 PHE cc_start: 0.8182 (m-80) cc_final: 0.7899 (m-80) REVERT: P 112 HIS cc_start: 0.6051 (t-90) cc_final: 0.5522 (t-90) REVERT: P 113 MET cc_start: 0.7755 (mmt) cc_final: 0.7255 (mmt) REVERT: P 142 MET cc_start: 0.7900 (tpt) cc_final: 0.7255 (tpp) REVERT: P 161 LYS cc_start: 0.8535 (mttt) cc_final: 0.8089 (mmtt) REVERT: P 162 ASP cc_start: 0.8455 (t0) cc_final: 0.7625 (m-30) REVERT: P 206 MET cc_start: 0.7451 (ppp) cc_final: 0.7238 (ppp) REVERT: P 253 ARG cc_start: 0.8341 (mmp80) cc_final: 0.7870 (mmm160) REVERT: U 329 ARG cc_start: 0.8902 (mmm160) cc_final: 0.8591 (tpp-160) REVERT: U 396 THR cc_start: 0.8641 (p) cc_final: 0.8306 (t) REVERT: Q 180 LYS cc_start: 0.6637 (tptt) cc_final: 0.6275 (tptt) REVERT: Q 184 GLN cc_start: 0.8042 (pp30) cc_final: 0.7834 (pp30) REVERT: Q 192 GLU cc_start: 0.8831 (tp30) cc_final: 0.8402 (tp30) REVERT: Q 201 HIS cc_start: 0.7078 (m90) cc_final: 0.6477 (m-70) REVERT: Q 252 LYS cc_start: 0.8049 (pttt) cc_final: 0.7787 (pttm) REVERT: T 475 MET cc_start: 0.3853 (tpp) cc_final: 0.3204 (ttp) outliers start: 2 outliers final: 0 residues processed: 464 average time/residue: 0.3688 time to fit residues: 268.8575 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 : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 53 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 261 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 106 optimal weight: 40.0000 chunk 215 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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** ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 GLN ** I 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 GLN ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 232 HIS M 71 ASN M 115 HIS M 156 HIS N 35 GLN ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 133 ASN ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.099278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.090795 restraints weight = 140152.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.090821 restraints weight = 127316.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.090738 restraints weight = 114407.593| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.6985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 24542 Z= 0.210 Angle : 0.704 11.155 33096 Z= 0.363 Chirality : 0.045 0.201 3766 Planarity : 0.005 0.049 4177 Dihedral : 4.940 39.850 3174 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.04 % Allowed : 1.48 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 2920 helix: 0.65 (0.12), residues: 1677 sheet: -0.06 (0.31), residues: 267 loop : -0.93 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L 72 HIS 0.016 0.001 HIS P 171 PHE 0.019 0.002 PHE N 123 TYR 0.017 0.002 TYR N 197 ARG 0.010 0.001 ARG O 196 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 1123) hydrogen bonds : angle 4.34502 ( 3360) covalent geometry : bond 0.00460 (24542) covalent geometry : angle 0.70437 (33096) *********************** 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 426 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 425 time to evaluate : 2.978 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 65 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7811 (mm-30) REVERT: H 93 LYS cc_start: 0.8654 (ttmt) cc_final: 0.8391 (ttpt) REVERT: H 130 MET cc_start: 0.8632 (mmp) cc_final: 0.7450 (ptm) REVERT: I 229 MET cc_start: 0.6793 (ppp) cc_final: 0.6382 (ppp) REVERT: I 334 ASN cc_start: 0.6943 (m-40) cc_final: 0.5788 (p0) REVERT: I 339 PHE cc_start: 0.7030 (t80) cc_final: 0.6704 (t80) REVERT: I 355 HIS cc_start: 0.7588 (p-80) cc_final: 0.7130 (p-80) REVERT: I 369 ASN cc_start: 0.8166 (t0) cc_final: 0.7612 (t0) REVERT: I 399 GLU cc_start: 0.8461 (pp20) cc_final: 0.7681 (pp20) REVERT: I 416 ASN cc_start: 0.7479 (t0) cc_final: 0.7227 (p0) REVERT: I 454 GLN cc_start: 0.7312 (mp10) cc_final: 0.7047 (mp10) REVERT: I 499 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7742 (mt-10) REVERT: I 500 LEU cc_start: 0.8865 (tp) cc_final: 0.8597 (tp) REVERT: I 503 ASN cc_start: 0.8198 (m-40) cc_final: 0.7911 (m110) REVERT: I 607 MET cc_start: 0.8319 (mmm) cc_final: 0.8081 (mmm) REVERT: I 613 ASN cc_start: 0.9076 (m-40) cc_final: 0.8786 (m-40) REVERT: K 36 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8168 (mt-10) REVERT: K 38 CYS cc_start: 0.8592 (m) cc_final: 0.8001 (t) REVERT: K 62 MET cc_start: 0.7757 (ttp) cc_final: 0.7361 (tmm) REVERT: K 63 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8002 (mm-40) REVERT: K 103 ASP cc_start: 0.8696 (m-30) cc_final: 0.8044 (t0) REVERT: K 215 MET cc_start: 0.5787 (mtt) cc_final: 0.5525 (mtt) REVERT: L 48 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7737 (mtpp) REVERT: L 99 ILE cc_start: 0.9218 (pt) cc_final: 0.8890 (pt) REVERT: L 116 ASN cc_start: 0.7051 (p0) cc_final: 0.6103 (p0) REVERT: L 144 LYS cc_start: 0.2533 (mttt) cc_final: 0.2267 (mttm) REVERT: L 230 MET cc_start: 0.7406 (tmm) cc_final: 0.7108 (tmm) REVERT: L 288 TYR cc_start: 0.8067 (m-10) cc_final: 0.7323 (m-80) REVERT: L 299 LEU cc_start: 0.8447 (mt) cc_final: 0.7850 (mt) REVERT: L 300 SER cc_start: 0.8522 (p) cc_final: 0.7893 (t) REVERT: L 334 TYR cc_start: 0.7957 (t80) cc_final: 0.7338 (t80) REVERT: M 33 ASP cc_start: 0.8475 (m-30) cc_final: 0.7991 (m-30) REVERT: M 45 LYS cc_start: 0.6632 (tttt) cc_final: 0.6252 (tttp) REVERT: M 64 ASP cc_start: 0.7592 (m-30) cc_final: 0.7114 (m-30) REVERT: M 94 LEU cc_start: 0.7762 (mt) cc_final: 0.7201 (pp) REVERT: M 107 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8197 (mp0) REVERT: N 154 TYR cc_start: 0.8773 (t80) cc_final: 0.8362 (t80) REVERT: N 211 GLN cc_start: 0.7254 (mp10) cc_final: 0.6882 (tp40) REVERT: N 314 ILE cc_start: 0.6651 (tt) cc_final: 0.6439 (mt) REVERT: N 331 MET cc_start: 0.8714 (pmm) cc_final: 0.8214 (pmm) REVERT: N 334 PHE cc_start: 0.8690 (m-10) cc_final: 0.8458 (m-10) REVERT: O 174 GLN cc_start: 0.8069 (pt0) cc_final: 0.7509 (tt0) REVERT: O 175 HIS cc_start: 0.7747 (t70) cc_final: 0.7367 (t-170) REVERT: O 180 LEU cc_start: 0.8809 (mt) cc_final: 0.8546 (mm) REVERT: O 182 GLU cc_start: 0.7581 (tp30) cc_final: 0.6778 (tp30) REVERT: O 222 TYR cc_start: 0.8158 (p90) cc_final: 0.7724 (p90) REVERT: O 284 PHE cc_start: 0.8248 (m-80) cc_final: 0.7991 (m-80) REVERT: P 142 MET cc_start: 0.7796 (tpt) cc_final: 0.7149 (tpp) REVERT: P 161 LYS cc_start: 0.8657 (mttt) cc_final: 0.8181 (mmtt) REVERT: P 162 ASP cc_start: 0.8591 (t0) cc_final: 0.7761 (m-30) REVERT: P 206 MET cc_start: 0.7555 (ppp) cc_final: 0.7322 (ppp) REVERT: P 253 ARG cc_start: 0.8398 (mmp80) cc_final: 0.8073 (mmm160) REVERT: U 243 MET cc_start: 0.7757 (mpp) cc_final: 0.7262 (mpp) REVERT: U 329 ARG cc_start: 0.8957 (mmm160) cc_final: 0.8683 (tpp-160) REVERT: U 396 THR cc_start: 0.8675 (p) cc_final: 0.8384 (t) REVERT: Q 180 LYS cc_start: 0.6724 (tptt) cc_final: 0.6524 (tptt) REVERT: Q 201 HIS cc_start: 0.7053 (m90) cc_final: 0.6828 (m-70) outliers start: 1 outliers final: 0 residues processed: 426 average time/residue: 0.3541 time to fit residues: 239.2748 Evaluate side-chains 335 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 334 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 170 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 275 optimal weight: 20.0000 chunk 221 optimal weight: 6.9990 chunk 167 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 30.0000 chunk 88 optimal weight: 0.6980 chunk 220 optimal weight: 6.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 ASN M 115 HIS ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.099111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.091062 restraints weight = 135896.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.090473 restraints weight = 117506.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.090577 restraints weight = 110622.586| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.7233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24542 Z= 0.171 Angle : 0.658 10.306 33096 Z= 0.336 Chirality : 0.044 0.215 3766 Planarity : 0.004 0.044 4177 Dihedral : 4.903 44.479 3174 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 2920 helix: 0.76 (0.12), residues: 1683 sheet: -0.15 (0.31), residues: 266 loop : -1.00 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 504 HIS 0.007 0.001 HIS O 281 PHE 0.016 0.002 PHE I 245 TYR 0.018 0.002 TYR N 269 ARG 0.007 0.001 ARG I 177 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 1123) hydrogen bonds : angle 4.26139 ( 3360) covalent geometry : bond 0.00375 (24542) covalent geometry : angle 0.65805 (33096) *********************** 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 431 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 2.800 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 65 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8009 (mt-10) REVERT: H 130 MET cc_start: 0.8598 (mmp) cc_final: 0.7472 (ptm) REVERT: H 141 MET cc_start: 0.8439 (mpp) cc_final: 0.7888 (mpp) REVERT: I 221 LYS cc_start: 0.5817 (tttt) cc_final: 0.5391 (tmtt) REVERT: I 229 MET cc_start: 0.6775 (ppp) cc_final: 0.6442 (ppp) REVERT: I 339 PHE cc_start: 0.6987 (t80) cc_final: 0.6699 (t80) REVERT: I 355 HIS cc_start: 0.7617 (p-80) cc_final: 0.7160 (p-80) REVERT: I 369 ASN cc_start: 0.8096 (t0) cc_final: 0.7545 (t0) REVERT: I 399 GLU cc_start: 0.8467 (pp20) cc_final: 0.7919 (pp20) REVERT: I 416 ASN cc_start: 0.7454 (t0) cc_final: 0.7201 (p0) REVERT: I 499 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7769 (mt-10) REVERT: I 500 LEU cc_start: 0.8814 (tp) cc_final: 0.8572 (tp) REVERT: I 503 ASN cc_start: 0.8119 (m-40) cc_final: 0.7823 (m110) REVERT: I 575 TYR cc_start: 0.8326 (m-10) cc_final: 0.7984 (m-10) REVERT: I 607 MET cc_start: 0.8364 (mmm) cc_final: 0.8161 (mmm) REVERT: I 613 ASN cc_start: 0.9022 (m-40) cc_final: 0.8758 (m-40) REVERT: K 62 MET cc_start: 0.7699 (ttp) cc_final: 0.7354 (tmm) REVERT: K 103 ASP cc_start: 0.8636 (m-30) cc_final: 0.7961 (t0) REVERT: K 124 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7804 (mtt90) REVERT: K 127 ARG cc_start: 0.8371 (tmm-80) cc_final: 0.8089 (tmm-80) REVERT: K 215 MET cc_start: 0.5877 (mtt) cc_final: 0.5637 (mtt) REVERT: L 116 ASN cc_start: 0.7089 (p0) cc_final: 0.6171 (p0) REVERT: L 230 MET cc_start: 0.7415 (tmm) cc_final: 0.7118 (tmm) REVERT: L 288 TYR cc_start: 0.8131 (m-10) cc_final: 0.7363 (m-80) REVERT: L 299 LEU cc_start: 0.8427 (mt) cc_final: 0.7858 (mt) REVERT: L 300 SER cc_start: 0.8514 (p) cc_final: 0.7879 (t) REVERT: L 334 TYR cc_start: 0.7950 (t80) cc_final: 0.7332 (t80) REVERT: M 33 ASP cc_start: 0.8411 (m-30) cc_final: 0.7993 (m-30) REVERT: M 45 LYS cc_start: 0.6503 (tttt) cc_final: 0.6075 (tttp) REVERT: M 64 ASP cc_start: 0.7532 (m-30) cc_final: 0.7052 (m-30) REVERT: N 154 TYR cc_start: 0.8728 (t80) cc_final: 0.8351 (t80) REVERT: N 211 GLN cc_start: 0.7271 (mp10) cc_final: 0.6927 (tp40) REVERT: O 178 PHE cc_start: 0.8526 (m-10) cc_final: 0.8190 (m-80) REVERT: O 182 GLU cc_start: 0.7719 (tp30) cc_final: 0.6987 (tp30) REVERT: O 222 TYR cc_start: 0.8110 (p90) cc_final: 0.7853 (p90) REVERT: P 142 MET cc_start: 0.7772 (tpt) cc_final: 0.7201 (tpp) REVERT: P 161 LYS cc_start: 0.8621 (mttt) cc_final: 0.8133 (mmtt) REVERT: P 162 ASP cc_start: 0.8538 (t0) cc_final: 0.7780 (m-30) REVERT: P 206 MET cc_start: 0.7593 (ppp) cc_final: 0.7382 (ppp) REVERT: P 222 TRP cc_start: 0.8014 (t-100) cc_final: 0.7780 (t-100) REVERT: P 253 ARG cc_start: 0.8432 (mmp80) cc_final: 0.8093 (mmm160) REVERT: U 243 MET cc_start: 0.7582 (mpp) cc_final: 0.6968 (mpp) REVERT: U 329 ARG cc_start: 0.8953 (mmm160) cc_final: 0.8729 (tpp-160) REVERT: U 396 THR cc_start: 0.8646 (p) cc_final: 0.8410 (t) REVERT: Q 131 MET cc_start: -0.3354 (mtt) cc_final: -0.3582 (mtt) REVERT: Q 143 MET cc_start: 0.7575 (ptm) cc_final: 0.7306 (ppp) REVERT: Q 165 MET cc_start: 0.7969 (mtp) cc_final: 0.7636 (mmm) REVERT: Q 180 LYS cc_start: 0.6813 (tptt) cc_final: 0.6540 (tptt) REVERT: Q 184 GLN cc_start: 0.8085 (pp30) cc_final: 0.7830 (pp30) REVERT: Q 201 HIS cc_start: 0.7158 (m90) cc_final: 0.6486 (m-70) REVERT: T 473 MET cc_start: -0.1771 (mtp) cc_final: -0.1987 (mtm) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.3391 time to fit residues: 233.0075 Evaluate side-chains 339 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 250 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 chunk 253 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 227 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** I 102 ASN ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 ASN M 115 HIS ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 GLN ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 175 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.100001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.091719 restraints weight = 134307.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.091693 restraints weight = 115353.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.091600 restraints weight = 107672.176| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.7296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24542 Z= 0.134 Angle : 0.624 10.128 33096 Z= 0.318 Chirality : 0.044 0.200 3766 Planarity : 0.004 0.043 4177 Dihedral : 4.732 45.557 3174 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2920 helix: 0.99 (0.13), residues: 1678 sheet: -0.16 (0.31), residues: 267 loop : -0.86 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP K 239 HIS 0.012 0.001 HIS P 171 PHE 0.018 0.001 PHE M 92 TYR 0.024 0.002 TYR U 365 ARG 0.006 0.000 ARG H 161 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 1123) hydrogen bonds : angle 4.13274 ( 3360) covalent geometry : bond 0.00296 (24542) covalent geometry : angle 0.62449 (33096) *********************** 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 436 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 436 time to evaluate : 2.963 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 65 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7991 (mt-10) REVERT: H 127 MET cc_start: 0.7785 (mtp) cc_final: 0.7186 (mtp) REVERT: H 130 MET cc_start: 0.8548 (mmp) cc_final: 0.7425 (ptm) REVERT: H 141 MET cc_start: 0.8311 (mpp) cc_final: 0.7985 (mpp) REVERT: I 221 LYS cc_start: 0.5679 (tttt) cc_final: 0.5263 (tmtt) REVERT: I 229 MET cc_start: 0.6630 (ppp) cc_final: 0.6336 (ppp) REVERT: I 339 PHE cc_start: 0.7009 (t80) cc_final: 0.6781 (t80) REVERT: I 355 HIS cc_start: 0.7505 (p-80) cc_final: 0.7052 (p-80) REVERT: I 369 ASN cc_start: 0.8225 (t0) cc_final: 0.7593 (t0) REVERT: I 372 LEU cc_start: 0.9108 (mt) cc_final: 0.8380 (mt) REVERT: I 382 GLU cc_start: 0.7605 (pm20) cc_final: 0.7286 (tp30) REVERT: I 399 GLU cc_start: 0.8430 (pp20) cc_final: 0.7848 (pp20) REVERT: I 416 ASN cc_start: 0.7441 (t0) cc_final: 0.7196 (p0) REVERT: I 499 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7764 (mt-10) REVERT: I 500 LEU cc_start: 0.8800 (tp) cc_final: 0.8586 (tp) REVERT: I 503 ASN cc_start: 0.8056 (m-40) cc_final: 0.7799 (m110) REVERT: I 530 MET cc_start: 0.7641 (ptt) cc_final: 0.7288 (ptm) REVERT: I 607 MET cc_start: 0.8304 (mmm) cc_final: 0.8101 (mmm) REVERT: I 613 ASN cc_start: 0.8998 (m-40) cc_final: 0.8706 (m-40) REVERT: K 62 MET cc_start: 0.7705 (ttp) cc_final: 0.7332 (tmm) REVERT: K 103 ASP cc_start: 0.8639 (m-30) cc_final: 0.8009 (t0) REVERT: K 124 ARG cc_start: 0.8159 (mtp85) cc_final: 0.7782 (mtt90) REVERT: K 127 ARG cc_start: 0.8345 (tmm-80) cc_final: 0.8061 (tmm-80) REVERT: L 116 ASN cc_start: 0.7314 (p0) cc_final: 0.6441 (p0) REVERT: L 230 MET cc_start: 0.7277 (tmm) cc_final: 0.6960 (tmm) REVERT: L 334 TYR cc_start: 0.7944 (t80) cc_final: 0.7287 (t80) REVERT: M 33 ASP cc_start: 0.8387 (m-30) cc_final: 0.7959 (m-30) REVERT: M 45 LYS cc_start: 0.6449 (tttt) cc_final: 0.5976 (tttp) REVERT: M 64 ASP cc_start: 0.7389 (m-30) cc_final: 0.6971 (m-30) REVERT: M 94 LEU cc_start: 0.7996 (mt) cc_final: 0.7585 (pp) REVERT: N 154 TYR cc_start: 0.8663 (t80) cc_final: 0.8355 (t80) REVERT: N 331 MET cc_start: 0.8724 (pmm) cc_final: 0.8181 (pmm) REVERT: O 174 GLN cc_start: 0.8079 (pm20) cc_final: 0.7547 (tt0) REVERT: O 175 HIS cc_start: 0.8122 (t70) cc_final: 0.7774 (t70) REVERT: O 180 LEU cc_start: 0.8731 (mt) cc_final: 0.8516 (mm) REVERT: O 182 GLU cc_start: 0.7682 (tp30) cc_final: 0.6913 (tp30) REVERT: O 222 TYR cc_start: 0.8005 (p90) cc_final: 0.7768 (p90) REVERT: P 142 MET cc_start: 0.7822 (tpt) cc_final: 0.7183 (tpp) REVERT: P 161 LYS cc_start: 0.8505 (mttt) cc_final: 0.8069 (mmtt) REVERT: P 162 ASP cc_start: 0.8481 (t0) cc_final: 0.7741 (m-30) REVERT: P 222 TRP cc_start: 0.7837 (t-100) cc_final: 0.7624 (t-100) REVERT: P 253 ARG cc_start: 0.8435 (mmp80) cc_final: 0.7960 (mmm160) REVERT: U 329 ARG cc_start: 0.8944 (mmm160) cc_final: 0.8674 (tpp-160) REVERT: U 396 THR cc_start: 0.8644 (p) cc_final: 0.8408 (t) REVERT: Q 131 MET cc_start: -0.3059 (mtt) cc_final: -0.3346 (mtt) REVERT: Q 143 MET cc_start: 0.7422 (ptm) cc_final: 0.7158 (ppp) REVERT: Q 165 MET cc_start: 0.7938 (mtp) cc_final: 0.7691 (mmm) REVERT: Q 180 LYS cc_start: 0.6831 (tptt) cc_final: 0.6588 (tptt) REVERT: Q 184 GLN cc_start: 0.8025 (pp30) cc_final: 0.7771 (pp30) REVERT: Q 201 HIS cc_start: 0.6968 (m90) cc_final: 0.6381 (m-70) REVERT: Q 252 LYS cc_start: 0.7875 (pttm) cc_final: 0.7150 (tmtt) REVERT: T 473 MET cc_start: -0.2051 (mtp) cc_final: -0.2281 (mtm) outliers start: 0 outliers final: 0 residues processed: 436 average time/residue: 0.3413 time to fit residues: 238.0866 Evaluate side-chains 332 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 256 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 152 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 chunk 249 optimal weight: 20.0000 chunk 236 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 239 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 ASN 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 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** Q 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.101084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.091477 restraints weight = 140022.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.091552 restraints weight = 115809.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.091490 restraints weight = 115358.353| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.7284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 24542 Z= 0.114 Angle : 0.609 9.778 33096 Z= 0.307 Chirality : 0.043 0.194 3766 Planarity : 0.004 0.043 4177 Dihedral : 4.595 44.423 3174 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.16), residues: 2920 helix: 1.19 (0.13), residues: 1669 sheet: -0.20 (0.31), residues: 267 loop : -0.78 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP K 239 HIS 0.007 0.001 HIS O 281 PHE 0.016 0.001 PHE I 432 TYR 0.023 0.001 TYR U 365 ARG 0.006 0.000 ARG H 161 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 1123) hydrogen bonds : angle 3.98753 ( 3360) covalent geometry : bond 0.00248 (24542) covalent geometry : angle 0.60948 (33096) ********************** 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 434 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 2.652 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 53 GLN cc_start: 0.9320 (mm-40) cc_final: 0.9087 (mp10) REVERT: H 65 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7990 (mt-10) REVERT: H 127 MET cc_start: 0.7869 (mtp) cc_final: 0.7335 (mtp) REVERT: H 130 MET cc_start: 0.8572 (mmp) cc_final: 0.7430 (ptm) REVERT: H 141 MET cc_start: 0.8294 (mpp) cc_final: 0.7987 (mpp) REVERT: I 221 LYS cc_start: 0.6136 (tttt) cc_final: 0.5654 (tmtt) REVERT: I 229 MET cc_start: 0.7118 (ppp) cc_final: 0.6788 (ppp) REVERT: I 339 PHE cc_start: 0.7051 (t80) cc_final: 0.6707 (t80) REVERT: I 355 HIS cc_start: 0.7582 (p-80) cc_final: 0.7111 (p-80) REVERT: I 369 ASN cc_start: 0.8202 (t0) cc_final: 0.7555 (t0) REVERT: I 372 LEU cc_start: 0.9043 (mt) cc_final: 0.8292 (mt) REVERT: I 382 GLU cc_start: 0.7586 (pm20) cc_final: 0.7241 (mm-30) REVERT: I 399 GLU cc_start: 0.8511 (pp20) cc_final: 0.7924 (pp20) REVERT: I 499 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7789 (mt-10) REVERT: I 500 LEU cc_start: 0.8823 (tp) cc_final: 0.8623 (tp) REVERT: I 503 ASN cc_start: 0.8064 (m-40) cc_final: 0.7830 (m110) REVERT: I 505 LEU cc_start: 0.8544 (mt) cc_final: 0.8331 (mt) REVERT: I 530 MET cc_start: 0.7669 (ptt) cc_final: 0.7321 (ptm) REVERT: I 613 ASN cc_start: 0.9008 (m-40) cc_final: 0.8686 (m-40) REVERT: I 643 TYR cc_start: 0.7842 (m-80) cc_final: 0.6516 (m-80) REVERT: K 62 MET cc_start: 0.7582 (ttp) cc_final: 0.7238 (tmm) REVERT: K 103 ASP cc_start: 0.8650 (m-30) cc_final: 0.7994 (t0) REVERT: K 124 ARG cc_start: 0.8205 (mtp85) cc_final: 0.7842 (mtt90) REVERT: K 127 ARG cc_start: 0.8334 (tmm-80) cc_final: 0.8074 (tmm-80) REVERT: L 116 ASN cc_start: 0.7212 (p0) cc_final: 0.6214 (p0) REVERT: L 124 LEU cc_start: 0.7927 (pp) cc_final: 0.7451 (pp) REVERT: L 127 MET cc_start: 0.6553 (pmm) cc_final: 0.6005 (ppp) REVERT: L 144 LYS cc_start: 0.2529 (mttt) cc_final: 0.2275 (mttp) REVERT: L 230 MET cc_start: 0.7171 (tmm) cc_final: 0.6853 (tmm) REVERT: L 288 TYR cc_start: 0.8040 (m-10) cc_final: 0.7384 (m-80) REVERT: L 299 LEU cc_start: 0.8406 (mt) cc_final: 0.7838 (mt) REVERT: L 300 SER cc_start: 0.8335 (t) cc_final: 0.7862 (m) REVERT: M 33 ASP cc_start: 0.8329 (m-30) cc_final: 0.7923 (m-30) REVERT: M 45 LYS cc_start: 0.6537 (tttt) cc_final: 0.6032 (tttp) REVERT: M 64 ASP cc_start: 0.7292 (m-30) cc_final: 0.6853 (m-30) REVERT: M 94 LEU cc_start: 0.7924 (mt) cc_final: 0.7512 (pp) REVERT: N 3 GLU cc_start: 0.7340 (tp30) cc_final: 0.6943 (pm20) REVERT: N 154 TYR cc_start: 0.8681 (t80) cc_final: 0.8326 (t80) REVERT: N 266 PHE cc_start: 0.8761 (t80) cc_final: 0.8555 (t80) REVERT: N 331 MET cc_start: 0.8761 (pmm) cc_final: 0.8203 (pmm) REVERT: O 175 HIS cc_start: 0.7918 (t70) cc_final: 0.7699 (t70) REVERT: O 182 GLU cc_start: 0.7612 (tp30) cc_final: 0.6829 (tp30) REVERT: O 284 PHE cc_start: 0.8323 (m-80) cc_final: 0.7745 (m-80) REVERT: P 142 MET cc_start: 0.7789 (tpt) cc_final: 0.7230 (tpp) REVERT: P 161 LYS cc_start: 0.8473 (mttt) cc_final: 0.8036 (mmtt) REVERT: P 162 ASP cc_start: 0.8479 (t0) cc_final: 0.7726 (m-30) REVERT: P 253 ARG cc_start: 0.8414 (mmp80) cc_final: 0.7990 (mmm160) REVERT: U 329 ARG cc_start: 0.8919 (mmm160) cc_final: 0.8696 (tpp-160) REVERT: U 396 THR cc_start: 0.8645 (p) cc_final: 0.8392 (t) REVERT: Q 131 MET cc_start: -0.2943 (mtt) cc_final: -0.3220 (mtt) REVERT: Q 143 MET cc_start: 0.7084 (ptm) cc_final: 0.6845 (ppp) REVERT: Q 180 LYS cc_start: 0.6750 (tptt) cc_final: 0.6487 (tptt) REVERT: Q 184 GLN cc_start: 0.8109 (pp30) cc_final: 0.7877 (pp30) REVERT: Q 201 HIS cc_start: 0.7237 (m90) cc_final: 0.6614 (m-70) REVERT: Q 252 LYS cc_start: 0.7881 (pttm) cc_final: 0.7166 (tmtt) REVERT: R 101 MET cc_start: 0.7916 (mmm) cc_final: 0.7431 (mtt) REVERT: T 473 MET cc_start: -0.1863 (mtp) cc_final: -0.2157 (mtm) outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.3269 time to fit residues: 227.6574 Evaluate side-chains 341 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 259 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 247 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 140 optimal weight: 0.0020 chunk 12 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 212 optimal weight: 10.0000 overall best weight: 2.3996 ------------------------------------------------------------------------------- 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** ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 ASN 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** O 153 HIS ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 171 HIS ** 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** Q 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.099900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.091506 restraints weight = 133843.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.091598 restraints weight = 112674.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.091437 restraints weight = 109129.836| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.7463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24542 Z= 0.132 Angle : 0.624 9.834 33096 Z= 0.315 Chirality : 0.043 0.202 3766 Planarity : 0.004 0.042 4177 Dihedral : 4.596 44.964 3174 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.16), residues: 2920 helix: 1.16 (0.13), residues: 1676 sheet: -0.20 (0.31), residues: 268 loop : -0.82 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP K 239 HIS 0.011 0.001 HIS P 171 PHE 0.017 0.001 PHE M 92 TYR 0.020 0.001 TYR U 365 ARG 0.005 0.001 ARG N 42 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 1123) hydrogen bonds : angle 4.01626 ( 3360) covalent geometry : bond 0.00293 (24542) covalent geometry : angle 0.62378 (33096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9861.65 seconds wall clock time: 172 minutes 0.49 seconds (10320.49 seconds total)