Starting phenix.real_space_refine on Fri Mar 6 00:31:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6voa_21259/03_2026/6voa_21259.cif Found real_map, /net/cci-nas-00/data/ceres_data/6voa_21259/03_2026/6voa_21259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6voa_21259/03_2026/6voa_21259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6voa_21259/03_2026/6voa_21259.map" model { file = "/net/cci-nas-00/data/ceres_data/6voa_21259/03_2026/6voa_21259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6voa_21259/03_2026/6voa_21259.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 95 5.16 5 C 16810 2.51 5 N 4832 2.21 5 O 5087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 160 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26824 Number of models: 1 Model: "" Number of chains: 9 Chain: "H" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 421 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "B" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 3465 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 414} Link IDs: {'PTRANS': 17, 'TRANS': 601} Chain breaks: 6 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1447 Unresolved non-hydrogen angles: 1874 Unresolved non-hydrogen dihedrals: 1184 Unresolved non-hydrogen chiralities: 150 Planarities with less than four sites: {'GLN:plan1': 16, 'PHE:plan': 23, 'ARG:plan': 21, 'HIS:plan': 15, 'TYR:plan': 15, 'ASP:plan': 32, 'ASN:plan1': 25, 'GLU:plan': 27, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 802 Chain: "E" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3114 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2411 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain breaks: 2 Chain: "C" Number of atoms: 3676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 3676 Classifications: {'peptide': 667} Incomplete info: {'truncation_to_alanine': 484} Link IDs: {'PTRANS': 25, 'TRANS': 641} Chain breaks: 8 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1687 Unresolved non-hydrogen angles: 2159 Unresolved non-hydrogen dihedrals: 1384 Unresolved non-hydrogen chiralities: 163 Planarities with less than four sites: {'ASP:plan': 34, 'ASN:plan1': 21, 'ARG:plan': 24, 'TYR:plan': 19, 'GLN:plan1': 30, 'HIS:plan': 13, 'PHE:plan': 22, 'GLU:plan': 37, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 910 Chain: "F" Number of atoms: 3797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3797 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 20, 'TRANS': 454} Chain breaks: 2 Chain: "I" Number of atoms: 6034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6034 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 31, 'TRANS': 732} Chain breaks: 5 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 816 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 5, 'TRANS': 159} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 676 Unresolved non-hydrogen dihedrals: 445 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLU:plan': 8, 'HIS:plan': 5, 'ASP:plan': 13, 'ASN:plan1': 6, 'GLN:plan1': 9, 'PHE:plan': 7, 'ARG:plan': 7, 'TYR:plan': 3, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 275 Chain: "D" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3090 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PTRANS': 33, 'TRANS': 494} Chain breaks: 2 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1077 Unresolved non-hydrogen angles: 1373 Unresolved non-hydrogen dihedrals: 884 Unresolved non-hydrogen chiralities: 114 Planarities with less than four sites: {'ASP:plan': 16, 'PHE:plan': 12, 'HIS:plan': 8, 'GLU:plan': 23, 'TYR:plan': 9, 'ARG:plan': 18, 'GLN:plan1': 14, 'ASN:plan1': 12, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 515 Time building chain proxies: 6.11, per 1000 atoms: 0.23 Number of scatterers: 26824 At special positions: 0 Unit cell: (125.28, 150.12, 207.36, 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 95 16.00 O 5087 8.00 N 4832 7.00 C 16810 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: 2.40 Conformation dependent library (CDL) restraints added in 1.3 seconds 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7454 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 45 sheets defined 35.3% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'H' and resid 38 through 58 removed outlier: 3.671A pdb=" N GLU H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA H 51 " --> pdb=" O MET H 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN H 52 " --> pdb=" O GLN H 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 38 No H-bonds generated for 'chain 'B' and resid 36 through 38' Processing helix chain 'B' and resid 339 through 359 removed outlier: 3.552A pdb=" N GLN B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 517 Processing helix chain 'B' and resid 560 through 575 removed outlier: 3.730A pdb=" N ALA B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 634 removed outlier: 3.687A pdb=" N GLU B 592 " --> pdb=" O VAL B 588 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP B 601 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 685 Processing helix chain 'B' and resid 688 through 703 removed outlier: 3.847A pdb=" N ASN B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL B 694 " --> pdb=" O PRO B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 716 Processing helix chain 'E' and resid 35 through 45 removed outlier: 3.738A pdb=" N ILE E 39 " --> pdb=" O GLN E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 63 Processing helix chain 'E' and resid 68 through 80 removed outlier: 3.551A pdb=" N VAL E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 100 through 114 removed outlier: 3.678A pdb=" N LEU E 104 " --> pdb=" O CYS E 100 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 removed outlier: 3.751A pdb=" N GLU E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 148 removed outlier: 4.272A pdb=" N CYS E 138 " --> pdb=" O ASP E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 165 Processing helix chain 'E' and resid 167 through 182 Processing helix chain 'E' and resid 183 through 197 removed outlier: 3.765A pdb=" N ALA E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE E 190 " --> pdb=" O LYS E 186 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE E 197 " --> pdb=" O LYS E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 215 Processing helix chain 'E' and resid 218 through 232 removed outlier: 3.667A pdb=" N TYR E 231 " --> pdb=" O ASN E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 249 removed outlier: 3.980A pdb=" N ALA E 241 " --> pdb=" O LYS E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 263 removed outlier: 3.790A pdb=" N ALA E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL E 262 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 283 Processing helix chain 'E' and resid 286 through 299 removed outlier: 3.903A pdb=" N CYS E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 317 Processing helix chain 'E' and resid 321 through 334 removed outlier: 3.900A pdb=" N HIS E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 350 removed outlier: 3.755A pdb=" N ASN E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 368 removed outlier: 3.574A pdb=" N ALA E 357 " --> pdb=" O ASP E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 385 removed outlier: 4.362A pdb=" N ASN E 375 " --> pdb=" O ASN E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 402 removed outlier: 3.746A pdb=" N ALA E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 423 removed outlier: 3.788A pdb=" N GLU E 416 " --> pdb=" O GLU E 412 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 133 removed outlier: 3.806A pdb=" N SER G 123 " --> pdb=" O ARG G 119 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE G 125 " --> pdb=" O TYR G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 260 removed outlier: 4.225A pdb=" N LEU G 243 " --> pdb=" O PRO G 239 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN G 260 " --> pdb=" O VAL G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 302 Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'C' and resid 336 through 367 Processing helix chain 'C' and resid 516 through 528 Processing helix chain 'C' and resid 569 through 587 removed outlier: 3.759A pdb=" N ILE C 573 " --> pdb=" O ASN C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 634 Proline residue: C 611 - end of helix removed outlier: 3.868A pdb=" N LEU C 625 " --> pdb=" O LYS C 621 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASP C 627 " --> pdb=" O VAL C 623 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ALA C 628 " --> pdb=" O GLN C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 639 removed outlier: 3.917A pdb=" N ASN C 638 " --> pdb=" O HIS C 635 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR C 639 " --> pdb=" O GLU C 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 635 through 639' Processing helix chain 'C' and resid 643 through 661 removed outlier: 3.813A pdb=" N ILE C 649 " --> pdb=" O GLU C 645 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU C 651 " --> pdb=" O ARG C 647 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU C 652 " --> pdb=" O CYS C 648 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ASP C 654 " --> pdb=" O LEU C 650 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS C 661 " --> pdb=" O GLN C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 684 removed outlier: 3.616A pdb=" N HIS C 666 " --> pdb=" O LYS C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 703 Processing helix chain 'C' and resid 704 through 715 Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 17 through 30 removed outlier: 3.617A pdb=" N GLN F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 48 removed outlier: 3.608A pdb=" N TRP F 37 " --> pdb=" O ASP F 33 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL F 48 " --> pdb=" O LEU F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 55 removed outlier: 3.604A pdb=" N ASP F 54 " --> pdb=" O ASP F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 66 removed outlier: 3.505A pdb=" N ILE F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP F 66 " --> pdb=" O GLU F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 167 through 172 removed outlier: 3.503A pdb=" N TYR F 171 " --> pdb=" O ASN F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 188 removed outlier: 4.264A pdb=" N ALA F 180 " --> pdb=" O LYS F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 206 Processing helix chain 'F' and resid 210 through 225 removed outlier: 3.650A pdb=" N LYS F 214 " --> pdb=" O ASP F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 241 removed outlier: 3.927A pdb=" N GLN F 233 " --> pdb=" O GLU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 257 Processing helix chain 'F' and resid 259 through 274 Processing helix chain 'F' and resid 277 through 291 removed outlier: 3.543A pdb=" N LEU F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 308 removed outlier: 3.648A pdb=" N ALA F 297 " --> pdb=" O ASN F 293 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU F 299 " --> pdb=" O SER F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 325 Processing helix chain 'F' and resid 327 through 341 removed outlier: 3.689A pdb=" N LEU F 338 " --> pdb=" O PHE F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 359 removed outlier: 3.971A pdb=" N PHE F 349 " --> pdb=" O ASN F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 376 removed outlier: 3.502A pdb=" N PHE F 369 " --> pdb=" O THR F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 397 Processing helix chain 'F' and resid 398 through 413 removed outlier: 3.746A pdb=" N ALA F 402 " --> pdb=" O ASP F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 431 Processing helix chain 'F' and resid 432 through 447 Processing helix chain 'F' and resid 451 through 465 Processing helix chain 'F' and resid 466 through 481 removed outlier: 3.734A pdb=" N LYS F 476 " --> pdb=" O ALA F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 498 Processing helix chain 'I' and resid 64 through 66 No H-bonds generated for 'chain 'I' and resid 64 through 66' Processing helix chain 'I' and resid 207 through 213 Processing helix chain 'I' and resid 377 through 396 removed outlier: 3.524A pdb=" N ASN I 396 " --> pdb=" O ILE I 392 " (cutoff:3.500A) Processing helix chain 'I' and resid 530 through 533 Processing helix chain 'I' and resid 558 through 563 Processing helix chain 'I' and resid 605 through 627 removed outlier: 3.682A pdb=" N LEU I 609 " --> pdb=" O GLN I 605 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TRP I 610 " --> pdb=" O PHE I 606 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU I 611 " --> pdb=" O GLU I 607 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE I 612 " --> pdb=" O ASP I 608 " (cutoff:3.500A) Processing helix chain 'I' and resid 645 through 686 removed outlier: 3.537A pdb=" N ILE I 649 " --> pdb=" O TYR I 645 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU I 668 " --> pdb=" O GLU I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 694 through 742 Processing helix chain 'I' and resid 745 through 757 Processing helix chain 'I' and resid 767 through 783 Processing helix chain 'I' and resid 787 through 794 Processing helix chain 'I' and resid 805 through 821 Processing helix chain 'A' and resid 32 through 37 removed outlier: 4.452A pdb=" N LYS A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.507A pdb=" N LYS A 119 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.817A pdb=" N LEU D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN D 141 " --> pdb=" O ASP D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.542A pdb=" N VAL D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 474 removed outlier: 3.557A pdb=" N MET D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 9 removed outlier: 4.768A pdb=" N GLU B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 22 removed outlier: 3.889A pdb=" N LYS B 39 " --> pdb=" O THR B 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 81 removed outlier: 3.990A pdb=" N PHE B 112 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP B 104 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASP B 110 " --> pdb=" O ASP B 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.962A pdb=" N PHE B 155 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 163 through 169 removed outlier: 3.924A pdb=" N SER B 165 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 188 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU B 199 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL B 190 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.942A pdb=" N SER B 208 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TRP B 236 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 250 removed outlier: 3.551A pdb=" N SER B 246 " --> pdb=" O GLY B 263 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AA9, first strand: chain 'B' and resid 383 through 390 Processing sheet with id=AB1, first strand: chain 'B' and resid 427 through 430 removed outlier: 4.422A pdb=" N ILE B 417 " --> pdb=" O HIS B 428 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 415 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE B 412 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY B 462 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 414 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS B 458 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N THR C 480 " --> pdb=" O PRO C 474 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN C 469 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE C 409 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR C 471 " --> pdb=" O VAL C 407 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL C 407 " --> pdb=" O TYR C 471 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR C 473 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 427 through 430 removed outlier: 4.422A pdb=" N ILE B 417 " --> pdb=" O HIS B 428 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 415 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE B 412 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY B 462 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 414 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS B 458 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 553 through 556 Processing sheet with id=AB4, first strand: chain 'G' and resid 13 through 15 removed outlier: 3.521A pdb=" N ASP G 32 " --> pdb=" O VAL G 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 37 through 40 removed outlier: 6.233A pdb=" N ALA G 94 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR G 81 " --> pdb=" O ALA G 94 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR G 96 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE G 79 " --> pdb=" O TYR G 96 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU G 98 " --> pdb=" O LEU G 77 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 141 through 142 removed outlier: 3.730A pdb=" N LYS G 141 " --> pdb=" O SER G 200 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG G 186 " --> pdb=" O THR G 183 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY G 178 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN G 165 " --> pdb=" O GLY G 178 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE G 180 " --> pdb=" O LYS G 163 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS G 163 " --> pdb=" O PHE G 180 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE G 182 " --> pdb=" O TYR G 161 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 206 through 210 removed outlier: 6.885A pdb=" N GLU G 223 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL G 209 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL G 221 " --> pdb=" O VAL G 209 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 314 through 316 Processing sheet with id=AB9, first strand: chain 'C' and resid 6 through 12 removed outlier: 4.968A pdb=" N ILE C 314 " --> pdb=" O TYR C 10 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TRP C 313 " --> pdb=" O THR C 309 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL C 306 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE C 292 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N SER C 308 " --> pdb=" O THR C 290 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 21 through 24 removed outlier: 3.798A pdb=" N LYS C 34 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 69 through 72 removed outlier: 3.653A pdb=" N LEU C 101 " --> pdb=" O GLY C 92 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 114 through 117 removed outlier: 6.264A pdb=" N CYS C 133 " --> pdb=" O ASP C 137 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ASP C 137 " --> pdb=" O CYS C 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 147 through 152 removed outlier: 4.115A pdb=" N ASP C 149 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL C 171 " --> pdb=" O CYS C 167 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR C 182 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLN C 176 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL C 180 " --> pdb=" O GLN C 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 190 through 193 Processing sheet with id=AC6, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AC7, first strand: chain 'C' and resid 244 through 247 removed outlier: 6.346A pdb=" N VAL C 266 " --> pdb=" O ASP C 282 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP C 282 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL C 268 " --> pdb=" O ARG C 280 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 384 through 387 removed outlier: 4.261A pdb=" N THR C 386 " --> pdb=" O SER C 395 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 510 through 512 removed outlier: 3.779A pdb=" N GLU C 562 " --> pdb=" O ARG C 559 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 6 through 13 removed outlier: 4.980A pdb=" N ASP I 8 " --> pdb=" O TYR I 358 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N TYR I 358 " --> pdb=" O ASP I 8 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TRP I 10 " --> pdb=" O CYS I 356 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU I 348 " --> pdb=" O ALA I 332 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA I 332 " --> pdb=" O LEU I 348 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 26 through 28 removed outlier: 3.574A pdb=" N ALA I 28 " --> pdb=" O LYS I 39 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 79 through 84 removed outlier: 4.766A pdb=" N GLN I 80 " --> pdb=" O LEU I 98 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU I 98 " --> pdb=" O GLN I 80 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU I 95 " --> pdb=" O TYR I 106 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR I 127 " --> pdb=" O VAL I 105 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 108 through 111 Processing sheet with id=AD5, first strand: chain 'I' and resid 138 through 141 Processing sheet with id=AD6, first strand: chain 'I' and resid 185 through 187 Processing sheet with id=AD7, first strand: chain 'I' and resid 245 through 251 removed outlier: 7.193A pdb=" N LEU I 263 " --> pdb=" O ILE I 246 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE I 248 " --> pdb=" O PHE I 261 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE I 261 " --> pdb=" O ILE I 248 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE I 250 " --> pdb=" O SER I 259 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N SER I 259 " --> pdb=" O ILE I 250 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 287 through 291 removed outlier: 3.765A pdb=" N CYS I 289 " --> pdb=" O GLY I 306 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N MET I 311 " --> pdb=" O ASN I 307 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU I 312 " --> pdb=" O ALA I 323 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA I 323 " --> pdb=" O LEU I 312 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE I 314 " --> pdb=" O LYS I 321 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR I 319 " --> pdb=" O GLN I 316 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 411 through 417 Processing sheet with id=AE1, first strand: chain 'I' and resid 471 through 474 removed outlier: 5.574A pdb=" N LYS I 454 " --> pdb=" O SER I 509 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER I 509 " --> pdb=" O LYS I 454 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 535 through 537 Processing sheet with id=AE3, first strand: chain 'A' and resid 21 through 22 removed outlier: 3.878A pdb=" N CYS A 22 " --> pdb=" O PHE A 68 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'A' and resid 57 through 59 Processing sheet with id=AE5, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AE6, first strand: chain 'D' and resid 265 through 266 Processing sheet with id=AE7, first strand: chain 'D' and resid 296 through 297 Processing sheet with id=AE8, first strand: chain 'D' and resid 487 through 493 Processing sheet with id=AE9, first strand: chain 'D' and resid 534 through 536 1393 hydrogen bonds defined for protein. 4014 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: 5.89 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4782 1.32 - 1.44: 6541 1.44 - 1.57: 15715 1.57 - 1.69: 0 1.69 - 1.82: 144 Bond restraints: 27182 Sorted by residual: bond pdb=" CA SER C 430 " pdb=" CB SER C 430 " ideal model delta sigma weight residual 1.530 1.457 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" CA ALA B 167 " pdb=" CB ALA B 167 " ideal model delta sigma weight residual 1.534 1.473 0.061 1.76e-02 3.23e+03 1.18e+01 bond pdb=" CA SER I 364 " pdb=" CB SER I 364 " ideal model delta sigma weight residual 1.531 1.481 0.050 1.52e-02 4.33e+03 1.07e+01 bond pdb=" N SER E 410 " pdb=" CA SER E 410 " ideal model delta sigma weight residual 1.456 1.498 -0.041 1.28e-02 6.10e+03 1.05e+01 bond pdb=" C PRO I 363 " pdb=" O PRO I 363 " ideal model delta sigma weight residual 1.233 1.195 0.037 1.16e-02 7.43e+03 1.04e+01 ... (remaining 27177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 36409 2.77 - 5.53: 536 5.53 - 8.30: 68 8.30 - 11.07: 18 11.07 - 13.84: 3 Bond angle restraints: 37034 Sorted by residual: angle pdb=" C GLY C 327 " pdb=" N PRO C 328 " pdb=" CA PRO C 328 " ideal model delta sigma weight residual 119.84 133.68 -13.84 1.25e+00 6.40e-01 1.23e+02 angle pdb=" C ASP B 172 " pdb=" CA ASP B 172 " pdb=" CB ASP B 172 " ideal model delta sigma weight residual 109.83 118.14 -8.31 9.90e-01 1.02e+00 7.04e+01 angle pdb=" C MET D 326 " pdb=" N PRO D 327 " pdb=" CA PRO D 327 " ideal model delta sigma weight residual 119.05 127.59 -8.54 1.11e+00 8.12e-01 5.92e+01 angle pdb=" N GLU D 164 " pdb=" CA GLU D 164 " pdb=" C GLU D 164 " ideal model delta sigma weight residual 111.28 119.29 -8.01 1.09e+00 8.42e-01 5.40e+01 angle pdb=" N CYS A 160 " pdb=" CA CYS A 160 " pdb=" C CYS A 160 " ideal model delta sigma weight residual 108.45 117.65 -9.20 1.26e+00 6.30e-01 5.33e+01 ... (remaining 37029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 14888 18.00 - 35.99: 1128 35.99 - 53.99: 189 53.99 - 71.99: 40 71.99 - 89.98: 20 Dihedral angle restraints: 16265 sinusoidal: 4791 harmonic: 11474 Sorted by residual: dihedral pdb=" CA LEU D 179 " pdb=" C LEU D 179 " pdb=" N SER D 180 " pdb=" CA SER D 180 " ideal model delta harmonic sigma weight residual 180.00 -150.05 -29.95 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" C ASP B 172 " pdb=" N ASP B 172 " pdb=" CA ASP B 172 " pdb=" CB ASP B 172 " ideal model delta harmonic sigma weight residual -122.60 -137.25 14.65 0 2.50e+00 1.60e-01 3.43e+01 dihedral pdb=" CA LYS D 69 " pdb=" C LYS D 69 " pdb=" N VAL D 70 " pdb=" CA VAL D 70 " ideal model delta harmonic sigma weight residual -180.00 -150.95 -29.05 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 16262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4093 0.098 - 0.196: 298 0.196 - 0.294: 36 0.294 - 0.391: 10 0.391 - 0.489: 3 Chirality restraints: 4440 Sorted by residual: chirality pdb=" CA ILE A 90 " pdb=" N ILE A 90 " pdb=" C ILE A 90 " pdb=" CB ILE A 90 " both_signs ideal model delta sigma weight residual False 2.43 1.94 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CA ASP B 172 " pdb=" N ASP B 172 " pdb=" C ASP B 172 " pdb=" CB ASP B 172 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CA PHE B 171 " pdb=" N PHE B 171 " pdb=" C PHE B 171 " pdb=" CB PHE B 171 " both_signs ideal model delta sigma weight residual False 2.51 2.98 -0.47 2.00e-01 2.50e+01 5.50e+00 ... (remaining 4437 not shown) Planarity restraints: 4915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE F 16 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C PHE F 16 " -0.058 2.00e-02 2.50e+03 pdb=" O PHE F 16 " 0.021 2.00e-02 2.50e+03 pdb=" N GLN F 17 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 250 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C PHE B 250 " -0.056 2.00e-02 2.50e+03 pdb=" O PHE B 250 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP B 251 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 322 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.16e+00 pdb=" C TRP D 322 " -0.049 2.00e-02 2.50e+03 pdb=" O TRP D 322 " 0.019 2.00e-02 2.50e+03 pdb=" N THR D 323 " 0.016 2.00e-02 2.50e+03 ... (remaining 4912 not shown) Histogram of nonbonded interaction distances: 1.11 - 1.87: 13 1.87 - 2.62: 324 2.62 - 3.38: 35004 3.38 - 4.14: 59291 4.14 - 4.90: 109571 Nonbonded interactions: 204203 Sorted by model distance: nonbonded pdb=" CB SER C 428 " pdb=" C THR C 444 " model vdw 1.107 3.670 nonbonded pdb=" CB SER C 428 " pdb=" O THR C 444 " model vdw 1.299 3.440 nonbonded pdb=" CB SER C 428 " pdb=" CA THR C 444 " model vdw 1.335 3.870 nonbonded pdb=" CA SER C 428 " pdb=" O THR C 444 " model vdw 1.484 3.470 nonbonded pdb=" CA GLY A 52 " pdb=" O ASP A 69 " model vdw 1.504 3.440 ... (remaining 204198 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: 2.830 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.210 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5747 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 27182 Z= 0.254 Angle : 0.834 13.837 37034 Z= 0.541 Chirality : 0.057 0.489 4440 Planarity : 0.004 0.050 4915 Dihedral : 14.092 89.984 8811 Min Nonbonded Distance : 1.107 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.77 % Favored : 90.72 % Rotamer: Outliers : 1.57 % Allowed : 5.91 % Favored : 92.52 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.12), residues: 3888 helix: -0.64 (0.13), residues: 1331 sheet: -2.26 (0.17), residues: 804 loop : -3.41 (0.12), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 12 TYR 0.016 0.001 TYR E 124 PHE 0.016 0.002 PHE C 678 TRP 0.017 0.001 TRP I 237 HIS 0.006 0.001 HIS G 190 Details of bonding type rmsd covalent geometry : bond 0.00422 (27182) covalent geometry : angle 0.83397 (37034) hydrogen bonds : bond 0.14396 ( 1375) hydrogen bonds : angle 6.34891 ( 4014) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 668 time to evaluate : 1.016 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: B 591 GLU cc_start: 0.7190 (pp20) cc_final: 0.6917 (tm-30) REVERT: B 599 LYS cc_start: 0.7694 (mmtt) cc_final: 0.7371 (mmmt) REVERT: B 705 ASN cc_start: 0.6740 (m-40) cc_final: 0.5625 (t0) REVERT: E 306 ILE cc_start: 0.7003 (mt) cc_final: 0.6219 (tp) REVERT: G 22 MET cc_start: 0.6610 (mtm) cc_final: 0.6369 (ptm) REVERT: G 131 TYR cc_start: 0.7115 (t80) cc_final: 0.6740 (t80) REVERT: G 190 HIS cc_start: 0.4866 (p-80) cc_final: 0.4154 (p-80) REVERT: F 202 SER cc_start: 0.8439 (m) cc_final: 0.7673 (t) REVERT: I 160 MET cc_start: 0.6450 (ttt) cc_final: 0.6096 (tpt) REVERT: I 699 LEU cc_start: 0.7218 (tp) cc_final: 0.7008 (tp) REVERT: D 586 MET cc_start: 0.6061 (mpp) cc_final: 0.5364 (mmm) outliers start: 33 outliers final: 8 residues processed: 696 average time/residue: 0.1825 time to fit residues: 197.7929 Evaluate side-chains 305 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 297 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain I residue 519 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.0020 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 50.0000 overall best weight: 4.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN B 664 ASN B 684 HIS B 693 GLN E 40 HIS E 84 GLN ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 GLN E 159 HIS E 167 HIS ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 HIS E 375 ASN ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN G 165 ASN G 176 ASN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 HIS F 162 ASN F 188 HIS F 233 GLN F 259 GLN F 307 GLN F 309 ASN F 311 HIS F 351 ASN ** F 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 GLN ** F 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 456 ASN F 496 GLN I 120 GLN ** I 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 201 GLN I 302 ASN I 471 GLN I 515 ASN I 672 GLN I 677 GLN I 693 GLN I 694 HIS I 705 GLN ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 764 GLN D 449 HIS ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.097621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.083072 restraints weight = 123208.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.084271 restraints weight = 78585.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.085230 restraints weight = 52158.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.085427 restraints weight = 49300.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.085488 restraints weight = 39964.518| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 27182 Z= 0.266 Angle : 0.810 11.256 37034 Z= 0.426 Chirality : 0.049 0.238 4440 Planarity : 0.005 0.068 4915 Dihedral : 5.979 84.537 4142 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.44 % Favored : 91.51 % Rotamer: Outliers : 5.53 % Allowed : 17.25 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.13), residues: 3888 helix: 0.43 (0.13), residues: 1371 sheet: -1.64 (0.18), residues: 819 loop : -2.99 (0.13), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 96 TYR 0.020 0.002 TYR B 648 PHE 0.041 0.003 PHE F 16 TRP 0.014 0.002 TRP E 273 HIS 0.018 0.002 HIS D 504 Details of bonding type rmsd covalent geometry : bond 0.00574 (27182) covalent geometry : angle 0.81021 (37034) hydrogen bonds : bond 0.04824 ( 1375) hydrogen bonds : angle 5.17247 ( 4014) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 289 time to evaluate : 1.203 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: H 26 MET cc_start: 0.6439 (mpp) cc_final: 0.6096 (mpp) REVERT: B 592 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8873 (pt0) REVERT: B 595 LYS cc_start: 0.8368 (tppt) cc_final: 0.8097 (mptt) REVERT: B 639 THR cc_start: 0.7465 (p) cc_final: 0.7152 (p) REVERT: B 653 ASP cc_start: 0.8190 (m-30) cc_final: 0.7651 (m-30) REVERT: E 185 ASP cc_start: 0.8270 (p0) cc_final: 0.7537 (p0) REVERT: E 246 MET cc_start: 0.9011 (mtp) cc_final: 0.8614 (mtm) REVERT: E 306 ILE cc_start: 0.8205 (mt) cc_final: 0.7937 (mt) REVERT: G 22 MET cc_start: 0.7915 (mtm) cc_final: 0.7368 (ptm) REVERT: G 121 TYR cc_start: 0.7350 (m-10) cc_final: 0.7150 (m-10) REVERT: G 181 PHE cc_start: 0.6807 (m-80) cc_final: 0.6114 (m-80) REVERT: G 190 HIS cc_start: 0.7012 (p-80) cc_final: 0.6218 (p-80) REVERT: G 193 MET cc_start: 0.7783 (tmm) cc_final: 0.7227 (mpp) REVERT: C 647 ARG cc_start: 0.7554 (ttm-80) cc_final: 0.7266 (ttm-80) REVERT: C 682 PHE cc_start: 0.7846 (m-10) cc_final: 0.7507 (m-80) REVERT: F 243 MET cc_start: 0.7059 (mmm) cc_final: 0.6672 (mmm) REVERT: F 252 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7867 (mtmm) REVERT: F 384 ASP cc_start: 0.6950 (m-30) cc_final: 0.5896 (m-30) REVERT: F 437 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8586 (mtpp) REVERT: I 78 ILE cc_start: 0.7163 (mt) cc_final: 0.6516 (mt) REVERT: I 92 MET cc_start: 0.7371 (ptt) cc_final: 0.7036 (ptm) REVERT: I 99 HIS cc_start: 0.7618 (m-70) cc_final: 0.7392 (m170) REVERT: I 308 HIS cc_start: 0.6196 (OUTLIER) cc_final: 0.5608 (m90) REVERT: I 578 MET cc_start: 0.6245 (tpt) cc_final: 0.5736 (tpp) REVERT: I 590 LEU cc_start: 0.8912 (tt) cc_final: 0.8582 (tt) REVERT: I 622 GLU cc_start: 0.9285 (tt0) cc_final: 0.8673 (tm-30) REVERT: D 586 MET cc_start: 0.6023 (mpp) cc_final: 0.4933 (mmm) outliers start: 116 outliers final: 64 residues processed: 367 average time/residue: 0.1698 time to fit residues: 102.7380 Evaluate side-chains 306 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 238 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain E residue 63 HIS Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 395 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 282 CYS Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 437 LYS Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 451 TYR Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 289 CYS Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 294 CYS Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 308 HIS Chi-restraints excluded: chain I residue 311 MET Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 609 LEU Chi-restraints excluded: chain I residue 621 GLN Chi-restraints excluded: chain I residue 773 ASP Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 566 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 323 optimal weight: 8.9990 chunk 372 optimal weight: 30.0000 chunk 163 optimal weight: 40.0000 chunk 99 optimal weight: 7.9990 chunk 266 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 258 optimal weight: 9.9990 chunk 301 optimal weight: 1.9990 chunk 374 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 221 optimal weight: 5.9990 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 ASN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 633 GLN ** F 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN F 422 ASN ** F 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 GLN ** D 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.094524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.081692 restraints weight = 125764.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.082005 restraints weight = 82476.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.081991 restraints weight = 65093.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.082362 restraints weight = 64505.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.082534 restraints weight = 53778.575| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 27182 Z= 0.277 Angle : 0.779 8.993 37034 Z= 0.408 Chirality : 0.048 0.257 4440 Planarity : 0.005 0.063 4915 Dihedral : 5.617 49.592 4131 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.26 % Favored : 90.69 % Rotamer: Outliers : 6.58 % Allowed : 19.64 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.13), residues: 3888 helix: 0.50 (0.13), residues: 1367 sheet: -1.54 (0.18), residues: 776 loop : -2.95 (0.13), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 129 TYR 0.025 0.002 TYR C 660 PHE 0.051 0.003 PHE E 413 TRP 0.021 0.003 TRP E 135 HIS 0.043 0.003 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00601 (27182) covalent geometry : angle 0.77888 (37034) hydrogen bonds : bond 0.04800 ( 1375) hydrogen bonds : angle 5.21434 ( 4014) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 238 time to evaluate : 1.041 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: B 636 ASP cc_start: 0.7393 (t0) cc_final: 0.7166 (t0) REVERT: E 44 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7346 (tt) REVERT: E 306 ILE cc_start: 0.8201 (mt) cc_final: 0.7984 (mt) REVERT: E 315 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7679 (tp) REVERT: G 120 LEU cc_start: 0.8221 (tp) cc_final: 0.7801 (tp) REVERT: G 121 TYR cc_start: 0.7588 (m-10) cc_final: 0.7336 (m-80) REVERT: G 181 PHE cc_start: 0.6309 (m-80) cc_final: 0.5567 (m-80) REVERT: G 190 HIS cc_start: 0.6620 (p-80) cc_final: 0.5949 (p-80) REVERT: C 682 PHE cc_start: 0.8130 (m-10) cc_final: 0.7749 (m-80) REVERT: F 58 GLU cc_start: 0.5868 (OUTLIER) cc_final: 0.5652 (mp0) REVERT: F 243 MET cc_start: 0.6951 (mmm) cc_final: 0.6467 (mmm) REVERT: F 252 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8040 (mtmm) REVERT: F 384 ASP cc_start: 0.6186 (m-30) cc_final: 0.5916 (m-30) REVERT: F 437 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8799 (mtpp) REVERT: I 78 ILE cc_start: 0.7481 (mt) cc_final: 0.6813 (mp) REVERT: I 99 HIS cc_start: 0.7523 (m-70) cc_final: 0.7287 (m170) REVERT: I 462 GLN cc_start: 0.4218 (mm-40) cc_final: 0.3592 (mm-40) REVERT: D 586 MET cc_start: 0.6442 (mpp) cc_final: 0.5383 (mmm) outliers start: 138 outliers final: 89 residues processed: 345 average time/residue: 0.1617 time to fit residues: 93.1983 Evaluate side-chains 304 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 210 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 705 ASN Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 63 HIS Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 279 CYS Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 398 MET Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 78 ASN Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 302 TYR Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 391 HIS Chi-restraints excluded: chain F residue 437 LYS Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 451 TYR Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 294 CYS Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 311 MET Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 477 MET Chi-restraints excluded: chain I residue 519 ILE Chi-restraints excluded: chain I residue 526 LYS Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 609 LEU Chi-restraints excluded: chain I residue 616 LEU Chi-restraints excluded: chain I residue 621 GLN Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 747 ASP Chi-restraints excluded: chain I residue 773 ASP Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 587 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 176 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 144 optimal weight: 50.0000 chunk 63 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 300 optimal weight: 10.0000 chunk 138 optimal weight: 0.0000 chunk 93 optimal weight: 1.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 15 GLN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 ASN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** G 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 ASN C 635 HIS ** F 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.094221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.080796 restraints weight = 125777.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.081901 restraints weight = 84086.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.081965 restraints weight = 57672.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.082259 restraints weight = 57441.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.082333 restraints weight = 52032.762| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 27182 Z= 0.203 Angle : 0.674 11.545 37034 Z= 0.354 Chirality : 0.045 0.192 4440 Planarity : 0.004 0.056 4915 Dihedral : 5.294 48.841 4130 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.05 % Favored : 91.90 % Rotamer: Outliers : 6.20 % Allowed : 21.40 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.13), residues: 3888 helix: 0.80 (0.14), residues: 1362 sheet: -1.55 (0.18), residues: 774 loop : -2.75 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 135 TYR 0.027 0.002 TYR C 660 PHE 0.054 0.002 PHE E 413 TRP 0.015 0.002 TRP I 9 HIS 0.010 0.002 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00438 (27182) covalent geometry : angle 0.67382 (37034) hydrogen bonds : bond 0.04226 ( 1375) hydrogen bonds : angle 4.89152 ( 4014) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 225 time to evaluate : 1.126 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: E 44 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7573 (tt) REVERT: E 173 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8497 (ttm) REVERT: E 315 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7689 (tp) REVERT: G 120 LEU cc_start: 0.8249 (tp) cc_final: 0.7806 (tp) REVERT: G 136 MET cc_start: 0.7384 (tpp) cc_final: 0.7136 (tpp) REVERT: G 190 HIS cc_start: 0.6760 (p-80) cc_final: 0.6127 (p-80) REVERT: C 636 GLU cc_start: 0.2543 (OUTLIER) cc_final: 0.1726 (mt-10) REVERT: F 137 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.7117 (pt) REVERT: F 243 MET cc_start: 0.6918 (mmm) cc_final: 0.6562 (mmm) REVERT: F 384 ASP cc_start: 0.6111 (m-30) cc_final: 0.5881 (m-30) REVERT: I 78 ILE cc_start: 0.7726 (mt) cc_final: 0.7513 (mt) REVERT: I 462 GLN cc_start: 0.4304 (mm-40) cc_final: 0.3834 (mm-40) REVERT: D 586 MET cc_start: 0.6344 (mpp) cc_final: 0.5684 (mmm) outliers start: 130 outliers final: 83 residues processed: 329 average time/residue: 0.1572 time to fit residues: 87.1629 Evaluate side-chains 292 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 204 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 63 HIS Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 173 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 279 CYS Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 108 PHE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 391 HIS Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 405 CYS Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 451 TYR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 45 PHE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 294 CYS Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 536 LEU Chi-restraints excluded: chain I residue 616 LEU Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 747 ASP Chi-restraints excluded: chain I residue 773 ASP Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 566 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 307 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 196 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 260 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 ASN G 74 ASN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN ** F 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 GLN ** I 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 652 HIS ** I 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 778 HIS ** D 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.095371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.082213 restraints weight = 124726.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.083036 restraints weight = 85178.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.083128 restraints weight = 58432.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.083464 restraints weight = 59739.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.083560 restraints weight = 49731.774| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27182 Z= 0.144 Angle : 0.613 9.742 37034 Z= 0.321 Chirality : 0.044 0.349 4440 Planarity : 0.004 0.048 4915 Dihedral : 4.937 49.087 4130 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.64 % Favored : 92.31 % Rotamer: Outliers : 5.39 % Allowed : 22.31 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.13), residues: 3888 helix: 1.13 (0.14), residues: 1354 sheet: -1.43 (0.18), residues: 796 loop : -2.59 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 129 TYR 0.031 0.001 TYR C 660 PHE 0.048 0.002 PHE E 413 TRP 0.013 0.001 TRP I 237 HIS 0.008 0.001 HIS I 94 Details of bonding type rmsd covalent geometry : bond 0.00309 (27182) covalent geometry : angle 0.61317 (37034) hydrogen bonds : bond 0.03908 ( 1375) hydrogen bonds : angle 4.57262 ( 4014) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 223 time to evaluate : 1.076 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: H 46 LYS cc_start: 0.8311 (mmtt) cc_final: 0.7621 (tptm) REVERT: B 599 LYS cc_start: 0.8439 (mmtt) cc_final: 0.8121 (pttt) REVERT: E 44 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7848 (tt) REVERT: E 373 LEU cc_start: 0.8284 (mm) cc_final: 0.8077 (tp) REVERT: G 120 LEU cc_start: 0.8190 (tp) cc_final: 0.7759 (tp) REVERT: G 136 MET cc_start: 0.7361 (tpp) cc_final: 0.7111 (tpp) REVERT: G 190 HIS cc_start: 0.6460 (p-80) cc_final: 0.6146 (p-80) REVERT: C 622 LYS cc_start: 0.7839 (mptt) cc_final: 0.7443 (ttmt) REVERT: C 636 GLU cc_start: 0.2744 (OUTLIER) cc_final: 0.1463 (mt-10) REVERT: C 647 ARG cc_start: 0.8060 (ttp-110) cc_final: 0.7333 (ptp-170) REVERT: F 243 MET cc_start: 0.6809 (mmm) cc_final: 0.6512 (mmm) REVERT: F 252 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7876 (ttmm) REVERT: F 313 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8398 (tp30) REVERT: F 384 ASP cc_start: 0.5719 (m-30) cc_final: 0.5498 (m-30) REVERT: I 78 ILE cc_start: 0.7666 (mt) cc_final: 0.7435 (mp) REVERT: I 95 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6092 (tt) REVERT: I 456 LYS cc_start: 0.2904 (OUTLIER) cc_final: 0.2526 (tptp) REVERT: I 462 GLN cc_start: 0.4250 (mm-40) cc_final: 0.3918 (mm-40) REVERT: D 558 LYS cc_start: 0.6332 (mttt) cc_final: 0.5815 (tptt) REVERT: D 586 MET cc_start: 0.6297 (mpp) cc_final: 0.5716 (mmm) outliers start: 113 outliers final: 72 residues processed: 308 average time/residue: 0.1565 time to fit residues: 81.2940 Evaluate side-chains 283 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 205 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 63 HIS Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 279 CYS Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 108 PHE Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 391 HIS Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 451 TYR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 45 PHE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 550 ILE Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 609 LEU Chi-restraints excluded: chain I residue 616 LEU Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 773 ASP Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 566 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 163 optimal weight: 40.0000 chunk 332 optimal weight: 0.2980 chunk 299 optimal weight: 20.0000 chunk 246 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 171 optimal weight: 20.0000 chunk 60 optimal weight: 0.9990 chunk 236 optimal weight: 4.9990 chunk 179 optimal weight: 20.0000 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN C 616 GLN C 633 GLN ** F 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 117 HIS ** I 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 778 HIS D 581 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.094861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.081182 restraints weight = 124759.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.082750 restraints weight = 79032.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.083279 restraints weight = 53331.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.083414 restraints weight = 49091.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.083542 restraints weight = 41412.857| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 27182 Z= 0.148 Angle : 0.607 9.063 37034 Z= 0.318 Chirality : 0.044 0.273 4440 Planarity : 0.004 0.051 4915 Dihedral : 4.811 48.922 4130 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.87 % Favored : 92.08 % Rotamer: Outliers : 6.05 % Allowed : 22.35 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.13), residues: 3888 helix: 1.24 (0.14), residues: 1352 sheet: -1.38 (0.18), residues: 788 loop : -2.51 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 129 TYR 0.021 0.001 TYR G 203 PHE 0.023 0.002 PHE F 182 TRP 0.013 0.001 TRP F 212 HIS 0.010 0.001 HIS F 449 Details of bonding type rmsd covalent geometry : bond 0.00323 (27182) covalent geometry : angle 0.60678 (37034) hydrogen bonds : bond 0.03826 ( 1375) hydrogen bonds : angle 4.50979 ( 4014) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 212 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 LYS cc_start: 0.8363 (mmtt) cc_final: 0.7744 (tptm) REVERT: E 44 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7906 (tt) REVERT: G 136 MET cc_start: 0.7477 (tpp) cc_final: 0.7241 (tpp) REVERT: G 190 HIS cc_start: 0.6405 (p-80) cc_final: 0.6141 (p-80) REVERT: C 622 LYS cc_start: 0.7791 (mptt) cc_final: 0.7467 (ttmt) REVERT: C 636 GLU cc_start: 0.3045 (OUTLIER) cc_final: 0.1644 (mt-10) REVERT: F 243 MET cc_start: 0.6851 (mmm) cc_final: 0.6555 (mmm) REVERT: F 252 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7991 (ttmm) REVERT: F 313 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8431 (tp30) REVERT: F 410 LEU cc_start: 0.7441 (mt) cc_final: 0.7184 (mt) REVERT: I 78 ILE cc_start: 0.7725 (mt) cc_final: 0.7513 (mp) REVERT: I 95 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.5906 (tt) REVERT: I 456 LYS cc_start: 0.2836 (OUTLIER) cc_final: 0.2504 (tptp) REVERT: D 558 LYS cc_start: 0.6403 (mttt) cc_final: 0.5998 (tptt) REVERT: D 586 MET cc_start: 0.6331 (mpp) cc_final: 0.5779 (mmm) outliers start: 127 outliers final: 88 residues processed: 315 average time/residue: 0.1461 time to fit residues: 77.8664 Evaluate side-chains 298 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 204 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 63 HIS Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 279 CYS Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 108 PHE Chi-restraints excluded: chain G residue 203 TYR Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 351 ASN Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 391 HIS Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 451 TYR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 45 PHE Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 536 LEU Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 609 LEU Chi-restraints excluded: chain I residue 616 LEU Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 696 ASP Chi-restraints excluded: chain I residue 747 ASP Chi-restraints excluded: chain I residue 773 ASP Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 563 ILE Chi-restraints excluded: chain D residue 566 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 233 optimal weight: 1.9990 chunk 265 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 147 optimal weight: 50.0000 chunk 14 optimal weight: 20.0000 chunk 165 optimal weight: 30.0000 chunk 322 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 GLN ** F 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 761 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.093536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.080674 restraints weight = 124852.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.081286 restraints weight = 84859.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.081451 restraints weight = 59529.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.081663 restraints weight = 59314.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.081725 restraints weight = 52898.011| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.6239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 27182 Z= 0.185 Angle : 0.649 11.621 37034 Z= 0.340 Chirality : 0.046 0.391 4440 Planarity : 0.004 0.061 4915 Dihedral : 4.950 48.415 4130 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.72 % Favored : 91.23 % Rotamer: Outliers : 5.86 % Allowed : 22.78 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.13), residues: 3888 helix: 1.13 (0.14), residues: 1357 sheet: -1.24 (0.18), residues: 761 loop : -2.56 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 712 TYR 0.031 0.002 TYR G 131 PHE 0.019 0.002 PHE F 160 TRP 0.015 0.002 TRP I 9 HIS 0.011 0.001 HIS F 449 Details of bonding type rmsd covalent geometry : bond 0.00406 (27182) covalent geometry : angle 0.64904 (37034) hydrogen bonds : bond 0.04034 ( 1375) hydrogen bonds : angle 4.64189 ( 4014) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 210 time to evaluate : 1.076 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: B 599 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8160 (pttt) REVERT: E 44 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8004 (tt) REVERT: E 315 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7694 (tp) REVERT: G 109 ILE cc_start: 0.8378 (mt) cc_final: 0.8133 (mp) REVERT: G 136 MET cc_start: 0.7530 (tpp) cc_final: 0.7264 (tpp) REVERT: G 190 HIS cc_start: 0.6282 (p-80) cc_final: 0.6038 (p-80) REVERT: F 243 MET cc_start: 0.6866 (mmm) cc_final: 0.6628 (mmm) REVERT: F 313 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8526 (tp30) REVERT: F 357 PHE cc_start: 0.8066 (t80) cc_final: 0.7505 (t80) REVERT: I 75 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6473 (mmp80) REVERT: I 95 LEU cc_start: 0.6652 (OUTLIER) cc_final: 0.6073 (tt) REVERT: I 349 SER cc_start: 0.8527 (t) cc_final: 0.8064 (p) REVERT: D 558 LYS cc_start: 0.6399 (mttt) cc_final: 0.5874 (tptt) REVERT: D 586 MET cc_start: 0.6198 (mpp) cc_final: 0.5872 (mmm) outliers start: 123 outliers final: 93 residues processed: 310 average time/residue: 0.1555 time to fit residues: 81.2281 Evaluate side-chains 296 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 198 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 63 HIS Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 157 GLN Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 273 TRP Chi-restraints excluded: chain E residue 279 CYS Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 108 PHE Chi-restraints excluded: chain G residue 203 TYR Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 229 GLU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 344 TYR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 391 HIS Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 451 TYR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 45 PHE Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 536 LEU Chi-restraints excluded: chain I residue 609 LEU Chi-restraints excluded: chain I residue 616 LEU Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 696 ASP Chi-restraints excluded: chain I residue 737 LEU Chi-restraints excluded: chain I residue 747 ASP Chi-restraints excluded: chain I residue 773 ASP Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 563 ILE Chi-restraints excluded: chain D residue 566 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 149 optimal weight: 50.0000 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 339 optimal weight: 9.9990 chunk 37 optimal weight: 30.0000 chunk 114 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 188 optimal weight: 40.0000 chunk 234 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 657 GLN F 205 HIS F 216 GLN ** F 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 HIS ** F 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 778 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.091794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.077941 restraints weight = 127460.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.078835 restraints weight = 85783.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.078786 restraints weight = 62584.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.079192 restraints weight = 58719.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.079379 restraints weight = 51531.507| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.6527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27182 Z= 0.180 Angle : 0.653 10.899 37034 Z= 0.341 Chirality : 0.045 0.287 4440 Planarity : 0.004 0.095 4915 Dihedral : 4.950 48.814 4130 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.51 % Favored : 91.44 % Rotamer: Outliers : 5.72 % Allowed : 23.12 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.13), residues: 3888 helix: 1.09 (0.14), residues: 1356 sheet: -1.27 (0.18), residues: 774 loop : -2.57 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 129 TYR 0.034 0.002 TYR G 131 PHE 0.018 0.002 PHE F 182 TRP 0.017 0.002 TRP G 168 HIS 0.010 0.001 HIS F 449 Details of bonding type rmsd covalent geometry : bond 0.00393 (27182) covalent geometry : angle 0.65295 (37034) hydrogen bonds : bond 0.04021 ( 1375) hydrogen bonds : angle 4.67294 ( 4014) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 213 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 LYS cc_start: 0.8726 (mmmt) cc_final: 0.7953 (tptm) REVERT: B 599 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8061 (pttt) REVERT: E 44 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7959 (tt) REVERT: G 136 MET cc_start: 0.7352 (tpp) cc_final: 0.7076 (tpp) REVERT: G 190 HIS cc_start: 0.6823 (p-80) cc_final: 0.6597 (p-80) REVERT: C 622 LYS cc_start: 0.7891 (mptt) cc_final: 0.7505 (ttmt) REVERT: F 243 MET cc_start: 0.6986 (mmm) cc_final: 0.6655 (mmm) REVERT: F 313 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8517 (tp30) REVERT: F 357 PHE cc_start: 0.8097 (t80) cc_final: 0.7564 (t80) REVERT: I 75 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6597 (mmp80) REVERT: I 95 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6406 (tt) REVERT: I 349 SER cc_start: 0.8517 (t) cc_final: 0.7967 (p) REVERT: I 456 LYS cc_start: 0.2961 (OUTLIER) cc_final: 0.2722 (tptp) REVERT: D 558 LYS cc_start: 0.6290 (mttt) cc_final: 0.5700 (tptt) REVERT: D 586 MET cc_start: 0.6397 (mpp) cc_final: 0.5823 (mmm) outliers start: 120 outliers final: 100 residues processed: 308 average time/residue: 0.1518 time to fit residues: 79.4907 Evaluate side-chains 303 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 198 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 63 HIS Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 144 CYS Chi-restraints excluded: chain E residue 157 GLN Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 273 TRP Chi-restraints excluded: chain E residue 279 CYS Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 108 PHE Chi-restraints excluded: chain G residue 203 TYR Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 229 GLU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 267 PHE Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 344 TYR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 451 TYR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 45 PHE Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 294 CYS Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 609 LEU Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 640 VAL Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 696 ASP Chi-restraints excluded: chain I residue 747 ASP Chi-restraints excluded: chain I residue 773 ASP Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 563 ILE Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 569 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 248 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 251 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 chunk 257 optimal weight: 0.2980 chunk 129 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 chunk 359 optimal weight: 50.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 ASN F 311 HIS ** F 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.093355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.079109 restraints weight = 124331.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.080489 restraints weight = 79379.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.080468 restraints weight = 51927.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.080780 restraints weight = 51731.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.081018 restraints weight = 44730.977| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.6586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 27182 Z= 0.127 Angle : 0.615 11.521 37034 Z= 0.319 Chirality : 0.044 0.219 4440 Planarity : 0.004 0.061 4915 Dihedral : 4.653 49.470 4130 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.56 % Favored : 92.39 % Rotamer: Outliers : 4.48 % Allowed : 24.88 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.13), residues: 3888 helix: 1.33 (0.14), residues: 1362 sheet: -1.26 (0.18), residues: 789 loop : -2.47 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 647 TYR 0.028 0.001 TYR G 131 PHE 0.019 0.002 PHE F 160 TRP 0.020 0.002 TRP I 610 HIS 0.009 0.001 HIS F 449 Details of bonding type rmsd covalent geometry : bond 0.00277 (27182) covalent geometry : angle 0.61547 (37034) hydrogen bonds : bond 0.03703 ( 1375) hydrogen bonds : angle 4.42175 ( 4014) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 216 time to evaluate : 1.031 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: H 23 ILE cc_start: 0.8362 (mt) cc_final: 0.8155 (tp) REVERT: H 46 LYS cc_start: 0.8764 (mmmt) cc_final: 0.7964 (tptm) REVERT: H 49 GLN cc_start: 0.8414 (tp-100) cc_final: 0.8110 (tp-100) REVERT: E 44 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7869 (tt) REVERT: E 342 MET cc_start: 0.7969 (ppp) cc_final: 0.7244 (ppp) REVERT: G 22 MET cc_start: 0.7656 (mtp) cc_final: 0.7455 (ttt) REVERT: G 109 ILE cc_start: 0.8178 (mt) cc_final: 0.7933 (mp) REVERT: G 136 MET cc_start: 0.7380 (tpp) cc_final: 0.7111 (tpp) REVERT: G 190 HIS cc_start: 0.6896 (p-80) cc_final: 0.6641 (p-80) REVERT: C 622 LYS cc_start: 0.7753 (mptt) cc_final: 0.7541 (ttpt) REVERT: C 626 ILE cc_start: 0.6181 (OUTLIER) cc_final: 0.5136 (mt) REVERT: C 636 GLU cc_start: 0.2979 (OUTLIER) cc_final: 0.2278 (mt-10) REVERT: C 650 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7233 (mm) REVERT: F 243 MET cc_start: 0.6878 (mmm) cc_final: 0.6524 (mmm) REVERT: F 252 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8304 (ttmm) REVERT: F 313 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8394 (tp30) REVERT: F 357 PHE cc_start: 0.8218 (t80) cc_final: 0.7625 (t80) REVERT: I 95 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6506 (tt) REVERT: I 349 SER cc_start: 0.8530 (t) cc_final: 0.7975 (p) REVERT: I 350 ASP cc_start: 0.8380 (p0) cc_final: 0.8159 (p0) REVERT: I 578 MET cc_start: 0.6813 (tpt) cc_final: 0.6384 (tpp) REVERT: D 540 LEU cc_start: 0.7629 (mt) cc_final: 0.7038 (mp) REVERT: D 558 LYS cc_start: 0.6146 (mttt) cc_final: 0.5520 (tttt) REVERT: D 586 MET cc_start: 0.6326 (mpp) cc_final: 0.5829 (mmm) outliers start: 94 outliers final: 73 residues processed: 291 average time/residue: 0.1551 time to fit residues: 76.7899 Evaluate side-chains 282 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 202 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 63 HIS Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 157 GLN Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 279 CYS Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 108 PHE Chi-restraints excluded: chain G residue 203 TYR Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 229 GLU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 344 TYR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 45 PHE Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 550 ILE Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 609 LEU Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 640 VAL Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 696 ASP Chi-restraints excluded: chain I residue 747 ASP Chi-restraints excluded: chain I residue 773 ASP Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 569 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 369 optimal weight: 20.0000 chunk 366 optimal weight: 20.0000 chunk 360 optimal weight: 20.0000 chunk 269 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 255 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 265 optimal weight: 8.9990 chunk 367 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 15 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 350 ASN G 60 HIS G 128 HIS ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 ASN C 598 ASN ** C 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 761 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.088714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.075528 restraints weight = 128481.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.076338 restraints weight = 82464.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.076906 restraints weight = 62531.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.076932 restraints weight = 49896.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.077017 restraints weight = 47419.361| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.7245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 27182 Z= 0.336 Angle : 0.871 11.892 37034 Z= 0.456 Chirality : 0.051 0.258 4440 Planarity : 0.005 0.094 4915 Dihedral : 5.840 48.749 4130 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.06 % Favored : 88.86 % Rotamer: Outliers : 4.67 % Allowed : 25.26 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.13), residues: 3888 helix: 0.35 (0.13), residues: 1365 sheet: -1.54 (0.18), residues: 764 loop : -2.74 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 15 TYR 0.035 0.003 TYR G 131 PHE 0.036 0.003 PHE I 684 TRP 0.030 0.004 TRP G 168 HIS 0.011 0.003 HIS F 449 Details of bonding type rmsd covalent geometry : bond 0.00730 (27182) covalent geometry : angle 0.87101 (37034) hydrogen bonds : bond 0.05172 ( 1375) hydrogen bonds : angle 5.50743 ( 4014) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 193 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 23 ILE cc_start: 0.8437 (mt) cc_final: 0.8169 (tp) REVERT: B 599 LYS cc_start: 0.8479 (mmtt) cc_final: 0.8214 (pttt) REVERT: E 44 ILE cc_start: 0.8475 (tt) cc_final: 0.8100 (tt) REVERT: E 315 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7957 (tp) REVERT: C 647 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7179 (ptp-170) REVERT: F 243 MET cc_start: 0.7288 (mmm) cc_final: 0.6981 (mmm) REVERT: F 313 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8123 (tp30) REVERT: F 357 PHE cc_start: 0.8329 (t80) cc_final: 0.7621 (t80) REVERT: I 95 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6539 (tt) REVERT: I 349 SER cc_start: 0.8541 (t) cc_final: 0.8098 (p) REVERT: I 462 GLN cc_start: 0.4682 (mm-40) cc_final: 0.4365 (mm-40) REVERT: I 513 GLU cc_start: 0.7809 (pm20) cc_final: 0.7474 (tp30) REVERT: D 558 LYS cc_start: 0.6450 (mttt) cc_final: 0.5776 (tttt) REVERT: D 586 MET cc_start: 0.6474 (mpp) cc_final: 0.6114 (mmm) outliers start: 98 outliers final: 76 residues processed: 269 average time/residue: 0.1484 time to fit residues: 68.6372 Evaluate side-chains 266 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 186 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain E residue 63 HIS Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 273 TRP Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 108 PHE Chi-restraints excluded: chain G residue 203 TYR Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 647 ARG Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 229 GLU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 344 TYR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 45 PHE Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 294 CYS Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 609 LEU Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain I residue 694 HIS Chi-restraints excluded: chain I residue 696 ASP Chi-restraints excluded: chain I residue 747 ASP Chi-restraints excluded: chain I residue 773 ASP Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 569 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 38 optimal weight: 50.0000 chunk 5 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 chunk 324 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 chunk 103 optimal weight: 0.0470 chunk 323 optimal weight: 20.0000 chunk 202 optimal weight: 0.9980 chunk 282 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 156 optimal weight: 40.0000 overall best weight: 2.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 677 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 HIS G 162 ASN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 ASN ** C 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.090718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.077430 restraints weight = 127311.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.078171 restraints weight = 79609.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.078680 restraints weight = 59534.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.078884 restraints weight = 49348.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.078952 restraints weight = 46066.750| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.7223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 27182 Z= 0.179 Angle : 0.690 10.574 37034 Z= 0.360 Chirality : 0.046 0.242 4440 Planarity : 0.004 0.067 4915 Dihedral : 5.258 48.736 4130 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.31 % Favored : 91.64 % Rotamer: Outliers : 3.81 % Allowed : 26.74 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.13), residues: 3888 helix: 0.88 (0.13), residues: 1349 sheet: -1.48 (0.18), residues: 756 loop : -2.64 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 647 TYR 0.028 0.002 TYR G 131 PHE 0.023 0.002 PHE I 684 TRP 0.022 0.002 TRP G 168 HIS 0.012 0.002 HIS F 449 Details of bonding type rmsd covalent geometry : bond 0.00394 (27182) covalent geometry : angle 0.69026 (37034) hydrogen bonds : bond 0.04218 ( 1375) hydrogen bonds : angle 4.95045 ( 4014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4085.04 seconds wall clock time: 71 minutes 43.81 seconds (4303.81 seconds total)