Starting phenix.real_space_refine on Fri Mar 6 02:14:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vnw_21251/03_2026/6vnw_21251.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vnw_21251/03_2026/6vnw_21251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vnw_21251/03_2026/6vnw_21251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vnw_21251/03_2026/6vnw_21251.map" model { file = "/net/cci-nas-00/data/ceres_data/6vnw_21251/03_2026/6vnw_21251.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vnw_21251/03_2026/6vnw_21251.cif" } resolution = 3.44 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= 0.005 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 114 5.16 5 C 17361 2.51 5 N 4848 2.21 5 O 5163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 187 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: 27486 Number of models: 1 Model: "" Number of chains: 8 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: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 3957 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 361} Link IDs: {'PTRANS': 22, 'TRANS': 636} Chain breaks: 4 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1256 Unresolved non-hydrogen angles: 1625 Unresolved non-hydrogen dihedrals: 1031 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'GLN:plan1': 12, 'PHE:plan': 18, 'ARG:plan': 19, 'HIS:plan': 15, 'TYR:plan': 14, 'ASP:plan': 26, 'ASN:plan1': 21, 'GLU:plan': 23, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 684 Chain: "E" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3107 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 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: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 3666 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 482} Link IDs: {'PTRANS': 25, 'TRANS': 639} Chain breaks: 8 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1679 Unresolved non-hydrogen angles: 2149 Unresolved non-hydrogen dihedrals: 1378 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': 35, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 902 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: "D" Number of atoms: 4093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4093 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 33, 'TRANS': 494} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 4.99, per 1000 atoms: 0.18 Number of scatterers: 27486 At special positions: 0 Unit cell: (124.8, 146.9, 205.4, 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 114 16.00 O 5163 8.00 N 4848 7.00 C 17361 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: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7214 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 46 sheets defined 36.2% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 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 490 through 494 removed outlier: 3.970A pdb=" N GLU B 494 " --> pdb=" O PRO B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 517 Processing helix chain 'B' and resid 560 through 575 Processing helix chain 'B' and resid 586 through 634 removed outlier: 3.548A pdb=" N GLU B 592 " --> pdb=" O VAL B 588 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP B 601 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 4.128A 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 689 through 704 removed outlier: 3.525A pdb=" N GLN B 693 " --> pdb=" O LYS B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 716 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.832A pdb=" N ILE E 44 " --> pdb=" O HIS E 40 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN E 45 " --> pdb=" O LEU E 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 45' Processing helix chain 'E' and resid 49 through 63 removed outlier: 3.608A pdb=" N ILE E 55 " --> pdb=" O CYS E 51 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN E 60 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 80 Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 100 through 114 removed outlier: 3.677A 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: 3.752A pdb=" N GLU E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 148 removed outlier: 4.273A 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: 3.979A 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: 3.805A 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: 3.904A 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 349 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: 3.758A 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: 3.869A 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: 4.936A pdb=" N ALA C 628 " --> pdb=" O GLN C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 639 removed outlier: 3.918A pdb=" N ASN C 638 " --> pdb=" O HIS C 635 " (cutoff:3.500A) removed outlier: 3.755A 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: 3.826A pdb=" N GLU C 651 " --> pdb=" O ARG C 647 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU C 652 " --> pdb=" O CYS C 648 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ASP C 654 " --> pdb=" O LEU C 650 " (cutoff:3.500A) removed outlier: 5.756A 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: 3.615A 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: 3.616A pdb=" N GLN F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 48 removed outlier: 3.607A pdb=" N TRP F 37 " --> pdb=" O ASP F 33 " (cutoff:3.500A) removed outlier: 3.882A 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 58 through 66 removed outlier: 4.153A pdb=" N GLU F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 3.643A 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: 3.651A 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: 3.690A 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: 3.747A 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: 4.167A pdb=" N TRP I 610 " --> pdb=" O PHE I 606 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU I 611 " --> pdb=" O GLU I 607 " (cutoff:3.500A) removed outlier: 4.092A 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 'D' and resid 132 through 137 removed outlier: 3.803A pdb=" N ASP D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 142 removed outlier: 3.896A pdb=" N GLN D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 153 removed outlier: 4.059A pdb=" N LYS D 153 " --> pdb=" O PRO D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 190 removed outlier: 3.575A pdb=" N HIS D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.568A 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 289 through 293 removed outlier: 4.768A pdb=" N GLU B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN D 365 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 357 " --> pdb=" O ASN D 365 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 367 " --> pdb=" O VAL D 355 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 22 removed outlier: 3.890A 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: 6.548A pdb=" N ASP B 104 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.182A 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: 4.392A 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: 4.423A 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: 6.778A 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: 4.670A 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: 4.423A 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: 6.778A 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 531 through 536 Processing sheet with id=AB4, first strand: chain 'G' and resid 13 through 15 removed outlier: 3.520A 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: 4.206A 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: 4.128A 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: 4.101A 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: 6.804A 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: 6.884A 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: 3.955A 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: 3.799A 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: 6.263A pdb=" N CYS C 133 " --> pdb=" O ASP C 137 " (cutoff:3.500A) removed outlier: 5.867A 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: 4.054A pdb=" N ASP C 282 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.628A 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: 5.559A pdb=" N TYR I 358 " --> pdb=" O ASP I 8 " (cutoff:3.500A) removed outlier: 4.313A 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: 3.581A 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: 6.555A 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: 3.732A 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: 5.573A pdb=" N LYS I 454 " --> pdb=" O SER I 509 " (cutoff:3.500A) removed outlier: 4.310A 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 'D' and resid 45 through 46 Processing sheet with id=AE4, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AE5, first strand: chain 'D' and resid 200 through 202 removed outlier: 3.706A pdb=" N ALA D 240 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ASP D 232 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE D 238 " --> pdb=" O ASP D 232 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 272 through 273 Processing sheet with id=AE7, first strand: chain 'D' and resid 295 through 297 removed outlier: 3.749A pdb=" N VAL D 296 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D 303 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU D 311 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR D 323 " --> pdb=" O LEU D 311 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY D 313 " --> pdb=" O LEU D 321 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 390 through 391 Processing sheet with id=AE9, first strand: chain 'D' and resid 487 through 493 Processing sheet with id=AF1, first strand: chain 'D' and resid 534 through 536 1414 hydrogen bonds defined for protein. 4053 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: 2.87 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: 4824 1.32 - 1.44: 6800 1.44 - 1.57: 16118 1.57 - 1.69: 0 1.69 - 1.82: 175 Bond restraints: 27917 Sorted by residual: bond pdb=" CA ALA B 167 " pdb=" CB ALA B 167 " ideal model delta sigma weight residual 1.534 1.474 0.060 1.76e-02 3.23e+03 1.15e+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 1.08e+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 1.196 0.037 1.16e-02 7.43e+03 1.01e+01 bond pdb=" N VAL B 257 " pdb=" CA VAL B 257 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.17e-02 7.31e+03 9.67e+00 ... (remaining 27912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 36662 1.92 - 3.84: 1017 3.84 - 5.76: 193 5.76 - 7.69: 48 7.69 - 9.61: 16 Bond angle restraints: 37936 Sorted by residual: 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 7.05e+01 angle pdb=" N THR B 487 " pdb=" CA THR B 487 " pdb=" C THR B 487 " ideal model delta sigma weight residual 108.07 116.75 -8.68 1.38e+00 5.25e-01 3.95e+01 angle pdb=" N HIS E 40 " pdb=" CA HIS E 40 " pdb=" C HIS E 40 " ideal model delta sigma weight residual 114.09 105.07 9.02 1.55e+00 4.16e-01 3.38e+01 angle pdb=" C ASP B 251 " pdb=" CA ASP B 251 " pdb=" CB ASP B 251 " ideal model delta sigma weight residual 111.70 103.14 8.56 1.48e+00 4.57e-01 3.34e+01 angle pdb=" N GLN F 17 " pdb=" CA GLN F 17 " pdb=" C GLN F 17 " ideal model delta sigma weight residual 112.72 105.67 7.05 1.28e+00 6.10e-01 3.03e+01 ... (remaining 37931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 15104 17.71 - 35.41: 1372 35.41 - 53.12: 252 53.12 - 70.82: 49 70.82 - 88.53: 26 Dihedral angle restraints: 16803 sinusoidal: 5682 harmonic: 11121 Sorted by residual: 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 -137.29 14.69 0 2.50e+00 1.60e-01 3.45e+01 dihedral pdb=" CA GLY D 50 " pdb=" C GLY D 50 " pdb=" N GLU D 51 " pdb=" CA GLU D 51 " ideal model delta harmonic sigma weight residual 180.00 150.77 29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA THR G 40 " pdb=" C THR G 40 " pdb=" N LYS G 41 " pdb=" CA LYS G 41 " ideal model delta harmonic sigma weight residual 180.00 -151.20 -28.80 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 16800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4125 0.096 - 0.193: 297 0.193 - 0.289: 28 0.289 - 0.385: 11 0.385 - 0.481: 3 Chirality restraints: 4464 Sorted by residual: 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 5.79e+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 5.56e+00 chirality pdb=" CA GLU B 259 " pdb=" N GLU B 259 " pdb=" C GLU B 259 " pdb=" CB GLU B 259 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.77e+00 ... (remaining 4461 not shown) Planarity restraints: 4968 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 3.20e-02 1.03e+01 pdb=" C PHE B 250 " -0.055 2.00e-02 2.50e+03 pdb=" O PHE B 250 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP B 251 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 347 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.10e+00 pdb=" C ALA E 347 " 0.049 2.00e-02 2.50e+03 pdb=" O ALA E 347 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU E 348 " -0.017 2.00e-02 2.50e+03 ... (remaining 4965 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 370 2.64 - 3.21: 24762 3.21 - 3.77: 40946 3.77 - 4.34: 55101 4.34 - 4.90: 91776 Nonbonded interactions: 212955 Sorted by model distance: nonbonded pdb=" O HIS E 40 " pdb=" ND1 HIS E 40 " model vdw 2.078 3.120 nonbonded pdb=" OE1 GLU F 2 " pdb=" OG1 THR I 134 " model vdw 2.202 3.040 nonbonded pdb=" CZ PHE I 724 " pdb=" O LEU I 759 " model vdw 2.205 3.340 nonbonded pdb=" OG1 THR G 83 " pdb=" OE1 GLU G 93 " model vdw 2.208 3.040 nonbonded pdb=" N LEU G 88 " pdb=" OE2 GLU F 379 " model vdw 2.222 3.120 ... (remaining 212950 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 individual isotropic 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.360 Find NCS groups from input model: 0.180 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 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 0.065 27917 Z= 0.251 Angle : 0.806 9.608 37936 Z= 0.483 Chirality : 0.055 0.481 4464 Planarity : 0.004 0.062 4968 Dihedral : 14.769 88.528 9589 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.12 % Favored : 91.74 % Rotamer: Outliers : 2.05 % Allowed : 6.87 % Favored : 91.08 % Cbeta Deviations : 0.19 % 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: -3.20 (0.12), residues: 3767 helix: -0.54 (0.13), residues: 1287 sheet: -2.28 (0.16), residues: 836 loop : -3.37 (0.13), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 12 TYR 0.023 0.002 TYR E 43 PHE 0.019 0.002 PHE D 46 TRP 0.017 0.002 TRP I 237 HIS 0.011 0.001 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00439 (27917) covalent geometry : angle 0.80632 (37936) hydrogen bonds : bond 0.13709 ( 1396) hydrogen bonds : angle 6.46679 ( 4053) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 690 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 LYS cc_start: 0.7672 (mtpt) cc_final: 0.7444 (mmtt) REVERT: B 555 THR cc_start: 0.5727 (m) cc_final: 0.5380 (m) REVERT: B 629 GLU cc_start: 0.7491 (tp30) cc_final: 0.7243 (mm-30) REVERT: B 660 ILE cc_start: 0.8300 (tp) cc_final: 0.8059 (mt) REVERT: B 684 HIS cc_start: 0.8044 (t70) cc_final: 0.7812 (t-90) REVERT: E 57 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7283 (tt0) REVERT: E 61 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5516 (tt0) REVERT: E 361 TYR cc_start: 0.6035 (m-80) cc_final: 0.5809 (m-80) REVERT: E 414 ASP cc_start: 0.5145 (m-30) cc_final: 0.4636 (m-30) REVERT: G 9 GLU cc_start: 0.7721 (mp0) cc_final: 0.7508 (mp0) REVERT: G 249 GLU cc_start: 0.7736 (pp20) cc_final: 0.7404 (pp20) REVERT: C 622 LYS cc_start: 0.7831 (mttt) cc_final: 0.7284 (mttt) REVERT: C 648 CYS cc_start: 0.7042 (m) cc_final: 0.6520 (p) REVERT: C 681 LYS cc_start: 0.6082 (pptt) cc_final: 0.5742 (mttt) REVERT: F 22 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6410 (tt) REVERT: F 79 SER cc_start: 0.8141 (t) cc_final: 0.7893 (p) REVERT: F 326 ASP cc_start: 0.8015 (p0) cc_final: 0.7581 (t0) REVERT: I 285 TYR cc_start: 0.8651 (p90) cc_final: 0.8407 (p90) REVERT: I 301 ILE cc_start: 0.8162 (mt) cc_final: 0.7754 (mt) REVERT: I 325 GLN cc_start: 0.8187 (tt0) cc_final: 0.7934 (tt0) outliers start: 51 outliers final: 16 residues processed: 729 average time/residue: 0.1783 time to fit residues: 203.4213 Evaluate side-chains 446 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 427 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 413 PHE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 225 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.0570 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 50.0000 chunk 298 optimal weight: 2.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN B 651 ASN B 705 ASN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 HIS ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 ASN G 74 ASN ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 ASN G 176 ASN G 190 HIS G 194 ASN G 205 GLN G 334 GLN C 610 HIS ** C 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 216 GLN F 233 GLN F 259 GLN F 307 GLN F 322 HIS F 350 ASN F 351 ASN ** F 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 HIS F 454 HIS F 456 ASN F 496 GLN I 120 GLN I 201 GLN I 651 HIS I 652 HIS I 672 GLN I 677 GLN I 693 GLN D 65 GLN D 74 HIS D 97 HIS D 197 GLN D 225 ASN D 291 GLN D 449 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.232352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.4252 r_free = 0.4252 target = 0.186087 restraints weight = 34842.415| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 5.25 r_work: 0.3715 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27917 Z= 0.167 Angle : 0.673 12.029 37936 Z= 0.347 Chirality : 0.046 0.197 4464 Planarity : 0.004 0.056 4968 Dihedral : 6.184 107.381 4075 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.53 % Favored : 93.44 % Rotamer: Outliers : 2.77 % Allowed : 15.82 % Favored : 81.41 % 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: -1.94 (0.13), residues: 3767 helix: 0.81 (0.14), residues: 1312 sheet: -1.84 (0.17), residues: 852 loop : -2.82 (0.14), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 598 TYR 0.027 0.002 TYR C 660 PHE 0.025 0.002 PHE B 501 TRP 0.014 0.001 TRP I 237 HIS 0.021 0.002 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00368 (27917) covalent geometry : angle 0.67313 (37936) hydrogen bonds : bond 0.04290 ( 1396) hydrogen bonds : angle 4.84055 ( 4053) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 454 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 506 ARG cc_start: 0.8247 (mmm160) cc_final: 0.7912 (mmm160) REVERT: B 555 THR cc_start: 0.7156 (m) cc_final: 0.6902 (m) REVERT: B 560 ASP cc_start: 0.6982 (t0) cc_final: 0.6713 (t0) REVERT: B 629 GLU cc_start: 0.8239 (tp30) cc_final: 0.7629 (mm-30) REVERT: B 660 ILE cc_start: 0.8630 (tp) cc_final: 0.8283 (mt) REVERT: B 684 HIS cc_start: 0.8101 (t70) cc_final: 0.7873 (t-90) REVERT: E 342 MET cc_start: 0.8230 (tmm) cc_final: 0.7913 (tmm) REVERT: G 82 ARG cc_start: 0.6580 (tpp-160) cc_final: 0.6310 (tpp-160) REVERT: G 129 ARG cc_start: 0.7954 (tpm170) cc_final: 0.7323 (ttp-110) REVERT: G 132 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8142 (pt0) REVERT: G 181 PHE cc_start: 0.8534 (m-80) cc_final: 0.8322 (m-10) REVERT: G 194 ASN cc_start: 0.7284 (OUTLIER) cc_final: 0.6916 (t160) REVERT: G 249 GLU cc_start: 0.8280 (pp20) cc_final: 0.7750 (pp20) REVERT: C 648 CYS cc_start: 0.7830 (m) cc_final: 0.7530 (m) REVERT: C 657 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7264 (mm-40) REVERT: C 670 LEU cc_start: 0.6516 (mp) cc_final: 0.6122 (mt) REVERT: F 62 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7128 (mm-30) REVERT: F 79 SER cc_start: 0.8405 (t) cc_final: 0.8008 (p) REVERT: F 326 ASP cc_start: 0.8054 (p0) cc_final: 0.7602 (t0) REVERT: F 469 ARG cc_start: 0.6997 (tpp80) cc_final: 0.6793 (tpp80) REVERT: I 16 ASP cc_start: 0.7313 (p0) cc_final: 0.6980 (p0) REVERT: I 243 GLU cc_start: 0.8065 (pm20) cc_final: 0.7791 (pm20) REVERT: I 411 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7484 (tp) REVERT: I 456 LYS cc_start: 0.7453 (mmmt) cc_final: 0.6961 (ttpp) REVERT: I 598 ARG cc_start: 0.7917 (ptp-110) cc_final: 0.7441 (ptp-110) REVERT: D 94 MET cc_start: 0.4336 (ttt) cc_final: 0.3563 (tpt) REVERT: D 333 MET cc_start: 0.6921 (mtm) cc_final: 0.6459 (ptp) outliers start: 69 outliers final: 35 residues processed: 503 average time/residue: 0.1679 time to fit residues: 136.4833 Evaluate side-chains 417 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 380 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain G residue 47 ARG Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 194 ASN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 205 TYR Chi-restraints excluded: chain I residue 249 CYS Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 411 LEU Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 485 VAL Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 583 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 272 optimal weight: 0.6980 chunk 188 optimal weight: 7.9990 chunk 301 optimal weight: 3.9990 chunk 337 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 156 optimal weight: 50.0000 chunk 117 optimal weight: 2.9990 chunk 341 optimal weight: 20.0000 chunk 91 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN B 608 GLN E 99 GLN E 106 GLN E 139 HIS ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 HIS G 102 ASN ** G 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 ASN F 123 GLN F 162 ASN F 188 HIS F 360 GLN ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 456 ASN I 73 HIS ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 HIS I 377 ASN I 420 ASN I 448 ASN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 515 ASN I 587 GLN I 717 GLN I 778 HIS D 97 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.207934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.162263 restraints weight = 34468.666| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.18 r_work: 0.3525 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.122 27917 Z= 0.378 Angle : 0.857 16.715 37936 Z= 0.442 Chirality : 0.053 0.283 4464 Planarity : 0.005 0.051 4968 Dihedral : 5.756 59.133 4043 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.10 % Favored : 91.82 % Rotamer: Outliers : 6.14 % Allowed : 18.19 % Favored : 75.66 % 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: -2.03 (0.13), residues: 3767 helix: 0.47 (0.14), residues: 1327 sheet: -1.80 (0.17), residues: 845 loop : -2.69 (0.14), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 509 TYR 0.033 0.003 TYR F 300 PHE 0.047 0.003 PHE I 45 TRP 0.028 0.003 TRP I 237 HIS 0.015 0.003 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00895 (27917) covalent geometry : angle 0.85735 (37936) hydrogen bonds : bond 0.05330 ( 1396) hydrogen bonds : angle 5.23813 ( 4053) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 413 time to evaluate : 1.037 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 7 MET cc_start: 0.7853 (tmm) cc_final: 0.7435 (tmm) REVERT: H 10 GLU cc_start: 0.8203 (mp0) cc_final: 0.7977 (mp0) REVERT: H 40 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8585 (m) REVERT: B 519 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7809 (mm) REVERT: B 575 PHE cc_start: 0.7666 (m-10) cc_final: 0.7410 (m-10) REVERT: E 58 GLN cc_start: 0.6224 (OUTLIER) cc_final: 0.5969 (tm-30) REVERT: E 110 SER cc_start: 0.8007 (OUTLIER) cc_final: 0.7502 (m) REVERT: E 123 VAL cc_start: 0.6194 (p) cc_final: 0.5975 (t) REVERT: E 235 ASN cc_start: 0.7447 (t0) cc_final: 0.7141 (t0) REVERT: E 245 MET cc_start: 0.8019 (ptt) cc_final: 0.7804 (ptp) REVERT: E 336 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7528 (tmtt) REVERT: E 423 LYS cc_start: 0.9044 (mmtm) cc_final: 0.8818 (mmtp) REVERT: G 19 SER cc_start: 0.8749 (p) cc_final: 0.8307 (t) REVERT: G 22 MET cc_start: 0.7956 (mtm) cc_final: 0.7719 (mtm) REVERT: G 76 ILE cc_start: 0.8303 (pt) cc_final: 0.8075 (mt) REVERT: G 129 ARG cc_start: 0.8208 (tpm170) cc_final: 0.7963 (ttp-110) REVERT: G 227 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7791 (mm110) REVERT: G 249 GLU cc_start: 0.8459 (pp20) cc_final: 0.7842 (pp20) REVERT: G 324 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8439 (tt) REVERT: C 652 GLU cc_start: 0.8494 (mp0) cc_final: 0.8120 (pt0) REVERT: C 657 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7294 (mm-40) REVERT: C 660 TYR cc_start: 0.7462 (t80) cc_final: 0.7235 (t80) REVERT: C 670 LEU cc_start: 0.6240 (mp) cc_final: 0.5874 (mt) REVERT: I 16 ASP cc_start: 0.7333 (p0) cc_final: 0.6895 (p0) REVERT: I 189 ARG cc_start: 0.8759 (mtp-110) cc_final: 0.8470 (mmm-85) REVERT: I 205 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.8312 (m-80) REVERT: I 271 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8178 (mt) REVERT: I 290 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.9057 (p90) REVERT: I 462 GLN cc_start: 0.8277 (mm-40) cc_final: 0.8043 (mm-40) REVERT: I 566 PHE cc_start: 0.7019 (OUTLIER) cc_final: 0.6140 (m-10) REVERT: I 589 THR cc_start: 0.7725 (m) cc_final: 0.7345 (m) REVERT: I 608 ASP cc_start: 0.8315 (m-30) cc_final: 0.7947 (m-30) REVERT: I 624 PHE cc_start: 0.8042 (m-10) cc_final: 0.7760 (m-10) REVERT: I 735 ILE cc_start: 0.8706 (pt) cc_final: 0.8467 (pt) REVERT: D 94 MET cc_start: 0.4513 (ttt) cc_final: 0.3667 (tpt) REVERT: D 307 ASN cc_start: 0.7998 (t0) cc_final: 0.7784 (t0) REVERT: D 333 MET cc_start: 0.6913 (mtm) cc_final: 0.6474 (ptp) REVERT: D 384 GLU cc_start: 0.3765 (OUTLIER) cc_final: 0.3503 (mp0) REVERT: D 457 TYR cc_start: 0.8521 (t80) cc_final: 0.8289 (t80) REVERT: D 488 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8349 (tt) REVERT: D 501 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8648 (tp) REVERT: D 583 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8061 (t0) REVERT: D 584 MET cc_start: 0.9019 (tpp) cc_final: 0.8719 (mmm) REVERT: D 590 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.5179 (pp) outliers start: 153 outliers final: 65 residues processed: 530 average time/residue: 0.1675 time to fit residues: 143.1659 Evaluate side-chains 427 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 348 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 264 CYS Chi-restraints excluded: chain E residue 412 GLU Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 47 ARG Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 92 MET Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 205 TYR Chi-restraints excluded: chain I residue 249 CYS Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 377 ASN Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 501 GLU Chi-restraints excluded: chain I residue 515 ASN Chi-restraints excluded: chain I residue 566 PHE Chi-restraints excluded: chain I residue 609 LEU Chi-restraints excluded: chain I residue 621 GLN Chi-restraints excluded: chain I residue 642 LEU Chi-restraints excluded: chain I residue 643 GLU Chi-restraints excluded: chain I residue 654 GLU Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain I residue 723 SER Chi-restraints excluded: chain I residue 733 LEU Chi-restraints excluded: chain I residue 765 GLU Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 590 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 168 optimal weight: 50.0000 chunk 98 optimal weight: 0.5980 chunk 93 optimal weight: 0.2980 chunk 164 optimal weight: 50.0000 chunk 65 optimal weight: 2.9990 chunk 170 optimal weight: 30.0000 chunk 203 optimal weight: 50.0000 chunk 111 optimal weight: 1.9990 chunk 329 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 326 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 642 ASN B 664 ASN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 GLN C 688 ASN F 265 ASN ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 308 HIS I 420 ASN I 515 ASN I 694 HIS I 717 GLN D 545 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.203572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.152899 restraints weight = 34106.715| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.99 r_work: 0.3373 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 27917 Z= 0.243 Angle : 0.689 10.179 37936 Z= 0.356 Chirality : 0.047 0.193 4464 Planarity : 0.004 0.051 4968 Dihedral : 5.296 59.379 4040 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.33 % Favored : 92.65 % Rotamer: Outliers : 3.94 % Allowed : 22.05 % Favored : 74.02 % 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: -1.56 (0.13), residues: 3767 helix: 1.03 (0.14), residues: 1320 sheet: -1.61 (0.18), residues: 831 loop : -2.51 (0.14), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 78 TYR 0.022 0.002 TYR E 236 PHE 0.028 0.002 PHE D 534 TRP 0.019 0.002 TRP I 9 HIS 0.014 0.002 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00575 (27917) covalent geometry : angle 0.68877 (37936) hydrogen bonds : bond 0.04336 ( 1396) hydrogen bonds : angle 4.78592 ( 4053) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 381 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 MET cc_start: 0.7624 (tmm) cc_final: 0.6956 (tmm) REVERT: H 9 ARG cc_start: 0.8444 (ttp-110) cc_final: 0.8205 (ttp80) REVERT: B 494 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8044 (tm-30) REVERT: B 519 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7765 (mm) REVERT: B 614 MET cc_start: 0.8581 (ttm) cc_final: 0.8306 (mtp) REVERT: B 706 ASN cc_start: 0.8076 (t0) cc_final: 0.7802 (t0) REVERT: E 58 GLN cc_start: 0.6413 (OUTLIER) cc_final: 0.6158 (tm-30) REVERT: E 75 LEU cc_start: 0.7657 (tp) cc_final: 0.7395 (tp) REVERT: E 112 PHE cc_start: 0.8115 (t80) cc_final: 0.7869 (t80) REVERT: E 191 TYR cc_start: 0.6772 (m-10) cc_final: 0.6352 (m-80) REVERT: E 232 ASP cc_start: 0.7012 (t0) cc_final: 0.6577 (t0) REVERT: E 359 ARG cc_start: 0.8332 (ptp90) cc_final: 0.8042 (mtm-85) REVERT: E 368 ASP cc_start: 0.7265 (t0) cc_final: 0.7004 (t0) REVERT: G 29 VAL cc_start: 0.8283 (p) cc_final: 0.7927 (m) REVERT: G 76 ILE cc_start: 0.8255 (pt) cc_final: 0.8024 (mt) REVERT: G 82 ARG cc_start: 0.6648 (tpp-160) cc_final: 0.6310 (tpp-160) REVERT: G 119 ARG cc_start: 0.8190 (tmm-80) cc_final: 0.7936 (ttt180) REVERT: G 168 TRP cc_start: 0.8491 (m-90) cc_final: 0.8148 (m-90) REVERT: G 227 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7874 (mm110) REVERT: G 249 GLU cc_start: 0.8460 (pp20) cc_final: 0.7664 (pp20) REVERT: C 652 GLU cc_start: 0.8374 (mp0) cc_final: 0.8120 (pt0) REVERT: C 669 ARG cc_start: 0.6860 (mmp80) cc_final: 0.6181 (mmp80) REVERT: C 670 LEU cc_start: 0.6089 (mp) cc_final: 0.5859 (mt) REVERT: F 79 SER cc_start: 0.8536 (t) cc_final: 0.8114 (p) REVERT: F 266 LEU cc_start: 0.8827 (tp) cc_final: 0.8621 (tp) REVERT: I 16 ASP cc_start: 0.7318 (p0) cc_final: 0.6983 (p0) REVERT: I 189 ARG cc_start: 0.8499 (mtp-110) cc_final: 0.8269 (ttt90) REVERT: I 309 ASN cc_start: 0.8324 (t0) cc_final: 0.7970 (t0) REVERT: I 563 PHE cc_start: 0.7538 (m-80) cc_final: 0.7314 (m-80) REVERT: I 566 PHE cc_start: 0.6969 (OUTLIER) cc_final: 0.5354 (m-80) REVERT: I 735 ILE cc_start: 0.8418 (pt) cc_final: 0.8208 (pt) REVERT: D 94 MET cc_start: 0.4548 (ttt) cc_final: 0.3500 (tpt) REVERT: D 227 GLU cc_start: 0.5596 (mm-30) cc_final: 0.5183 (tp30) REVERT: D 384 GLU cc_start: 0.3900 (OUTLIER) cc_final: 0.3638 (mp0) REVERT: D 581 HIS cc_start: 0.7006 (OUTLIER) cc_final: 0.6477 (m90) REVERT: D 590 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5485 (pp) outliers start: 98 outliers final: 57 residues processed: 454 average time/residue: 0.1673 time to fit residues: 124.0451 Evaluate side-chains 404 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 341 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 93 CYS Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 310 GLN Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 673 MET Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 92 MET Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain I residue 284 ASP Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 566 PHE Chi-restraints excluded: chain I residue 621 GLN Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain I residue 723 SER Chi-restraints excluded: chain I residue 733 LEU Chi-restraints excluded: chain I residue 765 GLU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 581 HIS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 590 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 63 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 308 optimal weight: 2.9990 chunk 272 optimal weight: 0.0870 chunk 186 optimal weight: 40.0000 chunk 358 optimal weight: 2.9990 chunk 280 optimal weight: 0.8980 chunk 355 optimal weight: 8.9990 chunk 196 optimal weight: 0.9990 chunk 369 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 375 ASN ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN I 155 GLN I 377 ASN I 515 ASN I 760 GLN D 307 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.207151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.155744 restraints weight = 33873.015| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.90 r_work: 0.3419 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 27917 Z= 0.145 Angle : 0.617 12.508 37936 Z= 0.317 Chirality : 0.044 0.191 4464 Planarity : 0.004 0.049 4968 Dihedral : 4.903 58.683 4040 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.82 % Favored : 93.15 % Rotamer: Outliers : 3.78 % Allowed : 23.33 % Favored : 72.89 % 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: -1.12 (0.14), residues: 3767 helix: 1.49 (0.14), residues: 1324 sheet: -1.42 (0.18), residues: 839 loop : -2.33 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 78 TYR 0.020 0.001 TYR C 660 PHE 0.032 0.002 PHE E 413 TRP 0.017 0.001 TRP I 9 HIS 0.010 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00335 (27917) covalent geometry : angle 0.61690 (37936) hydrogen bonds : bond 0.03803 ( 1396) hydrogen bonds : angle 4.41207 ( 4053) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 382 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 MET cc_start: 0.7573 (tmm) cc_final: 0.6880 (tmm) REVERT: H 9 ARG cc_start: 0.8409 (ttp-110) cc_final: 0.8110 (ttp80) REVERT: B 494 GLU cc_start: 0.8524 (tm-30) cc_final: 0.7943 (tm-30) REVERT: B 519 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7820 (mm) REVERT: B 574 PHE cc_start: 0.8183 (t80) cc_final: 0.7955 (t80) REVERT: E 191 TYR cc_start: 0.6985 (m-80) cc_final: 0.6354 (m-80) REVERT: E 217 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7012 (mt) REVERT: E 359 ARG cc_start: 0.8248 (ptp90) cc_final: 0.7982 (mtm-85) REVERT: E 368 ASP cc_start: 0.7475 (t0) cc_final: 0.7216 (t0) REVERT: G 29 VAL cc_start: 0.8308 (p) cc_final: 0.7944 (m) REVERT: G 82 ARG cc_start: 0.6556 (tpp-160) cc_final: 0.6205 (tpp-160) REVERT: G 119 ARG cc_start: 0.8183 (tmm-80) cc_final: 0.7983 (ttt180) REVERT: G 168 TRP cc_start: 0.8388 (m-90) cc_final: 0.8112 (m-90) REVERT: G 227 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7834 (mm110) REVERT: G 249 GLU cc_start: 0.8360 (pp20) cc_final: 0.7468 (pp20) REVERT: C 681 LYS cc_start: 0.4445 (OUTLIER) cc_final: 0.3853 (mttt) REVERT: F 79 SER cc_start: 0.8494 (t) cc_final: 0.8090 (p) REVERT: F 265 ASN cc_start: 0.8171 (m-40) cc_final: 0.7875 (m-40) REVERT: I 16 ASP cc_start: 0.7295 (p0) cc_final: 0.7034 (p0) REVERT: I 147 LYS cc_start: 0.8321 (mmtt) cc_final: 0.8104 (mmtm) REVERT: I 309 ASN cc_start: 0.8176 (t0) cc_final: 0.7837 (t0) REVERT: I 735 ILE cc_start: 0.8539 (pt) cc_final: 0.8332 (pt) REVERT: I 818 ARG cc_start: 0.6662 (tpt170) cc_final: 0.6389 (ttt180) REVERT: D 94 MET cc_start: 0.4475 (ttt) cc_final: 0.3333 (tpt) REVERT: D 227 GLU cc_start: 0.5524 (mm-30) cc_final: 0.5127 (tp30) REVERT: D 384 GLU cc_start: 0.3862 (OUTLIER) cc_final: 0.3634 (mp0) REVERT: D 590 LEU cc_start: 0.5578 (OUTLIER) cc_final: 0.5326 (pp) outliers start: 94 outliers final: 49 residues processed: 448 average time/residue: 0.1572 time to fit residues: 115.6352 Evaluate side-chains 408 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 354 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 93 CYS Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 282 CYS Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 375 GLU Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 515 ASN Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 609 LEU Chi-restraints excluded: chain I residue 654 GLU Chi-restraints excluded: chain I residue 733 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 590 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 46 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 291 optimal weight: 0.7980 chunk 211 optimal weight: 0.9980 chunk 73 optimal weight: 0.0770 chunk 151 optimal weight: 7.9990 chunk 230 optimal weight: 0.0980 chunk 302 optimal weight: 0.8980 chunk 233 optimal weight: 0.9990 chunk 315 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 HIS ** C 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 515 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.206827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.156028 restraints weight = 33925.752| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.72 r_work: 0.3450 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27917 Z= 0.132 Angle : 0.610 15.162 37936 Z= 0.310 Chirality : 0.044 0.176 4464 Planarity : 0.004 0.058 4968 Dihedral : 4.744 58.607 4038 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.24 % Favored : 93.74 % Rotamer: Outliers : 4.30 % Allowed : 23.49 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3767 helix: 1.69 (0.14), residues: 1323 sheet: -1.36 (0.18), residues: 859 loop : -2.22 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 514 TYR 0.022 0.001 TYR C 660 PHE 0.023 0.002 PHE D 534 TRP 0.016 0.001 TRP I 9 HIS 0.008 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00303 (27917) covalent geometry : angle 0.61005 (37936) hydrogen bonds : bond 0.03663 ( 1396) hydrogen bonds : angle 4.27578 ( 4053) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 380 time to evaluate : 0.981 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: H 7 MET cc_start: 0.7230 (tmm) cc_final: 0.6514 (tmm) REVERT: H 9 ARG cc_start: 0.8391 (ttp-110) cc_final: 0.8102 (ttp80) REVERT: B 494 GLU cc_start: 0.8492 (tm-30) cc_final: 0.7946 (tm-30) REVERT: B 519 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7874 (mm) REVERT: B 574 PHE cc_start: 0.8264 (t80) cc_final: 0.7932 (t80) REVERT: E 217 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7001 (mt) REVERT: E 232 ASP cc_start: 0.7101 (t0) cc_final: 0.6653 (t0) REVERT: E 317 MET cc_start: 0.8302 (mtp) cc_final: 0.8018 (mtp) REVERT: E 359 ARG cc_start: 0.8260 (ptp90) cc_final: 0.8020 (mtm-85) REVERT: E 368 ASP cc_start: 0.7650 (t0) cc_final: 0.7258 (t0) REVERT: E 423 LYS cc_start: 0.9180 (mmtp) cc_final: 0.8963 (mmtp) REVERT: G 29 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.7946 (m) REVERT: G 82 ARG cc_start: 0.6606 (tpp-160) cc_final: 0.6074 (tpp-160) REVERT: G 168 TRP cc_start: 0.8351 (m-90) cc_final: 0.8068 (m-90) REVERT: G 249 GLU cc_start: 0.8212 (pp20) cc_final: 0.7334 (pp20) REVERT: C 646 TYR cc_start: 0.7040 (m-80) cc_final: 0.6801 (m-80) REVERT: C 669 ARG cc_start: 0.6903 (mmp80) cc_final: 0.6395 (mmp80) REVERT: F 62 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7815 (mm-30) REVERT: F 63 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.8014 (ttm) REVERT: F 79 SER cc_start: 0.8465 (t) cc_final: 0.8050 (p) REVERT: F 265 ASN cc_start: 0.8104 (m-40) cc_final: 0.7726 (m110) REVERT: F 344 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7631 (t80) REVERT: I 160 MET cc_start: 0.8448 (ttm) cc_final: 0.8227 (ttm) REVERT: I 309 ASN cc_start: 0.8092 (t0) cc_final: 0.7795 (t0) REVERT: I 608 ASP cc_start: 0.8491 (m-30) cc_final: 0.8191 (m-30) REVERT: I 733 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8694 (tp) REVERT: D 94 MET cc_start: 0.4260 (ttt) cc_final: 0.3147 (tpt) REVERT: D 155 MET cc_start: 0.0995 (mmm) cc_final: 0.0730 (mtp) REVERT: D 227 GLU cc_start: 0.5166 (mm-30) cc_final: 0.4758 (tp30) REVERT: D 384 GLU cc_start: 0.3993 (OUTLIER) cc_final: 0.3764 (mp0) REVERT: D 581 HIS cc_start: 0.6589 (OUTLIER) cc_final: 0.6120 (m90) REVERT: D 590 LEU cc_start: 0.5540 (OUTLIER) cc_final: 0.5288 (pp) outliers start: 107 outliers final: 64 residues processed: 460 average time/residue: 0.1574 time to fit residues: 119.4687 Evaluate side-chains 434 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 361 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 93 CYS Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 310 GLN Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 282 CYS Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 344 TYR Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 642 LEU Chi-restraints excluded: chain I residue 654 GLU Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain I residue 733 LEU Chi-restraints excluded: chain I residue 749 ILE Chi-restraints excluded: chain I residue 799 LEU Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 581 HIS Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 590 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 260 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 370 optimal weight: 0.5980 chunk 248 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 292 optimal weight: 0.6980 chunk 223 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 247 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 GLN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 132 GLN I 276 GLN I 420 ASN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 515 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.206261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.155725 restraints weight = 33924.577| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.99 r_work: 0.3408 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27917 Z= 0.154 Angle : 0.624 13.372 37936 Z= 0.317 Chirality : 0.045 0.194 4464 Planarity : 0.004 0.054 4968 Dihedral : 4.702 57.758 4038 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.66 % Favored : 93.31 % Rotamer: Outliers : 4.50 % Allowed : 23.69 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 3767 helix: 1.71 (0.14), residues: 1315 sheet: -1.21 (0.18), residues: 846 loop : -2.15 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 647 TYR 0.017 0.001 TYR C 660 PHE 0.029 0.002 PHE E 112 TRP 0.017 0.001 TRP I 9 HIS 0.007 0.001 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00359 (27917) covalent geometry : angle 0.62356 (37936) hydrogen bonds : bond 0.03738 ( 1396) hydrogen bonds : angle 4.27201 ( 4053) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 357 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 MET cc_start: 0.7160 (tmm) cc_final: 0.6420 (tmm) REVERT: B 519 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7952 (mm) REVERT: B 574 PHE cc_start: 0.8352 (t80) cc_final: 0.7993 (t80) REVERT: E 217 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.6980 (mt) REVERT: E 359 ARG cc_start: 0.8288 (ptp90) cc_final: 0.8070 (mtm-85) REVERT: E 368 ASP cc_start: 0.7809 (t0) cc_final: 0.7447 (t0) REVERT: G 29 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.7981 (m) REVERT: G 82 ARG cc_start: 0.6489 (tpp-160) cc_final: 0.6122 (tpp-160) REVERT: G 249 GLU cc_start: 0.8273 (pp20) cc_final: 0.7560 (pp20) REVERT: C 626 ILE cc_start: 0.8134 (tp) cc_final: 0.7677 (tt) REVERT: C 652 GLU cc_start: 0.8456 (pt0) cc_final: 0.7942 (mp0) REVERT: F 62 GLU cc_start: 0.8263 (mm-30) cc_final: 0.6718 (mm-30) REVERT: F 79 SER cc_start: 0.8539 (t) cc_final: 0.8129 (p) REVERT: F 344 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7899 (t80) REVERT: I 71 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8372 (tt0) REVERT: I 160 MET cc_start: 0.8452 (ttm) cc_final: 0.8244 (ttm) REVERT: I 265 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8245 (pt0) REVERT: I 309 ASN cc_start: 0.8113 (t0) cc_final: 0.7825 (t0) REVERT: I 456 LYS cc_start: 0.7699 (tttm) cc_final: 0.7385 (ttpp) REVERT: I 597 GLN cc_start: 0.6597 (pt0) cc_final: 0.6295 (pt0) REVERT: I 608 ASP cc_start: 0.8560 (m-30) cc_final: 0.8256 (m-30) REVERT: D 94 MET cc_start: 0.4120 (ttt) cc_final: 0.3024 (tpt) REVERT: D 155 MET cc_start: 0.1006 (mmm) cc_final: 0.0724 (mtp) REVERT: D 227 GLU cc_start: 0.5093 (mm-30) cc_final: 0.4689 (tp30) REVERT: D 384 GLU cc_start: 0.4039 (OUTLIER) cc_final: 0.3808 (mp0) REVERT: D 581 HIS cc_start: 0.6774 (OUTLIER) cc_final: 0.6307 (m90) outliers start: 112 outliers final: 74 residues processed: 444 average time/residue: 0.1587 time to fit residues: 116.0305 Evaluate side-chains 430 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 348 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 93 CYS Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 310 GLN Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 282 CYS Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 344 TYR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain I residue 265 GLU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 515 ASN Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 609 LEU Chi-restraints excluded: chain I residue 642 LEU Chi-restraints excluded: chain I residue 654 GLU Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain I residue 733 LEU Chi-restraints excluded: chain I residue 749 ILE Chi-restraints excluded: chain I residue 799 LEU Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 358 TYR Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 581 HIS Chi-restraints excluded: chain D residue 583 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 135 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 186 optimal weight: 50.0000 chunk 343 optimal weight: 5.9990 chunk 373 optimal weight: 0.7980 chunk 344 optimal weight: 7.9990 chunk 168 optimal weight: 50.0000 chunk 298 optimal weight: 0.0980 chunk 171 optimal weight: 40.0000 chunk 233 optimal weight: 0.9980 chunk 324 optimal weight: 10.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN E 99 GLN E 106 GLN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN I 276 GLN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 515 ASN I 672 GLN D 307 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.203287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.146397 restraints weight = 34260.384| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.02 r_work: 0.3452 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 27917 Z= 0.218 Angle : 0.671 12.579 37936 Z= 0.342 Chirality : 0.046 0.196 4464 Planarity : 0.004 0.046 4968 Dihedral : 4.863 57.123 4038 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.98 % Favored : 92.99 % Rotamer: Outliers : 4.06 % Allowed : 24.46 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.14), residues: 3767 helix: 1.49 (0.14), residues: 1333 sheet: -1.21 (0.18), residues: 849 loop : -2.21 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 514 TYR 0.021 0.002 TYR F 300 PHE 0.045 0.002 PHE I 279 TRP 0.019 0.002 TRP I 9 HIS 0.013 0.001 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00515 (27917) covalent geometry : angle 0.67098 (37936) hydrogen bonds : bond 0.04028 ( 1396) hydrogen bonds : angle 4.39817 ( 4053) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 354 time to evaluate : 0.803 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: H 7 MET cc_start: 0.7414 (tmm) cc_final: 0.6650 (tmm) REVERT: H 22 ASP cc_start: 0.8082 (t0) cc_final: 0.7831 (t0) REVERT: B 519 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8038 (mm) REVERT: B 535 PHE cc_start: 0.7364 (m-80) cc_final: 0.7113 (m-80) REVERT: B 574 PHE cc_start: 0.8445 (t80) cc_final: 0.8033 (t80) REVERT: B 594 ARG cc_start: 0.8290 (ttm110) cc_final: 0.8075 (ttp-170) REVERT: B 700 ASP cc_start: 0.7831 (m-30) cc_final: 0.7539 (m-30) REVERT: B 709 MET cc_start: 0.7743 (ptm) cc_final: 0.7492 (ptm) REVERT: E 112 PHE cc_start: 0.8719 (t80) cc_final: 0.8370 (t80) REVERT: E 217 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7041 (mt) REVERT: E 368 ASP cc_start: 0.8141 (t0) cc_final: 0.7938 (t0) REVERT: E 412 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7166 (tm-30) REVERT: G 249 GLU cc_start: 0.8311 (pp20) cc_final: 0.7569 (pp20) REVERT: C 626 ILE cc_start: 0.8232 (tp) cc_final: 0.7816 (tt) REVERT: C 652 GLU cc_start: 0.8247 (pt0) cc_final: 0.7961 (mp0) REVERT: F 79 SER cc_start: 0.8637 (t) cc_final: 0.8207 (p) REVERT: F 265 ASN cc_start: 0.8209 (m-40) cc_final: 0.7741 (m110) REVERT: F 344 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.8237 (t80) REVERT: I 160 MET cc_start: 0.8577 (ttm) cc_final: 0.8347 (ttm) REVERT: I 265 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8273 (pt0) REVERT: I 309 ASN cc_start: 0.8249 (t0) cc_final: 0.7946 (t0) REVERT: D 94 MET cc_start: 0.3889 (ttt) cc_final: 0.2851 (tpt) REVERT: D 155 MET cc_start: 0.1168 (mmm) cc_final: 0.0921 (mtp) REVERT: D 227 GLU cc_start: 0.5212 (mm-30) cc_final: 0.4766 (tp30) REVERT: D 384 GLU cc_start: 0.4051 (OUTLIER) cc_final: 0.3766 (mp0) REVERT: D 581 HIS cc_start: 0.7141 (OUTLIER) cc_final: 0.6606 (m90) outliers start: 101 outliers final: 77 residues processed: 434 average time/residue: 0.1568 time to fit residues: 111.5535 Evaluate side-chains 425 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 342 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 310 GLN Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 282 CYS Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 344 TYR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain I residue 265 GLU Chi-restraints excluded: chain I residue 284 ASP Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 607 GLU Chi-restraints excluded: chain I residue 642 LEU Chi-restraints excluded: chain I residue 654 GLU Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain I residue 733 LEU Chi-restraints excluded: chain I residue 749 ILE Chi-restraints excluded: chain I residue 799 LEU Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 358 TYR Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 581 HIS Chi-restraints excluded: chain D residue 583 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 96 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 138 optimal weight: 9.9990 chunk 233 optimal weight: 0.5980 chunk 288 optimal weight: 0.5980 chunk 200 optimal weight: 20.0000 chunk 195 optimal weight: 0.9990 chunk 164 optimal weight: 40.0000 chunk 28 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 GLN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN I 276 GLN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.204992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.155043 restraints weight = 33930.606| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.84 r_work: 0.3398 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27917 Z= 0.154 Angle : 0.633 13.135 37936 Z= 0.320 Chirality : 0.045 0.229 4464 Planarity : 0.004 0.048 4968 Dihedral : 4.713 58.115 4038 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.26 % Favored : 93.71 % Rotamer: Outliers : 3.90 % Allowed : 24.82 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3767 helix: 1.67 (0.14), residues: 1335 sheet: -1.18 (0.18), residues: 863 loop : -2.12 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 9 TYR 0.018 0.001 TYR F 10 PHE 0.026 0.002 PHE E 112 TRP 0.016 0.001 TRP I 9 HIS 0.007 0.001 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00359 (27917) covalent geometry : angle 0.63296 (37936) hydrogen bonds : bond 0.03712 ( 1396) hydrogen bonds : angle 4.25087 ( 4053) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 349 time to evaluate : 1.113 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: H 22 ASP cc_start: 0.7990 (t0) cc_final: 0.7720 (t0) REVERT: B 519 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8046 (mm) REVERT: B 574 PHE cc_start: 0.8378 (t80) cc_final: 0.7975 (t80) REVERT: B 594 ARG cc_start: 0.8319 (ttm110) cc_final: 0.8083 (ttp-170) REVERT: B 700 ASP cc_start: 0.7850 (m-30) cc_final: 0.7403 (m-30) REVERT: B 709 MET cc_start: 0.7821 (ptm) cc_final: 0.7521 (ptm) REVERT: E 112 PHE cc_start: 0.8667 (t80) cc_final: 0.8443 (t80) REVERT: E 191 TYR cc_start: 0.7117 (m-80) cc_final: 0.6844 (m-80) REVERT: E 342 MET cc_start: 0.8854 (tmm) cc_final: 0.8425 (tmm) REVERT: G 29 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.7977 (m) REVERT: G 77 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7600 (mt) REVERT: G 82 ARG cc_start: 0.6651 (tpp-160) cc_final: 0.6282 (tpp-160) REVERT: G 249 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7482 (pp20) REVERT: G 305 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: C 626 ILE cc_start: 0.8118 (tp) cc_final: 0.7760 (tt) REVERT: C 648 CYS cc_start: 0.7767 (m) cc_final: 0.7512 (p) REVERT: F 62 GLU cc_start: 0.8144 (mm-30) cc_final: 0.6737 (mm-30) REVERT: F 79 SER cc_start: 0.8514 (t) cc_final: 0.8075 (p) REVERT: F 265 ASN cc_start: 0.8174 (m-40) cc_final: 0.7700 (m110) REVERT: F 344 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7976 (t80) REVERT: I 160 MET cc_start: 0.8453 (ttm) cc_final: 0.8246 (ttm) REVERT: I 265 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8171 (pt0) REVERT: I 309 ASN cc_start: 0.8168 (t0) cc_final: 0.7872 (t0) REVERT: I 456 LYS cc_start: 0.7948 (tttm) cc_final: 0.7617 (ttpp) REVERT: D 94 MET cc_start: 0.3768 (ttt) cc_final: 0.2799 (tpt) REVERT: D 155 MET cc_start: 0.1085 (mmm) cc_final: 0.0850 (mtp) REVERT: D 227 GLU cc_start: 0.5121 (mm-30) cc_final: 0.4657 (tp30) REVERT: D 274 ILE cc_start: 0.2166 (OUTLIER) cc_final: 0.1784 (mt) REVERT: D 384 GLU cc_start: 0.3978 (OUTLIER) cc_final: 0.3707 (mp0) REVERT: D 581 HIS cc_start: 0.6835 (OUTLIER) cc_final: 0.6358 (m90) REVERT: D 583 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7887 (t0) outliers start: 97 outliers final: 77 residues processed: 425 average time/residue: 0.1561 time to fit residues: 109.6786 Evaluate side-chains 426 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 338 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain G residue 310 GLN Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 282 CYS Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 344 TYR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain I residue 265 GLU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 607 GLU Chi-restraints excluded: chain I residue 642 LEU Chi-restraints excluded: chain I residue 654 GLU Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain I residue 733 LEU Chi-restraints excluded: chain I residue 749 ILE Chi-restraints excluded: chain I residue 799 LEU Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 358 TYR Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 581 HIS Chi-restraints excluded: chain D residue 583 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 31 optimal weight: 9.9990 chunk 252 optimal weight: 1.9990 chunk 320 optimal weight: 0.6980 chunk 369 optimal weight: 0.6980 chunk 352 optimal weight: 1.9990 chunk 249 optimal weight: 0.7980 chunk 241 optimal weight: 2.9990 chunk 236 optimal weight: 0.8980 chunk 312 optimal weight: 2.9990 chunk 170 optimal weight: 50.0000 chunk 233 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.205334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.155159 restraints weight = 33941.611| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.80 r_work: 0.3390 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27917 Z= 0.149 Angle : 0.638 11.664 37936 Z= 0.321 Chirality : 0.045 0.296 4464 Planarity : 0.004 0.048 4968 Dihedral : 4.693 58.441 4038 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.50 % Favored : 93.47 % Rotamer: Outliers : 3.73 % Allowed : 25.10 % 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: -0.69 (0.14), residues: 3767 helix: 1.75 (0.14), residues: 1333 sheet: -1.05 (0.18), residues: 854 loop : -2.09 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 9 TYR 0.019 0.001 TYR F 10 PHE 0.025 0.002 PHE E 112 TRP 0.016 0.001 TRP I 9 HIS 0.008 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00347 (27917) covalent geometry : angle 0.63751 (37936) hydrogen bonds : bond 0.03665 ( 1396) hydrogen bonds : angle 4.20629 ( 4053) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 336 time to evaluate : 0.777 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: B 519 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8080 (mm) REVERT: B 535 PHE cc_start: 0.7412 (m-80) cc_final: 0.7163 (m-80) REVERT: B 574 PHE cc_start: 0.8367 (t80) cc_final: 0.7981 (t80) REVERT: B 594 ARG cc_start: 0.8347 (ttm110) cc_final: 0.8118 (ttp-170) REVERT: B 700 ASP cc_start: 0.7807 (m-30) cc_final: 0.7376 (m-30) REVERT: E 112 PHE cc_start: 0.8768 (t80) cc_final: 0.8558 (t80) REVERT: E 342 MET cc_start: 0.8828 (tmm) cc_final: 0.8427 (tmm) REVERT: E 359 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8097 (mtt90) REVERT: G 29 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.7989 (m) REVERT: G 77 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7586 (mt) REVERT: G 82 ARG cc_start: 0.6631 (tpp-160) cc_final: 0.6265 (tpp-160) REVERT: G 249 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7499 (pp20) REVERT: C 626 ILE cc_start: 0.8140 (tp) cc_final: 0.7774 (tt) REVERT: F 62 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7487 (mt-10) REVERT: F 79 SER cc_start: 0.8510 (t) cc_final: 0.8065 (p) REVERT: F 344 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7964 (t80) REVERT: I 265 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8185 (pt0) REVERT: I 309 ASN cc_start: 0.8117 (t0) cc_final: 0.7820 (t0) REVERT: D 94 MET cc_start: 0.3618 (ttt) cc_final: 0.2718 (tpt) REVERT: D 155 MET cc_start: 0.1034 (mmm) cc_final: 0.0800 (mtp) REVERT: D 200 ILE cc_start: 0.7761 (mt) cc_final: 0.7324 (tp) REVERT: D 227 GLU cc_start: 0.5115 (mm-30) cc_final: 0.4662 (tp30) REVERT: D 384 GLU cc_start: 0.3981 (OUTLIER) cc_final: 0.3709 (mp0) REVERT: D 581 HIS cc_start: 0.6829 (OUTLIER) cc_final: 0.6362 (m90) REVERT: D 583 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7999 (t0) outliers start: 93 outliers final: 77 residues processed: 407 average time/residue: 0.1597 time to fit residues: 106.7374 Evaluate side-chains 426 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 340 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 310 GLN Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 282 CYS Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 344 TYR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain I residue 265 GLU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 607 GLU Chi-restraints excluded: chain I residue 609 LEU Chi-restraints excluded: chain I residue 642 LEU Chi-restraints excluded: chain I residue 654 GLU Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain I residue 733 LEU Chi-restraints excluded: chain I residue 749 ILE Chi-restraints excluded: chain I residue 799 LEU Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 358 TYR Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 581 HIS Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 590 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 225 optimal weight: 1.9990 chunk 219 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 280 optimal weight: 0.7980 chunk 318 optimal weight: 0.7980 chunk 163 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 chunk 38 optimal weight: 30.0000 chunk 107 optimal weight: 3.9990 chunk 329 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 GLN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN ** I 471 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 = 0.4407 r_free = 0.4407 target = 0.201813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.153172 restraints weight = 33724.069| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.79 r_work: 0.3389 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 27917 Z= 0.207 Angle : 0.681 14.463 37936 Z= 0.342 Chirality : 0.047 0.288 4464 Planarity : 0.004 0.049 4968 Dihedral : 4.825 57.885 4038 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.25 % Favored : 92.73 % Rotamer: Outliers : 4.02 % Allowed : 24.94 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 3767 helix: 1.55 (0.14), residues: 1334 sheet: -1.09 (0.18), residues: 860 loop : -2.12 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 9 TYR 0.020 0.002 TYR C 660 PHE 0.026 0.002 PHE D 534 TRP 0.019 0.002 TRP I 9 HIS 0.012 0.001 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00492 (27917) covalent geometry : angle 0.68097 (37936) hydrogen bonds : bond 0.03962 ( 1396) hydrogen bonds : angle 4.36715 ( 4053) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6677.68 seconds wall clock time: 114 minutes 51.41 seconds (6891.41 seconds total)