Starting phenix.real_space_refine on Thu Mar 5 13:34:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tw3_26149/03_2026/7tw3_26149.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tw3_26149/03_2026/7tw3_26149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tw3_26149/03_2026/7tw3_26149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tw3_26149/03_2026/7tw3_26149.map" model { file = "/net/cci-nas-00/data/ceres_data/7tw3_26149/03_2026/7tw3_26149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tw3_26149/03_2026/7tw3_26149.cif" } resolution = 4.4 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= 0.005 sd= 0.057 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 86 5.16 5 C 14576 2.51 5 N 3924 2.21 5 O 4055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22641 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6563 Classifications: {'peptide': 830} Link IDs: {'PTRANS': 49, 'TRANS': 780} Chain breaks: 3 Chain: "B" Number of atoms: 6435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6435 Classifications: {'peptide': 814} Link IDs: {'PTRANS': 49, 'TRANS': 764} Chain breaks: 3 Chain: "E" Number of atoms: 5236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5236 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 633} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 4407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 4407 Classifications: {'peptide': 635} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PTRANS': 34, 'TRANS': 600} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 547 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'ASN:plan1': 7, 'HIS:plan': 9, 'GLN:plan1': 6, 'GLU:plan': 5, 'ASP:plan': 8, 'ARG:plan': 3, 'TYR:plan': 4, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 195 Time building chain proxies: 5.02, per 1000 atoms: 0.22 Number of scatterers: 22641 At special positions: 0 Unit cell: (113.3, 138.6, 258.5, 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 86 16.00 O 4055 8.00 N 3924 7.00 C 14576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 1.4 seconds 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5508 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 19 sheets defined 51.9% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 43 through 47 removed outlier: 3.642A pdb=" N HIS A 47 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 116 removed outlier: 3.674A pdb=" N LYS A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 149 through 157 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 194 through 201 removed outlier: 3.690A pdb=" N CYS A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 277 through 290 Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 303 through 316 removed outlier: 3.854A pdb=" N LEU A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 335 removed outlier: 3.907A pdb=" N LEU A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 347 removed outlier: 3.560A pdb=" N TYR A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 390 removed outlier: 3.630A pdb=" N VAL A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 402 through 431 removed outlier: 3.966A pdb=" N LEU A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 436 through 455 removed outlier: 3.847A pdb=" N LEU A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 483 removed outlier: 3.779A pdb=" N LEU A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 507 removed outlier: 3.805A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 517 through 547 removed outlier: 3.695A pdb=" N GLN A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 593 removed outlier: 3.870A pdb=" N ASN A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 removed outlier: 3.527A pdb=" N PHE A 608 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 624 removed outlier: 3.640A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 667 Processing helix chain 'A' and resid 667 through 690 removed outlier: 3.670A pdb=" N ALA A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 695 removed outlier: 3.712A pdb=" N LYS A 695 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 719 removed outlier: 3.573A pdb=" N PHE A 719 " --> pdb=" O VAL A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 738 Processing helix chain 'A' and resid 760 through 773 removed outlier: 3.503A pdb=" N LEU A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 786 through 799 removed outlier: 4.009A pdb=" N GLY A 790 " --> pdb=" O ALA A 786 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 791 " --> pdb=" O VAL A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 811 removed outlier: 3.754A pdb=" N ASP A 807 " --> pdb=" O ILE A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.530A pdb=" N LYS A 826 " --> pdb=" O VAL A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 853 removed outlier: 3.710A pdb=" N LEU A 835 " --> pdb=" O TRP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 858 through 872 removed outlier: 3.636A pdb=" N VAL A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL A 867 " --> pdb=" O LEU A 863 " (cutoff:3.500A) Proline residue: A 868 - end of helix Processing helix chain 'A' and resid 873 through 877 Processing helix chain 'A' and resid 879 through 887 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 127 through 142 removed outlier: 3.825A pdb=" N VAL B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 149 through 158 removed outlier: 4.029A pdb=" N ARG B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 194 through 201 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.894A pdb=" N GLU B 291 " --> pdb=" O THR B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 303 through 317 removed outlier: 4.194A pdb=" N LEU B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 334 removed outlier: 3.691A pdb=" N SER B 334 " --> pdb=" O ALA B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 331 through 334' Processing helix chain 'B' and resid 335 through 349 removed outlier: 3.637A pdb=" N GLN B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 390 removed outlier: 3.602A pdb=" N VAL B 383 " --> pdb=" O PHE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 399 Processing helix chain 'B' and resid 402 through 431 removed outlier: 3.932A pdb=" N LEU B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 436 through 455 removed outlier: 3.742A pdb=" N LEU B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE B 451 " --> pdb=" O GLN B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 483 removed outlier: 3.824A pdb=" N LEU B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 507 removed outlier: 3.730A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 516 Processing helix chain 'B' and resid 517 through 547 removed outlier: 3.660A pdb=" N GLN B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 593 removed outlier: 3.846A pdb=" N ASN B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 removed outlier: 3.612A pdb=" N PHE B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 624 removed outlier: 3.595A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 667 Processing helix chain 'B' and resid 667 through 690 removed outlier: 3.659A pdb=" N ALA B 671 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 695 removed outlier: 3.704A pdb=" N LYS B 695 " --> pdb=" O PRO B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 719 removed outlier: 3.645A pdb=" N PHE B 719 " --> pdb=" O VAL B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 738 removed outlier: 3.517A pdb=" N SER B 731 " --> pdb=" O THR B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 773 removed outlier: 3.508A pdb=" N LEU B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 786 through 799 removed outlier: 4.028A pdb=" N GLY B 790 " --> pdb=" O ALA B 786 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 791 " --> pdb=" O VAL B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 811 removed outlier: 3.798A pdb=" N ASP B 807 " --> pdb=" O ILE B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 827 removed outlier: 3.536A pdb=" N LYS B 826 " --> pdb=" O VAL B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 853 removed outlier: 3.603A pdb=" N LEU B 835 " --> pdb=" O TRP B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 858 through 865 removed outlier: 3.558A pdb=" N VAL B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 872 removed outlier: 3.803A pdb=" N LEU B 869 " --> pdb=" O LEU B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 877 Processing helix chain 'B' and resid 879 through 887 Processing helix chain 'E' and resid 13 through 21 removed outlier: 4.122A pdb=" N ASN E 17 " --> pdb=" O GLN E 13 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 58 Processing helix chain 'E' and resid 151 through 159 removed outlier: 3.640A pdb=" N ARG E 155 " --> pdb=" O ASN E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 197 Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.559A pdb=" N SER E 206 " --> pdb=" O GLU E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 227 removed outlier: 3.684A pdb=" N VAL E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL E 227 " --> pdb=" O LYS E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 243 removed outlier: 3.897A pdb=" N ASN E 243 " --> pdb=" O GLY E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 257 Processing helix chain 'E' and resid 264 through 269 removed outlier: 3.784A pdb=" N ALA E 268 " --> pdb=" O ASP E 265 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N TRP E 269 " --> pdb=" O GLY E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 283 Processing helix chain 'E' and resid 368 through 374 Processing helix chain 'E' and resid 375 through 379 removed outlier: 3.902A pdb=" N LEU E 378 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 375 through 379' Processing helix chain 'E' and resid 381 through 390 removed outlier: 3.677A pdb=" N ASN E 390 " --> pdb=" O PHE E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 435 Processing helix chain 'E' and resid 441 through 458 removed outlier: 3.840A pdb=" N GLU E 457 " --> pdb=" O LYS E 453 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 550 through 552 No H-bonds generated for 'chain 'E' and resid 550 through 552' Processing helix chain 'G' and resid 176 through 183 Processing helix chain 'G' and resid 185 through 196 removed outlier: 3.519A pdb=" N ALA G 189 " --> pdb=" O ASP G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 216 removed outlier: 3.545A pdb=" N TYR G 216 " --> pdb=" O ILE G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 227 Processing helix chain 'G' and resid 241 through 250 Processing helix chain 'G' and resid 251 through 261 Processing helix chain 'G' and resid 274 through 283 removed outlier: 3.586A pdb=" N ASN G 282 " --> pdb=" O CYS G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 294 removed outlier: 3.702A pdb=" N SER G 288 " --> pdb=" O HIS G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 315 Processing helix chain 'G' and resid 317 through 328 Processing helix chain 'G' and resid 340 through 349 Processing helix chain 'G' and resid 350 through 361 removed outlier: 3.675A pdb=" N ALA G 354 " --> pdb=" O HIS G 350 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL G 356 " --> pdb=" O ARG G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 381 Processing helix chain 'G' and resid 384 through 394 Processing helix chain 'G' and resid 406 through 415 Processing helix chain 'G' and resid 416 through 426 removed outlier: 3.598A pdb=" N VAL G 420 " --> pdb=" O HIS G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 445 Processing helix chain 'G' and resid 449 through 459 removed outlier: 3.563A pdb=" N ASN G 459 " --> pdb=" O TYR G 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 479 removed outlier: 3.857A pdb=" N ARG G 479 " --> pdb=" O HIS G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 483 through 492 removed outlier: 3.879A pdb=" N LYS G 487 " --> pdb=" O THR G 483 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU G 488 " --> pdb=" O ASN G 484 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN G 492 " --> pdb=" O LEU G 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 505 through 514 Processing helix chain 'G' and resid 515 through 525 removed outlier: 3.750A pdb=" N GLU G 524 " --> pdb=" O LEU G 520 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS G 525 " --> pdb=" O ALA G 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 538 through 547 removed outlier: 3.884A pdb=" N VAL G 542 " --> pdb=" O THR G 538 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA G 543 " --> pdb=" O PRO G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 549 through 558 removed outlier: 4.356A pdb=" N GLU G 553 " --> pdb=" O VAL G 549 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU G 554 " --> pdb=" O ARG G 550 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG G 558 " --> pdb=" O LEU G 554 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 579 removed outlier: 3.639A pdb=" N HIS G 578 " --> pdb=" O HIS G 574 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N HIS G 579 " --> pdb=" O VAL G 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 589 removed outlier: 4.132A pdb=" N VAL G 585 " --> pdb=" O ASN G 581 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU G 587 " --> pdb=" O ASP G 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 604 through 613 removed outlier: 3.811A pdb=" N ILE G 608 " --> pdb=" O THR G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 616 through 623 Processing helix chain 'G' and resid 637 through 646 removed outlier: 3.632A pdb=" N GLU G 645 " --> pdb=" O LEU G 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 649 through 654 Processing helix chain 'G' and resid 670 through 679 Processing helix chain 'G' and resid 680 through 691 Processing helix chain 'G' and resid 703 through 712 Processing helix chain 'G' and resid 713 through 724 removed outlier: 4.153A pdb=" N LEU G 720 " --> pdb=" O LEU G 716 " (cutoff:3.500A) Processing helix chain 'G' and resid 736 through 745 Processing helix chain 'G' and resid 746 through 756 Processing helix chain 'G' and resid 769 through 777 Processing helix chain 'G' and resid 779 through 790 removed outlier: 4.045A pdb=" N VAL G 785 " --> pdb=" O SER G 781 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL G 788 " --> pdb=" O ASP G 784 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 removed outlier: 4.009A pdb=" N ALA A 35 " --> pdb=" O ARG E 638 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA E 598 " --> pdb=" O VAL E 685 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 87 removed outlier: 7.210A pdb=" N LEU A 61 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ARG A 80 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A 59 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS A 56 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR A 227 " --> pdb=" O LYS A 56 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TYR A 58 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL A 229 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU A 60 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL A 231 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLN A 62 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ARG A 263 " --> pdb=" O SER A 224 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ALA A 226 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A 265 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU A 228 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL A 267 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU A 230 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU A 269 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ARG A 263 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL A 119 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ARG A 246 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU A 121 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN A 248 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU A 123 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ALA A 250 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 removed outlier: 7.210A pdb=" N LEU A 61 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ARG A 80 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A 59 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 319 through 321 removed outlier: 3.730A pdb=" N LEU A 319 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 321 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AA6, first strand: chain 'A' and resid 739 through 742 removed outlier: 7.003A pdb=" N VAL A 740 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN A 752 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 87 removed outlier: 7.297A pdb=" N LEU B 61 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ARG B 80 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 59 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 118 through 123 removed outlier: 4.550A pdb=" N VAL B 119 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ARG B 246 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU B 121 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLN B 248 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 123 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ALA B 250 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N VAL B 245 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 11.251A pdb=" N LEU B 268 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 11.568A pdb=" N LEU B 247 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 11.956A pdb=" N PHE B 266 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 10.853A pdb=" N GLU B 249 " --> pdb=" O PHE B 264 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N PHE B 264 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA B 226 " --> pdb=" O PHE B 264 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N PHE B 266 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 228 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU B 268 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU B 230 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 59 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ARG B 80 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU B 61 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 462 through 463 removed outlier: 3.567A pdb=" N SER B 725 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 739 through 742 removed outlier: 7.028A pdb=" N VAL B 740 " --> pdb=" O GLN B 754 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 752 " --> pdb=" O GLY B 742 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.851A pdb=" N GLU E 96 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER E 105 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL E 94 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR E 107 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ALA E 92 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 32 through 34 removed outlier: 6.692A pdb=" N LEU E 119 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLN E 133 " --> pdb=" O TYR E 117 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR E 117 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR E 135 " --> pdb=" O GLY E 115 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY E 115 " --> pdb=" O THR E 135 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 163 through 168 Processing sheet with id=AB5, first strand: chain 'E' and resid 363 through 367 removed outlier: 4.901A pdb=" N THR E 330 " --> pdb=" O LEU E 349 " (cutoff:3.500A) removed outlier: 12.186A pdb=" N THR E 328 " --> pdb=" O PRO E 351 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL E 288 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LYS E 421 " --> pdb=" O VAL E 288 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER E 419 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N PHE E 292 " --> pdb=" O ASN E 417 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASN E 417 " --> pdb=" O PHE E 292 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 303 through 308 removed outlier: 5.765A pdb=" N ILE E 304 " --> pdb=" O VAL E 394 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TRP E 396 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU E 306 " --> pdb=" O TRP E 396 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 408 through 409 removed outlier: 6.069A pdb=" N LEU E 485 " --> pdb=" O CYS E 586 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 408 through 409 removed outlier: 6.665A pdb=" N ALA E 515 " --> pdb=" O LYS E 525 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LYS E 525 " --> pdb=" O ALA E 515 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 475 through 480 Processing sheet with id=AC1, first strand: chain 'E' and resid 590 through 593 1081 hydrogen bonds defined for protein. 3102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.60 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7417 1.34 - 1.46: 5073 1.46 - 1.58: 10501 1.58 - 1.71: 0 1.71 - 1.83: 141 Bond restraints: 23132 Sorted by residual: bond pdb=" N VAL A 173 " pdb=" CA VAL A 173 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.09e+01 bond pdb=" N GLY E 299 " pdb=" CA GLY E 299 " ideal model delta sigma weight residual 1.445 1.475 -0.030 9.90e-03 1.02e+04 9.26e+00 bond pdb=" N LYS A 174 " pdb=" CA LYS A 174 " ideal model delta sigma weight residual 1.453 1.488 -0.036 1.18e-02 7.18e+03 9.15e+00 bond pdb=" N VAL G 717 " pdb=" CA VAL G 717 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.30e-02 5.92e+03 8.47e+00 bond pdb=" N ARG E 635 " pdb=" CA ARG E 635 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.79e+00 ... (remaining 23127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 30579 2.01 - 4.01: 747 4.01 - 6.02: 108 6.02 - 8.03: 20 8.03 - 10.03: 5 Bond angle restraints: 31459 Sorted by residual: angle pdb=" N PHE B 583 " pdb=" CA PHE B 583 " pdb=" CB PHE B 583 " ideal model delta sigma weight residual 110.12 104.47 5.65 1.47e+00 4.63e-01 1.48e+01 angle pdb=" CA GLN B 186 " pdb=" CB GLN B 186 " pdb=" CG GLN B 186 " ideal model delta sigma weight residual 114.10 121.74 -7.64 2.00e+00 2.50e-01 1.46e+01 angle pdb=" CA MET A 31 " pdb=" CB MET A 31 " pdb=" CG MET A 31 " ideal model delta sigma weight residual 114.10 121.45 -7.35 2.00e+00 2.50e-01 1.35e+01 angle pdb=" N VAL G 717 " pdb=" CA VAL G 717 " pdb=" C VAL G 717 " ideal model delta sigma weight residual 111.81 108.69 3.12 8.60e-01 1.35e+00 1.32e+01 angle pdb=" CA MET A 559 " pdb=" CB MET A 559 " pdb=" CG MET A 559 " ideal model delta sigma weight residual 114.10 120.96 -6.86 2.00e+00 2.50e-01 1.18e+01 ... (remaining 31454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 12683 18.00 - 36.00: 994 36.00 - 54.00: 144 54.00 - 72.00: 30 72.00 - 90.00: 29 Dihedral angle restraints: 13880 sinusoidal: 5382 harmonic: 8498 Sorted by residual: dihedral pdb=" CA LEU G 174 " pdb=" C LEU G 174 " pdb=" N PRO G 175 " pdb=" CA PRO G 175 " ideal model delta harmonic sigma weight residual 180.00 150.39 29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA LYS G 548 " pdb=" C LYS G 548 " pdb=" N VAL G 549 " pdb=" CA VAL G 549 " ideal model delta harmonic sigma weight residual 180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA VAL G 435 " pdb=" C VAL G 435 " pdb=" N LYS G 436 " pdb=" CA LYS G 436 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 13877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2406 0.036 - 0.072: 867 0.072 - 0.108: 300 0.108 - 0.144: 90 0.144 - 0.180: 14 Chirality restraints: 3677 Sorted by residual: chirality pdb=" CA HIS G 343 " pdb=" N HIS G 343 " pdb=" C HIS G 343 " pdb=" CB HIS G 343 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" CA TYR B 555 " pdb=" N TYR B 555 " pdb=" C TYR B 555 " pdb=" CB TYR B 555 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CA VAL B 267 " pdb=" N VAL B 267 " pdb=" C VAL B 267 " pdb=" CB VAL B 267 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.15e-01 ... (remaining 3674 not shown) Planarity restraints: 4026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 197 " -0.022 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C THR B 197 " 0.076 2.00e-02 2.50e+03 pdb=" O THR B 197 " -0.028 2.00e-02 2.50e+03 pdb=" N GLN B 198 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 89 " -0.019 2.00e-02 2.50e+03 2.28e-02 1.30e+01 pdb=" CG TRP E 89 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP E 89 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP E 89 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP E 89 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP E 89 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 89 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 89 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 89 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 89 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 583 " -0.029 2.00e-02 2.50e+03 2.61e-02 1.19e+01 pdb=" CG PHE B 583 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE B 583 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 583 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 583 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 583 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 583 " -0.005 2.00e-02 2.50e+03 ... (remaining 4023 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 299 2.66 - 3.22: 21477 3.22 - 3.78: 33625 3.78 - 4.34: 43910 4.34 - 4.90: 71994 Nonbonded interactions: 171305 Sorted by model distance: nonbonded pdb=" OE1 GLU A 472 " pdb=" OH TYR A 486 " model vdw 2.104 3.040 nonbonded pdb=" OE1 GLU B 472 " pdb=" OH TYR B 486 " model vdw 2.129 3.040 nonbonded pdb=" O PRO A 568 " pdb=" ND2 ASN B 569 " model vdw 2.130 3.120 nonbonded pdb=" OD1 ASN A 642 " pdb=" OG SER A 644 " model vdw 2.142 3.040 nonbonded pdb=" O PRO B 271 " pdb=" OH TYR B 278 " model vdw 2.161 3.040 ... (remaining 171300 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 55 through 894) selection = (chain 'B' and (resid 55 through 348 or resid 369 through 894)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.890 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 0.059 23132 Z= 0.216 Angle : 0.750 10.033 31459 Z= 0.403 Chirality : 0.044 0.180 3677 Planarity : 0.006 0.069 4026 Dihedral : 13.703 89.999 8372 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.08 % Allowed : 1.26 % Favored : 98.66 % 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: -1.98 (0.13), residues: 2918 helix: -0.73 (0.13), residues: 1353 sheet: -0.69 (0.26), residues: 348 loop : -2.12 (0.14), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 249 TYR 0.023 0.002 TYR B 555 PHE 0.060 0.002 PHE B 583 TRP 0.061 0.002 TRP E 89 HIS 0.016 0.001 HIS E 632 Details of bonding type rmsd covalent geometry : bond 0.00434 (23132) covalent geometry : angle 0.74953 (31459) hydrogen bonds : bond 0.14264 ( 1067) hydrogen bonds : angle 6.03135 ( 3102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.743 Fit side-chains REVERT: A 31 MET cc_start: 0.1246 (ttt) cc_final: 0.0980 (ttt) REVERT: A 559 MET cc_start: 0.4628 (ttp) cc_final: 0.3446 (mmt) REVERT: A 586 MET cc_start: 0.6599 (mmm) cc_final: 0.5928 (mmm) REVERT: A 587 MET cc_start: 0.8565 (mmp) cc_final: 0.8170 (mmp) REVERT: A 776 MET cc_start: 0.6205 (mmp) cc_final: 0.5958 (mtt) REVERT: B 317 CYS cc_start: 0.8646 (m) cc_final: 0.7767 (p) REVERT: B 696 MET cc_start: 0.3965 (mtp) cc_final: 0.3291 (mtp) REVERT: E 456 MET cc_start: 0.8772 (mmm) cc_final: 0.8385 (tmm) REVERT: G 311 MET cc_start: 0.7900 (tpt) cc_final: 0.7499 (tpt) REVERT: G 485 MET cc_start: 0.7769 (mmm) cc_final: 0.7552 (mmm) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.1292 time to fit residues: 19.6489 Evaluate side-chains 77 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 191 GLN B 198 GLN B 569 ASN E 100 GLN ** G 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.072963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.051713 restraints weight = 181211.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.051184 restraints weight = 116902.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.051022 restraints weight = 94325.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.051200 restraints weight = 90026.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.051400 restraints weight = 72047.869| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23132 Z= 0.113 Angle : 0.554 7.022 31459 Z= 0.277 Chirality : 0.039 0.147 3677 Planarity : 0.005 0.053 4026 Dihedral : 4.409 25.114 3141 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 2918 helix: 0.60 (0.14), residues: 1377 sheet: -0.22 (0.27), residues: 338 loop : -1.47 (0.15), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 591 TYR 0.017 0.001 TYR E 637 PHE 0.018 0.001 PHE B 583 TRP 0.031 0.001 TRP E 89 HIS 0.006 0.001 HIS E 632 Details of bonding type rmsd covalent geometry : bond 0.00234 (23132) covalent geometry : angle 0.55414 (31459) hydrogen bonds : bond 0.03855 ( 1067) hydrogen bonds : angle 4.47858 ( 3102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 66 MET cc_start: 0.4694 (tmm) cc_final: 0.4294 (tmm) REVERT: A 76 MET cc_start: 0.9013 (tpt) cc_final: 0.8713 (tpp) REVERT: A 167 LEU cc_start: 0.4916 (mm) cc_final: 0.4500 (tp) REVERT: A 559 MET cc_start: 0.4455 (ttp) cc_final: 0.3578 (tmm) REVERT: A 586 MET cc_start: 0.6578 (mmm) cc_final: 0.6020 (mmm) REVERT: A 587 MET cc_start: 0.8629 (mmp) cc_final: 0.8240 (mmp) REVERT: A 696 MET cc_start: 0.5440 (tpt) cc_final: 0.4945 (tpp) REVERT: A 776 MET cc_start: 0.6257 (mmp) cc_final: 0.5902 (mtt) REVERT: B 317 CYS cc_start: 0.8724 (m) cc_final: 0.7555 (p) REVERT: B 696 MET cc_start: 0.4139 (mtp) cc_final: 0.3453 (mtp) REVERT: E 81 ILE cc_start: 0.8983 (mp) cc_final: 0.8532 (tp) REVERT: E 276 CYS cc_start: 0.9237 (t) cc_final: 0.9024 (t) REVERT: E 456 MET cc_start: 0.9210 (mmm) cc_final: 0.8600 (tmm) REVERT: G 311 MET cc_start: 0.8492 (tpt) cc_final: 0.8054 (tpt) REVERT: G 319 ASP cc_start: 0.8370 (p0) cc_final: 0.8106 (p0) REVERT: G 485 MET cc_start: 0.8353 (mmm) cc_final: 0.8151 (mmm) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1183 time to fit residues: 17.9889 Evaluate side-chains 79 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 203 optimal weight: 20.0000 chunk 250 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 chunk 58 optimal weight: 30.0000 chunk 131 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 273 optimal weight: 20.0000 chunk 145 optimal weight: 0.2980 chunk 267 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 173 optimal weight: 0.0870 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 GLN ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS G 561 HIS ** G 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 640 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.072668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.054549 restraints weight = 181597.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.052707 restraints weight = 117434.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.053303 restraints weight = 95167.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.053154 restraints weight = 77726.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.053242 restraints weight = 81707.300| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23132 Z= 0.107 Angle : 0.513 7.281 31459 Z= 0.255 Chirality : 0.038 0.154 3677 Planarity : 0.004 0.052 4026 Dihedral : 4.067 20.202 3141 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.90 % 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: 0.21 (0.15), residues: 2918 helix: 1.24 (0.14), residues: 1383 sheet: 0.00 (0.28), residues: 332 loop : -1.10 (0.16), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 635 TYR 0.012 0.001 TYR A 824 PHE 0.015 0.001 PHE E 79 TRP 0.012 0.001 TRP E 89 HIS 0.005 0.001 HIS E 632 Details of bonding type rmsd covalent geometry : bond 0.00228 (23132) covalent geometry : angle 0.51267 (31459) hydrogen bonds : bond 0.03400 ( 1067) hydrogen bonds : angle 4.14035 ( 3102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8666 (tpt) cc_final: 0.8370 (tpp) REVERT: A 167 LEU cc_start: 0.4744 (mm) cc_final: 0.4393 (tp) REVERT: A 559 MET cc_start: 0.4319 (ttp) cc_final: 0.3278 (tmm) REVERT: A 586 MET cc_start: 0.6830 (mmm) cc_final: 0.6050 (mmm) REVERT: A 587 MET cc_start: 0.8546 (mmp) cc_final: 0.8110 (mmp) REVERT: A 776 MET cc_start: 0.6160 (mmp) cc_final: 0.5822 (mtt) REVERT: B 317 CYS cc_start: 0.8641 (m) cc_final: 0.7484 (p) REVERT: B 559 MET cc_start: 0.2694 (mmt) cc_final: 0.0937 (tpt) REVERT: B 696 MET cc_start: 0.2521 (mtp) cc_final: 0.1889 (mtp) REVERT: E 81 ILE cc_start: 0.8886 (mp) cc_final: 0.8513 (tp) REVERT: E 456 MET cc_start: 0.9195 (mmm) cc_final: 0.8601 (tmm) REVERT: G 311 MET cc_start: 0.8734 (tpt) cc_final: 0.8412 (tpt) REVERT: G 319 ASP cc_start: 0.8577 (p0) cc_final: 0.8269 (p0) REVERT: G 485 MET cc_start: 0.8273 (mmm) cc_final: 0.7970 (mmm) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.1162 time to fit residues: 17.9027 Evaluate side-chains 75 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 241 optimal weight: 0.8980 chunk 37 optimal weight: 30.0000 chunk 3 optimal weight: 5.9990 chunk 68 optimal weight: 30.0000 chunk 99 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 148 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 164 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS A 87 ASN ** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 GLN G 194 GLN ** G 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.069755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.047987 restraints weight = 184028.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.046664 restraints weight = 113803.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.046899 restraints weight = 98105.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.047144 restraints weight = 82681.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.047129 restraints weight = 73731.493| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23132 Z= 0.258 Angle : 0.695 11.912 31459 Z= 0.349 Chirality : 0.042 0.185 3677 Planarity : 0.005 0.084 4026 Dihedral : 4.588 22.445 3141 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.04 % Allowed : 3.98 % Favored : 95.97 % 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: 0.23 (0.15), residues: 2918 helix: 1.22 (0.14), residues: 1395 sheet: -0.26 (0.28), residues: 333 loop : -0.98 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 287 TYR 0.018 0.002 TYR E 167 PHE 0.026 0.002 PHE E 181 TRP 0.014 0.002 TRP E 324 HIS 0.010 0.002 HIS G 350 Details of bonding type rmsd covalent geometry : bond 0.00543 (23132) covalent geometry : angle 0.69499 (31459) hydrogen bonds : bond 0.04267 ( 1067) hydrogen bonds : angle 4.57744 ( 3102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.0379 (ttm) cc_final: -0.0087 (tpp) REVERT: A 76 MET cc_start: 0.9012 (tpt) cc_final: 0.8717 (tpp) REVERT: A 167 LEU cc_start: 0.4903 (mm) cc_final: 0.4212 (tp) REVERT: A 559 MET cc_start: 0.4239 (ttp) cc_final: 0.3191 (tmm) REVERT: A 578 MET cc_start: 0.8418 (mtt) cc_final: 0.8209 (mtt) REVERT: A 587 MET cc_start: 0.8615 (mmp) cc_final: 0.8190 (mmp) REVERT: A 776 MET cc_start: 0.6095 (mmp) cc_final: 0.5619 (mtt) REVERT: B 317 CYS cc_start: 0.8832 (m) cc_final: 0.8045 (t) REVERT: B 696 MET cc_start: 0.3176 (mtp) cc_final: 0.2502 (mtp) REVERT: E 456 MET cc_start: 0.9286 (mmm) cc_final: 0.8688 (tmm) REVERT: G 311 MET cc_start: 0.8674 (tpt) cc_final: 0.8373 (tpt) REVERT: G 485 MET cc_start: 0.8288 (mmm) cc_final: 0.7963 (mmm) outliers start: 1 outliers final: 1 residues processed: 79 average time/residue: 0.1106 time to fit residues: 15.5319 Evaluate side-chains 74 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 250 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 216 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 286 optimal weight: 50.0000 chunk 63 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 ASN G 614 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.071247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.050225 restraints weight = 180695.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.048895 restraints weight = 124877.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.048736 restraints weight = 107775.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.048848 restraints weight = 106595.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.048928 restraints weight = 81402.126| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23132 Z= 0.121 Angle : 0.527 7.681 31459 Z= 0.262 Chirality : 0.039 0.141 3677 Planarity : 0.004 0.048 4026 Dihedral : 4.196 20.177 3141 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 0.54 (0.15), residues: 2918 helix: 1.45 (0.14), residues: 1412 sheet: -0.12 (0.27), residues: 333 loop : -0.83 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 512 TYR 0.013 0.001 TYR A 390 PHE 0.008 0.001 PHE E 79 TRP 0.017 0.001 TRP B 662 HIS 0.005 0.001 HIS E 632 Details of bonding type rmsd covalent geometry : bond 0.00253 (23132) covalent geometry : angle 0.52658 (31459) hydrogen bonds : bond 0.03363 ( 1067) hydrogen bonds : angle 4.18581 ( 3102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 66 MET cc_start: 0.4747 (tmm) cc_final: 0.4368 (tmm) REVERT: A 76 MET cc_start: 0.9039 (tpt) cc_final: 0.8757 (tpp) REVERT: A 167 LEU cc_start: 0.4943 (mm) cc_final: 0.4314 (tp) REVERT: A 559 MET cc_start: 0.4435 (ttp) cc_final: 0.3450 (tmm) REVERT: A 578 MET cc_start: 0.8404 (mtt) cc_final: 0.8196 (mtt) REVERT: A 586 MET cc_start: 0.6865 (mmm) cc_final: 0.6285 (mmm) REVERT: A 587 MET cc_start: 0.8654 (mmp) cc_final: 0.8199 (mmp) REVERT: A 776 MET cc_start: 0.6152 (mmp) cc_final: 0.5626 (mtt) REVERT: B 317 CYS cc_start: 0.8867 (m) cc_final: 0.7896 (t) REVERT: B 559 MET cc_start: 0.3135 (mmt) cc_final: 0.1472 (tpt) REVERT: B 696 MET cc_start: 0.3614 (mtp) cc_final: 0.2946 (mtp) REVERT: E 456 MET cc_start: 0.9258 (mmm) cc_final: 0.8587 (tmm) REVERT: G 311 MET cc_start: 0.8642 (tpt) cc_final: 0.8347 (tpt) REVERT: G 443 MET cc_start: 0.8667 (tpt) cc_final: 0.8424 (tpp) REVERT: G 485 MET cc_start: 0.8374 (mmm) cc_final: 0.8001 (mmm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1201 time to fit residues: 17.3669 Evaluate side-chains 73 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 88 optimal weight: 0.9980 chunk 216 optimal weight: 4.9990 chunk 61 optimal weight: 30.0000 chunk 70 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 21 optimal weight: 0.0970 chunk 49 optimal weight: 0.0050 chunk 122 optimal weight: 40.0000 chunk 187 optimal weight: 5.9990 chunk 232 optimal weight: 0.7980 chunk 231 optimal weight: 10.0000 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** G 251 ASN ** 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 = 0.3939 r_free = 0.3939 target = 0.072598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.052353 restraints weight = 188386.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.050399 restraints weight = 134761.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.050833 restraints weight = 115510.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.050693 restraints weight = 104718.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.050795 restraints weight = 84116.350| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23132 Z= 0.108 Angle : 0.510 7.209 31459 Z= 0.252 Chirality : 0.038 0.141 3677 Planarity : 0.004 0.046 4026 Dihedral : 3.985 19.126 3141 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.16), residues: 2918 helix: 1.64 (0.14), residues: 1415 sheet: 0.05 (0.27), residues: 335 loop : -0.73 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 558 TYR 0.014 0.001 TYR E 518 PHE 0.010 0.001 PHE B 583 TRP 0.016 0.001 TRP B 662 HIS 0.004 0.001 HIS G 541 Details of bonding type rmsd covalent geometry : bond 0.00231 (23132) covalent geometry : angle 0.50961 (31459) hydrogen bonds : bond 0.03123 ( 1067) hydrogen bonds : angle 4.03531 ( 3102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 76 MET cc_start: 0.8920 (tpt) cc_final: 0.8680 (tpp) REVERT: A 167 LEU cc_start: 0.4896 (mm) cc_final: 0.4341 (tp) REVERT: A 559 MET cc_start: 0.4393 (ttp) cc_final: 0.3616 (tpp) REVERT: A 587 MET cc_start: 0.8655 (mmp) cc_final: 0.8199 (mmp) REVERT: A 776 MET cc_start: 0.5907 (mmp) cc_final: 0.5357 (mtt) REVERT: B 317 CYS cc_start: 0.8851 (m) cc_final: 0.7801 (t) REVERT: B 559 MET cc_start: 0.3207 (mmt) cc_final: 0.1495 (tpt) REVERT: B 696 MET cc_start: 0.3923 (mtp) cc_final: 0.3324 (mtp) REVERT: E 456 MET cc_start: 0.9200 (mmm) cc_final: 0.8525 (tmm) REVERT: G 485 MET cc_start: 0.8341 (mmm) cc_final: 0.7965 (mmm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1212 time to fit residues: 17.5088 Evaluate side-chains 75 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 21 optimal weight: 0.0970 chunk 126 optimal weight: 40.0000 chunk 137 optimal weight: 20.0000 chunk 196 optimal weight: 0.6980 chunk 185 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 76 optimal weight: 0.0970 chunk 81 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 240 optimal weight: 0.6980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS B 521 GLN ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 GLN G 251 ASN G 347 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.073333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.051974 restraints weight = 188088.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.050878 restraints weight = 128818.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.051514 restraints weight = 101425.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.051493 restraints weight = 84602.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.051713 restraints weight = 72514.819| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23132 Z= 0.086 Angle : 0.497 7.588 31459 Z= 0.242 Chirality : 0.038 0.138 3677 Planarity : 0.004 0.042 4026 Dihedral : 3.794 19.599 3141 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % 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: 0.93 (0.16), residues: 2918 helix: 1.74 (0.14), residues: 1411 sheet: 0.30 (0.28), residues: 331 loop : -0.65 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 558 TYR 0.017 0.001 TYR E 476 PHE 0.008 0.001 PHE E 79 TRP 0.015 0.001 TRP B 662 HIS 0.004 0.001 HIS G 541 Details of bonding type rmsd covalent geometry : bond 0.00183 (23132) covalent geometry : angle 0.49744 (31459) hydrogen bonds : bond 0.02874 ( 1067) hydrogen bonds : angle 3.89293 ( 3102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.4820 (mm) cc_final: 0.4392 (tp) REVERT: A 559 MET cc_start: 0.4254 (ttp) cc_final: 0.3502 (tpp) REVERT: A 586 MET cc_start: 0.6846 (mmm) cc_final: 0.6270 (mmm) REVERT: A 587 MET cc_start: 0.8632 (mmp) cc_final: 0.8164 (mmp) REVERT: B 317 CYS cc_start: 0.8766 (m) cc_final: 0.7635 (t) REVERT: B 559 MET cc_start: 0.3140 (mmt) cc_final: 0.1513 (tpt) REVERT: B 696 MET cc_start: 0.3656 (mtp) cc_final: 0.2997 (mtp) REVERT: B 712 MET cc_start: 0.4009 (ttp) cc_final: 0.3662 (ppp) REVERT: E 456 MET cc_start: 0.9151 (mmm) cc_final: 0.8522 (tmm) REVERT: G 311 MET cc_start: 0.8376 (tpt) cc_final: 0.7871 (tpt) REVERT: G 443 MET cc_start: 0.8625 (tpt) cc_final: 0.8398 (tpp) REVERT: G 485 MET cc_start: 0.8330 (mmm) cc_final: 0.7982 (mmm) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1187 time to fit residues: 18.0867 Evaluate side-chains 77 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 111 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 187 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 250 optimal weight: 0.6980 chunk 289 optimal weight: 50.0000 chunk 170 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 80 optimal weight: 0.0980 overall best weight: 3.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 GLN ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 HIS E 653 GLN G 579 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.071523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.050965 restraints weight = 187811.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.049117 restraints weight = 133925.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.049346 restraints weight = 112274.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.049401 restraints weight = 99796.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.049742 restraints weight = 78482.379| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23132 Z= 0.200 Angle : 0.591 8.935 31459 Z= 0.296 Chirality : 0.040 0.164 3677 Planarity : 0.004 0.055 4026 Dihedral : 4.087 19.817 3141 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: 0.78 (0.16), residues: 2918 helix: 1.63 (0.14), residues: 1407 sheet: -0.03 (0.28), residues: 337 loop : -0.66 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 352 TYR 0.017 0.001 TYR E 518 PHE 0.033 0.001 PHE A 104 TRP 0.012 0.001 TRP A 723 HIS 0.010 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00423 (23132) covalent geometry : angle 0.59132 (31459) hydrogen bonds : bond 0.03537 ( 1067) hydrogen bonds : angle 4.22454 ( 3102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.9060 (tpt) cc_final: 0.8731 (tpp) REVERT: A 167 LEU cc_start: 0.4774 (mm) cc_final: 0.4412 (tp) REVERT: A 559 MET cc_start: 0.4556 (ttp) cc_final: 0.3758 (tpp) REVERT: A 578 MET cc_start: 0.8261 (mtt) cc_final: 0.8045 (mtt) REVERT: A 586 MET cc_start: 0.7016 (mmm) cc_final: 0.5486 (tpt) REVERT: A 587 MET cc_start: 0.8641 (mmp) cc_final: 0.8039 (mmp) REVERT: A 721 MET cc_start: 0.4932 (mmp) cc_final: 0.4686 (mmp) REVERT: B 317 CYS cc_start: 0.8882 (m) cc_final: 0.8079 (t) REVERT: B 559 MET cc_start: 0.3098 (mmt) cc_final: 0.1460 (tpt) REVERT: B 696 MET cc_start: 0.3651 (mtp) cc_final: 0.3072 (mtp) REVERT: B 712 MET cc_start: 0.4055 (ttp) cc_final: 0.3586 (tmm) REVERT: E 456 MET cc_start: 0.9210 (mmm) cc_final: 0.8524 (tmm) REVERT: G 311 MET cc_start: 0.8543 (tpt) cc_final: 0.8022 (tpt) REVERT: G 443 MET cc_start: 0.8784 (tpt) cc_final: 0.8567 (tpp) REVERT: G 485 MET cc_start: 0.8258 (mmm) cc_final: 0.7913 (mmm) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1170 time to fit residues: 17.2314 Evaluate side-chains 75 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 201 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 170 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 230 optimal weight: 0.9990 chunk 225 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 169 optimal weight: 20.0000 chunk 159 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 GLN G 579 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.072087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.051641 restraints weight = 188421.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.049858 restraints weight = 134056.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.050151 restraints weight = 111883.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.050246 restraints weight = 97719.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.050465 restraints weight = 78499.764| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23132 Z= 0.128 Angle : 0.533 7.831 31459 Z= 0.264 Chirality : 0.039 0.154 3677 Planarity : 0.004 0.042 4026 Dihedral : 3.975 19.587 3141 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.16), residues: 2918 helix: 1.68 (0.14), residues: 1418 sheet: 0.09 (0.28), residues: 333 loop : -0.67 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 146 TYR 0.010 0.001 TYR E 167 PHE 0.026 0.001 PHE A 104 TRP 0.014 0.001 TRP B 662 HIS 0.008 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00274 (23132) covalent geometry : angle 0.53306 (31459) hydrogen bonds : bond 0.03117 ( 1067) hydrogen bonds : angle 4.02748 ( 3102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8973 (tpt) cc_final: 0.8626 (tpp) REVERT: A 167 LEU cc_start: 0.4760 (mm) cc_final: 0.4339 (tp) REVERT: A 435 MET cc_start: 0.5967 (ttm) cc_final: 0.4745 (tpt) REVERT: A 559 MET cc_start: 0.4946 (ttp) cc_final: 0.4106 (tpp) REVERT: A 586 MET cc_start: 0.7029 (mmm) cc_final: 0.6407 (mmm) REVERT: A 587 MET cc_start: 0.8687 (mmp) cc_final: 0.8202 (mmp) REVERT: B 317 CYS cc_start: 0.8784 (m) cc_final: 0.7974 (t) REVERT: B 696 MET cc_start: 0.3531 (mtp) cc_final: 0.2966 (mtp) REVERT: B 712 MET cc_start: 0.4071 (ttp) cc_final: 0.3580 (tmm) REVERT: E 234 GLN cc_start: 0.6621 (pm20) cc_final: 0.4942 (pp30) REVERT: E 456 MET cc_start: 0.9179 (mmm) cc_final: 0.8467 (tmm) REVERT: G 311 MET cc_start: 0.8444 (tpt) cc_final: 0.8015 (tpt) REVERT: G 485 MET cc_start: 0.8345 (mmm) cc_final: 0.8015 (mmm) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1110 time to fit residues: 16.7039 Evaluate side-chains 76 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 266 optimal weight: 10.0000 chunk 47 optimal weight: 30.0000 chunk 290 optimal weight: 50.0000 chunk 127 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 277 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 227 optimal weight: 1.9990 chunk 284 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 GLN G 504 HIS G 574 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.069113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.047777 restraints weight = 182738.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.046684 restraints weight = 127384.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.046699 restraints weight = 102088.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.046704 restraints weight = 102166.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.047024 restraints weight = 79097.194| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23132 Z= 0.258 Angle : 0.694 12.591 31459 Z= 0.350 Chirality : 0.042 0.160 3677 Planarity : 0.005 0.051 4026 Dihedral : 4.533 20.879 3141 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: 0.50 (0.16), residues: 2918 helix: 1.36 (0.14), residues: 1401 sheet: -0.26 (0.28), residues: 345 loop : -0.69 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 287 TYR 0.021 0.002 TYR E 167 PHE 0.026 0.002 PHE A 104 TRP 0.016 0.002 TRP A 723 HIS 0.012 0.002 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00537 (23132) covalent geometry : angle 0.69437 (31459) hydrogen bonds : bond 0.04083 ( 1067) hydrogen bonds : angle 4.48934 ( 3102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5836 Ramachandran restraints generated. 2918 Oldfield, 0 Emsley, 2918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8983 (tpt) cc_final: 0.8687 (tpp) REVERT: A 167 LEU cc_start: 0.4207 (mm) cc_final: 0.3873 (tp) REVERT: A 435 MET cc_start: 0.5957 (ttm) cc_final: 0.4642 (tpt) REVERT: A 559 MET cc_start: 0.5044 (ttp) cc_final: 0.3914 (tmm) REVERT: A 586 MET cc_start: 0.7101 (mmm) cc_final: 0.5466 (tpt) REVERT: A 587 MET cc_start: 0.8622 (mmp) cc_final: 0.8018 (mmp) REVERT: B 317 CYS cc_start: 0.8819 (m) cc_final: 0.8229 (t) REVERT: B 696 MET cc_start: 0.3031 (mtp) cc_final: 0.2433 (mtp) REVERT: B 712 MET cc_start: 0.4292 (ttp) cc_final: 0.3735 (tmm) REVERT: B 741 MET cc_start: 0.0038 (ptt) cc_final: -0.0219 (ptt) REVERT: G 311 MET cc_start: 0.8478 (tpt) cc_final: 0.8055 (tpt) REVERT: G 485 MET cc_start: 0.8285 (mmm) cc_final: 0.8053 (mmm) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1199 time to fit residues: 17.7776 Evaluate side-chains 73 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 96 optimal weight: 0.9990 chunk 107 optimal weight: 0.0970 chunk 242 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 214 optimal weight: 5.9990 chunk 278 optimal weight: 30.0000 chunk 275 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 268 optimal weight: 4.9990 chunk 255 optimal weight: 0.7980 chunk 71 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 HIS ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.071311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.050852 restraints weight = 181550.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.048503 restraints weight = 126103.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.049000 restraints weight = 95226.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.049108 restraints weight = 77141.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.049135 restraints weight = 71568.153| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23132 Z= 0.096 Angle : 0.540 8.656 31459 Z= 0.264 Chirality : 0.039 0.156 3677 Planarity : 0.004 0.042 4026 Dihedral : 4.036 19.535 3141 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.16), residues: 2918 helix: 1.61 (0.14), residues: 1412 sheet: 0.12 (0.28), residues: 335 loop : -0.60 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 248 TYR 0.017 0.001 TYR E 518 PHE 0.019 0.001 PHE A 104 TRP 0.015 0.001 TRP B 662 HIS 0.006 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00204 (23132) covalent geometry : angle 0.54043 (31459) hydrogen bonds : bond 0.03050 ( 1067) hydrogen bonds : angle 4.00329 ( 3102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3296.06 seconds wall clock time: 57 minutes 54.36 seconds (3474.36 seconds total)