Starting phenix.real_space_refine on Sun Feb 18 18:26:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tw3_26149/02_2024/7tw3_26149.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tw3_26149/02_2024/7tw3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tw3_26149/02_2024/7tw3_26149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tw3_26149/02_2024/7tw3_26149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tw3_26149/02_2024/7tw3_26149.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tw3_26149/02_2024/7tw3_26149.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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 Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: {'GLN:plan1': 6, 'HIS:plan': 9, 'TYR:plan': 4, 'ASN:plan1': 7, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 195 Time building chain proxies: 11.52, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 8.36 Conformation dependent library (CDL) restraints added in 4.3 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: 2.51 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: 8.26 Time building geometry restraints manager: 9.04 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: 95.22 - 103.02: 180 103.02 - 110.81: 8409 110.81 - 118.61: 10265 118.61 - 126.40: 12233 126.40 - 134.20: 372 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 2.440 nonbonded pdb=" OE1 GLU B 472 " pdb=" OH TYR B 486 " model vdw 2.129 2.440 nonbonded pdb=" O PRO A 568 " pdb=" ND2 ASN B 569 " model vdw 2.130 2.520 nonbonded pdb=" OD1 ASN A 642 " pdb=" OG SER A 644 " model vdw 2.142 2.440 nonbonded pdb=" O PRO B 271 " pdb=" OH TYR B 278 " model vdw 2.161 2.440 ... (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 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: 3.100 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: 12.850 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 58.800 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.160 ------------------------------------------------------------------------------- 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= 0.286 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (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 TRP 0.061 0.002 TRP E 89 HIS 0.016 0.001 HIS E 632 PHE 0.060 0.002 PHE B 583 TYR 0.023 0.002 TYR B 555 ARG 0.013 0.001 ARG G 249 *********************** 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 fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 2.482 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: 0.8773 (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: 0.3051 time to fit residues: 46.2976 Evaluate side-chains 77 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 247 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 75 optimal weight: 0.1980 chunk 149 optimal weight: 50.0000 chunk 118 optimal weight: 4.9990 chunk 229 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN B 198 GLN ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 653 GLN G 640 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23132 Z= 0.186 Angle : 0.555 6.490 31459 Z= 0.280 Chirality : 0.039 0.141 3677 Planarity : 0.005 0.053 4026 Dihedral : 4.403 24.492 3141 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 2918 helix: 0.59 (0.14), residues: 1378 sheet: -0.19 (0.27), residues: 342 loop : -1.48 (0.15), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 89 HIS 0.007 0.001 HIS E 632 PHE 0.016 0.001 PHE E 79 TYR 0.011 0.001 TYR B 555 ARG 0.004 0.000 ARG B 155 *********************** 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 81 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 2.570 Fit side-chains REVERT: A 31 MET cc_start: 0.0409 (ttt) cc_final: -0.0062 (ttm) REVERT: A 76 MET cc_start: 0.9451 (tpt) cc_final: 0.9223 (tpp) REVERT: A 167 LEU cc_start: 0.5041 (mm) cc_final: 0.4543 (tp) REVERT: A 559 MET cc_start: 0.4352 (ttp) cc_final: 0.3521 (tmm) REVERT: A 586 MET cc_start: 0.6734 (mmm) cc_final: 0.6021 (mmm) REVERT: A 587 MET cc_start: 0.8561 (mmp) cc_final: 0.8151 (mmp) REVERT: A 696 MET cc_start: 0.5270 (tpt) cc_final: 0.4743 (tpp) REVERT: A 776 MET cc_start: 0.6008 (mmp) cc_final: 0.5765 (mtt) REVERT: B 317 CYS cc_start: 0.8694 (m) cc_final: 0.7756 (p) REVERT: B 696 MET cc_start: 0.3689 (mtp) cc_final: 0.2998 (mtp) REVERT: B 776 MET cc_start: 0.7876 (tpp) cc_final: 0.7596 (tpp) REVERT: E 81 ILE cc_start: 0.8973 (mp) cc_final: 0.8581 (tp) REVERT: E 456 MET cc_start: 0.8812 (mmm) cc_final: 0.8386 (tmm) REVERT: G 311 MET cc_start: 0.8225 (tpt) cc_final: 0.7882 (tpt) REVERT: G 319 ASP cc_start: 0.8361 (p0) cc_final: 0.8122 (p0) REVERT: G 443 MET cc_start: 0.8584 (tpt) cc_final: 0.8379 (tpp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2912 time to fit residues: 42.0653 Evaluate side-chains 75 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 147 optimal weight: 50.0000 chunk 82 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 73 optimal weight: 30.0000 chunk 266 optimal weight: 10.0000 chunk 287 optimal weight: 40.0000 chunk 237 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 213 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS B 134 GLN ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 GLN G 227 ASN ** G 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS G 561 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23132 Z= 0.310 Angle : 0.624 9.569 31459 Z= 0.316 Chirality : 0.040 0.142 3677 Planarity : 0.005 0.059 4026 Dihedral : 4.499 23.050 3141 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.04 % Allowed : 4.44 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 2918 helix: 1.10 (0.14), residues: 1382 sheet: -0.18 (0.27), residues: 338 loop : -1.23 (0.16), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 662 HIS 0.011 0.001 HIS G 482 PHE 0.020 0.001 PHE E 181 TYR 0.016 0.001 TYR E 518 ARG 0.005 0.001 ARG G 352 *********************** 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 83 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.0970 (ttt) cc_final: 0.0566 (ttt) REVERT: A 76 MET cc_start: 0.9438 (tpt) cc_final: 0.9221 (tpp) REVERT: A 559 MET cc_start: 0.4492 (ttp) cc_final: 0.3620 (tmm) REVERT: A 587 MET cc_start: 0.8592 (mmp) cc_final: 0.8166 (mmp) REVERT: A 776 MET cc_start: 0.6031 (mmp) cc_final: 0.5690 (mtt) REVERT: B 317 CYS cc_start: 0.8787 (m) cc_final: 0.8009 (p) REVERT: B 696 MET cc_start: 0.3576 (mtp) cc_final: 0.2838 (mtp) REVERT: B 776 MET cc_start: 0.8128 (tpp) cc_final: 0.7833 (tpp) REVERT: E 456 MET cc_start: 0.8853 (mmm) cc_final: 0.8457 (tmm) outliers start: 1 outliers final: 1 residues processed: 83 average time/residue: 0.3114 time to fit residues: 45.8149 Evaluate side-chains 76 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 263 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 127 optimal weight: 30.0000 chunk 178 optimal weight: 3.9990 chunk 267 optimal weight: 0.9980 chunk 283 optimal weight: 8.9990 chunk 139 optimal weight: 40.0000 chunk 253 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 447 GLN G 613 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2078 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= 0.218 Angle : 0.553 8.786 31459 Z= 0.276 Chirality : 0.039 0.141 3677 Planarity : 0.004 0.053 4026 Dihedral : 4.348 21.647 3141 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 2918 helix: 1.37 (0.14), residues: 1390 sheet: -0.17 (0.27), residues: 343 loop : -1.01 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 662 HIS 0.006 0.001 HIS G 482 PHE 0.018 0.001 PHE B 266 TYR 0.013 0.001 TYR E 167 ARG 0.010 0.000 ARG G 558 *********************** 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 80 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.5083 (mm) cc_final: 0.4613 (tp) REVERT: A 559 MET cc_start: 0.4494 (ttp) cc_final: 0.3528 (tmm) REVERT: A 586 MET cc_start: 0.6913 (mmm) cc_final: 0.6208 (mmm) REVERT: A 587 MET cc_start: 0.8605 (mmp) cc_final: 0.8138 (mmp) REVERT: A 776 MET cc_start: 0.5990 (mmp) cc_final: 0.5562 (mtt) REVERT: B 317 CYS cc_start: 0.8843 (m) cc_final: 0.8041 (p) REVERT: B 559 MET cc_start: 0.3404 (mmt) cc_final: 0.1745 (tpt) REVERT: B 696 MET cc_start: 0.3666 (mtp) cc_final: 0.3013 (mtp) REVERT: B 776 MET cc_start: 0.8267 (tpp) cc_final: 0.7947 (tpp) REVERT: E 456 MET cc_start: 0.8816 (mmm) cc_final: 0.8407 (tmm) REVERT: G 311 MET cc_start: 0.8305 (tpt) cc_final: 0.7906 (tpt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2952 time to fit residues: 42.2960 Evaluate side-chains 73 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 235 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 210 optimal weight: 6.9990 chunk 116 optimal weight: 30.0000 chunk 241 optimal weight: 0.7980 chunk 195 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 254 optimal weight: 5.9990 chunk 71 optimal weight: 50.0000 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 347 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2334 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= 0.166 Angle : 0.515 7.889 31459 Z= 0.255 Chirality : 0.038 0.146 3677 Planarity : 0.004 0.044 4026 Dihedral : 4.111 18.938 3141 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 2918 helix: 1.59 (0.14), residues: 1398 sheet: -0.10 (0.27), residues: 348 loop : -0.84 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 662 HIS 0.005 0.001 HIS G 541 PHE 0.013 0.001 PHE E 652 TYR 0.012 0.001 TYR G 546 ARG 0.007 0.000 ARG G 512 *********************** 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 80 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.0130 (ttm) cc_final: -0.0366 (tpp) REVERT: A 167 LEU cc_start: 0.5126 (mm) cc_final: 0.4754 (tp) REVERT: A 435 MET cc_start: 0.5642 (ttt) cc_final: 0.4654 (mpp) REVERT: A 559 MET cc_start: 0.4533 (ttp) cc_final: 0.3809 (tpp) REVERT: A 586 MET cc_start: 0.6998 (mmm) cc_final: 0.5331 (tpt) REVERT: A 587 MET cc_start: 0.8600 (mmp) cc_final: 0.8002 (mmp) REVERT: A 721 MET cc_start: 0.4264 (mmp) cc_final: 0.3992 (mmp) REVERT: A 776 MET cc_start: 0.6021 (mmp) cc_final: 0.5546 (mtt) REVERT: B 317 CYS cc_start: 0.8870 (m) cc_final: 0.7959 (p) REVERT: B 559 MET cc_start: 0.3345 (mmt) cc_final: 0.1735 (tpt) REVERT: B 696 MET cc_start: 0.3770 (mtp) cc_final: 0.3136 (mtp) REVERT: B 776 MET cc_start: 0.8314 (tpp) cc_final: 0.7980 (tpp) REVERT: E 456 MET cc_start: 0.8771 (mmm) cc_final: 0.8307 (tmm) REVERT: G 311 MET cc_start: 0.8314 (tpt) cc_final: 0.7949 (tpt) REVERT: G 485 MET cc_start: 0.8514 (mmp) cc_final: 0.8192 (mmm) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.4272 time to fit residues: 61.1831 Evaluate side-chains 74 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 95 optimal weight: 0.5980 chunk 255 optimal weight: 0.0070 chunk 55 optimal weight: 30.0000 chunk 166 optimal weight: 0.7980 chunk 69 optimal weight: 50.0000 chunk 283 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 148 optimal weight: 50.0000 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 653 GLN G 215 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2480 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= 0.130 Angle : 0.497 7.084 31459 Z= 0.243 Chirality : 0.038 0.154 3677 Planarity : 0.004 0.041 4026 Dihedral : 3.930 17.810 3141 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 2918 helix: 1.71 (0.14), residues: 1402 sheet: 0.06 (0.27), residues: 338 loop : -0.73 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 662 HIS 0.006 0.001 HIS B 101 PHE 0.008 0.001 PHE E 79 TYR 0.011 0.001 TYR G 546 ARG 0.005 0.000 ARG G 512 *********************** 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 88 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 2.647 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.0141 (ttm) cc_final: -0.0403 (tpp) REVERT: A 167 LEU cc_start: 0.4809 (mm) cc_final: 0.4477 (tp) REVERT: A 435 MET cc_start: 0.5504 (ttt) cc_final: 0.4729 (mpp) REVERT: A 559 MET cc_start: 0.4517 (ttp) cc_final: 0.3770 (tpp) REVERT: A 578 MET cc_start: 0.8452 (mpp) cc_final: 0.8136 (mpp) REVERT: A 586 MET cc_start: 0.6965 (mmm) cc_final: 0.5318 (tpt) REVERT: A 587 MET cc_start: 0.8582 (mmp) cc_final: 0.7948 (mmp) REVERT: B 317 CYS cc_start: 0.8852 (m) cc_final: 0.7946 (p) REVERT: B 696 MET cc_start: 0.3423 (mtp) cc_final: 0.2808 (mtp) REVERT: B 776 MET cc_start: 0.8335 (tpp) cc_final: 0.7990 (tpp) REVERT: E 456 MET cc_start: 0.8754 (mmm) cc_final: 0.8305 (tmm) REVERT: G 319 ASP cc_start: 0.8686 (p0) cc_final: 0.8474 (p0) REVERT: G 485 MET cc_start: 0.8502 (mmp) cc_final: 0.8260 (mmm) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2874 time to fit residues: 45.3905 Evaluate side-chains 75 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 273 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 160 optimal weight: 8.9990 chunk 238 optimal weight: 0.6980 chunk 158 optimal weight: 30.0000 chunk 282 optimal weight: 30.0000 chunk 176 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- 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 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 HIS E 653 GLN ** G 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 23132 Z= 0.446 Angle : 0.758 13.101 31459 Z= 0.382 Chirality : 0.043 0.217 3677 Planarity : 0.005 0.063 4026 Dihedral : 4.676 21.915 3141 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 2918 helix: 1.26 (0.14), residues: 1399 sheet: -0.46 (0.27), residues: 336 loop : -0.86 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 643 HIS 0.015 0.002 HIS G 350 PHE 0.021 0.002 PHE E 134 TYR 0.022 0.002 TYR E 637 ARG 0.012 0.001 ARG G 352 *********************** 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 81 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 2.687 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.0316 (ttm) cc_final: -0.0277 (tpp) REVERT: A 167 LEU cc_start: 0.5298 (mm) cc_final: 0.4359 (tp) REVERT: A 435 MET cc_start: 0.5938 (ttt) cc_final: 0.5393 (mmt) REVERT: A 559 MET cc_start: 0.4585 (ttp) cc_final: 0.3869 (tpp) REVERT: A 586 MET cc_start: 0.7090 (mmm) cc_final: 0.5470 (tpt) REVERT: A 587 MET cc_start: 0.8615 (mmp) cc_final: 0.8008 (mmp) REVERT: B 317 CYS cc_start: 0.8926 (m) cc_final: 0.8262 (p) REVERT: B 696 MET cc_start: 0.3945 (mtp) cc_final: 0.3414 (mtp) REVERT: B 776 MET cc_start: 0.8294 (tpp) cc_final: 0.7968 (tpp) REVERT: G 311 MET cc_start: 0.8252 (tpt) cc_final: 0.7840 (tpt) REVERT: G 485 MET cc_start: 0.8490 (mmp) cc_final: 0.8077 (mmm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2930 time to fit residues: 42.3829 Evaluate side-chains 73 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 174 optimal weight: 3.9990 chunk 112 optimal weight: 0.0570 chunk 168 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 179 optimal weight: 0.7980 chunk 192 optimal weight: 0.9980 chunk 139 optimal weight: 30.0000 chunk 26 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 overall best weight: 0.7700 ------------------------------------------------------------------------------- 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 819 HIS B 101 HIS ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3062 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= 0.139 Angle : 0.532 8.592 31459 Z= 0.260 Chirality : 0.039 0.147 3677 Planarity : 0.004 0.042 4026 Dihedral : 4.112 18.437 3141 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.16), residues: 2918 helix: 1.63 (0.14), residues: 1412 sheet: -0.15 (0.27), residues: 351 loop : -0.70 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 662 HIS 0.005 0.001 HIS G 482 PHE 0.011 0.001 PHE A 411 TYR 0.013 0.001 TYR E 518 ARG 0.004 0.000 ARG A 233 *********************** 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 87 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.0189 (ttm) cc_final: -0.0332 (tpp) REVERT: A 167 LEU cc_start: 0.5013 (mm) cc_final: 0.4116 (tp) REVERT: A 435 MET cc_start: 0.5596 (ttt) cc_final: 0.5070 (mmt) REVERT: A 559 MET cc_start: 0.4654 (ttp) cc_final: 0.3944 (tpp) REVERT: A 586 MET cc_start: 0.7029 (mmm) cc_final: 0.5383 (tpt) REVERT: A 587 MET cc_start: 0.8651 (mmp) cc_final: 0.8024 (mmp) REVERT: B 317 CYS cc_start: 0.8853 (m) cc_final: 0.8100 (p) REVERT: B 696 MET cc_start: 0.3960 (mtp) cc_final: 0.3426 (mtp) REVERT: B 776 MET cc_start: 0.8326 (tpp) cc_final: 0.7990 (tpp) REVERT: E 456 MET cc_start: 0.8822 (mmm) cc_final: 0.8212 (tmm) REVERT: G 311 MET cc_start: 0.8167 (tpt) cc_final: 0.7730 (tpt) REVERT: G 485 MET cc_start: 0.8558 (mmp) cc_final: 0.8326 (mmm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.3005 time to fit residues: 46.1684 Evaluate side-chains 76 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 256 optimal weight: 4.9990 chunk 270 optimal weight: 30.0000 chunk 246 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 114 optimal weight: 20.0000 chunk 206 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 237 optimal weight: 8.9990 chunk 248 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3219 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= 0.196 Angle : 0.545 8.225 31459 Z= 0.269 Chirality : 0.039 0.150 3677 Planarity : 0.004 0.042 4026 Dihedral : 4.077 18.911 3141 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.16), residues: 2918 helix: 1.70 (0.14), residues: 1402 sheet: -0.12 (0.27), residues: 352 loop : -0.61 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 662 HIS 0.006 0.001 HIS A 163 PHE 0.010 0.001 PHE E 134 TYR 0.014 0.001 TYR A 818 ARG 0.004 0.000 ARG E 155 *********************** 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 82 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.0230 (ttm) cc_final: -0.0319 (tpp) REVERT: A 167 LEU cc_start: 0.4608 (mm) cc_final: 0.3865 (tp) REVERT: A 435 MET cc_start: 0.5729 (ttt) cc_final: 0.5196 (mmt) REVERT: A 559 MET cc_start: 0.4813 (ttp) cc_final: 0.4083 (tpp) REVERT: A 586 MET cc_start: 0.6886 (mmm) cc_final: 0.5200 (tpt) REVERT: A 587 MET cc_start: 0.8595 (mmp) cc_final: 0.7954 (mmp) REVERT: B 317 CYS cc_start: 0.8903 (m) cc_final: 0.8195 (p) REVERT: B 696 MET cc_start: 0.3941 (mtp) cc_final: 0.3408 (mtp) REVERT: B 776 MET cc_start: 0.8345 (tpp) cc_final: 0.8117 (tpp) REVERT: G 311 MET cc_start: 0.8209 (tpt) cc_final: 0.7821 (tpt) REVERT: G 485 MET cc_start: 0.8592 (mmp) cc_final: 0.8298 (mmm) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.3024 time to fit residues: 44.3415 Evaluate side-chains 76 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 172 optimal weight: 4.9990 chunk 278 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 132 optimal weight: 30.0000 chunk 193 optimal weight: 8.9990 chunk 291 optimal weight: 40.0000 chunk 268 optimal weight: 9.9990 chunk 232 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 142 optimal weight: 50.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 GLN ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 555 ASN ** E 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 504 HIS ** G 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 23132 Z= 0.454 Angle : 0.824 15.587 31459 Z= 0.418 Chirality : 0.045 0.271 3677 Planarity : 0.006 0.065 4026 Dihedral : 5.170 26.828 3141 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 2918 helix: 0.92 (0.14), residues: 1399 sheet: -0.82 (0.27), residues: 343 loop : -0.86 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 723 HIS 0.014 0.002 HIS G 350 PHE 0.018 0.002 PHE E 134 TYR 0.031 0.003 TYR A 278 ARG 0.011 0.001 ARG G 352 ********************** 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 75 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.0391 (ttm) cc_final: -0.0282 (tpp) REVERT: A 167 LEU cc_start: 0.4549 (mm) cc_final: 0.3746 (tp) REVERT: A 435 MET cc_start: 0.6493 (ttt) cc_final: 0.5998 (mmt) REVERT: A 559 MET cc_start: 0.5116 (ttp) cc_final: 0.4123 (tmm) REVERT: A 586 MET cc_start: 0.7040 (mmm) cc_final: 0.5482 (tpt) REVERT: A 587 MET cc_start: 0.8619 (mmp) cc_final: 0.7975 (mmm) REVERT: B 317 CYS cc_start: 0.8982 (m) cc_final: 0.8430 (p) REVERT: B 696 MET cc_start: 0.3763 (mtp) cc_final: 0.3298 (mtp) REVERT: G 311 MET cc_start: 0.8354 (tpt) cc_final: 0.7952 (tpt) REVERT: G 485 MET cc_start: 0.8641 (mmp) cc_final: 0.8287 (mmm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.3471 time to fit residues: 46.0391 Evaluate side-chains 68 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 184 optimal weight: 0.7980 chunk 247 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 64 optimal weight: 30.0000 chunk 232 optimal weight: 0.0770 chunk 97 optimal weight: 20.0000 chunk 239 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 40.0000 overall best weight: 2.3542 ------------------------------------------------------------------------------- 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 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.069870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.048513 restraints weight = 181223.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.046850 restraints weight = 133768.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.046989 restraints weight = 106495.955| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23132 Z= 0.219 Angle : 0.595 8.296 31459 Z= 0.299 Chirality : 0.040 0.159 3677 Planarity : 0.004 0.060 4026 Dihedral : 4.588 22.580 3141 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 2918 helix: 1.38 (0.14), residues: 1388 sheet: -0.61 (0.26), residues: 353 loop : -0.70 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 662 HIS 0.008 0.001 HIS E 632 PHE 0.050 0.001 PHE B 583 TYR 0.018 0.001 TYR E 167 ARG 0.018 0.000 ARG A 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3260.96 seconds wall clock time: 61 minutes 24.31 seconds (3684.31 seconds total)