Starting phenix.real_space_refine on Thu Jun 19 18:17:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tw3_26149/06_2025/7tw3_26149.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tw3_26149/06_2025/7tw3_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_26149/06_2025/7tw3_26149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tw3_26149/06_2025/7tw3_26149.map" model { file = "/net/cci-nas-00/data/ceres_data/7tw3_26149/06_2025/7tw3_26149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tw3_26149/06_2025/7tw3_26149.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.71, per 1000 atoms: 0.61 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: 6.04 Conformation dependent library (CDL) restraints added in 2.9 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: 2.96 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: 8.03 Time building geometry restraints manager: 7.04 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: 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: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 52.350 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.740 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.14264 ( 1067) hydrogen bonds : angle 6.03135 ( 3102) covalent geometry : bond 0.00434 (23132) covalent geometry : angle 0.74953 (31459) *********************** 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 : 2.700 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: 0.3100 time to fit residues: 47.4603 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 : 2.702 ------------------------------------------------------------------------------- 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: 10.0000 chunk 75 optimal weight: 3.9990 chunk 149 optimal weight: 40.0000 chunk 118 optimal weight: 10.0000 chunk 229 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 chunk 266 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN B 144 GLN B 198 GLN B 569 ASN ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 653 GLN ** G 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 640 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.072169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.054517 restraints weight = 182102.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.052568 restraints weight = 120890.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.053028 restraints weight = 99433.897| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1026 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= 0.144 Angle : 0.573 6.452 31459 Z= 0.289 Chirality : 0.039 0.149 3677 Planarity : 0.005 0.054 4026 Dihedral : 4.470 25.353 3141 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.18 % 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: -0.50 (0.15), residues: 2918 helix: 0.62 (0.14), residues: 1380 sheet: -0.22 (0.27), residues: 338 loop : -1.47 (0.15), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 89 HIS 0.007 0.001 HIS E 632 PHE 0.016 0.001 PHE E 79 TYR 0.014 0.001 TYR B 555 ARG 0.005 0.000 ARG G 591 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 1067) hydrogen bonds : angle 4.52257 ( 3102) covalent geometry : bond 0.00302 (23132) covalent geometry : angle 0.57282 (31459) *********************** 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 to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 2.857 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.0707 (ttt) cc_final: 0.0216 (ttm) REVERT: A 76 MET cc_start: 0.8678 (tpt) cc_final: 0.8452 (tpp) REVERT: A 167 LEU cc_start: 0.4709 (mm) cc_final: 0.4118 (tp) REVERT: A 559 MET cc_start: 0.4249 (ttp) cc_final: 0.3293 (tmm) REVERT: A 586 MET cc_start: 0.6886 (mmm) cc_final: 0.6125 (mmm) REVERT: A 587 MET cc_start: 0.8518 (mmp) cc_final: 0.8120 (mmp) REVERT: A 696 MET cc_start: 0.4619 (tpt) cc_final: 0.4177 (tpp) REVERT: A 776 MET cc_start: 0.6324 (mmp) cc_final: 0.6013 (mtt) REVERT: B 317 CYS cc_start: 0.8440 (m) cc_final: 0.7262 (p) REVERT: B 696 MET cc_start: 0.2508 (mtp) cc_final: 0.1972 (mtp) REVERT: B 776 MET cc_start: 0.7965 (tpp) cc_final: 0.7683 (tpp) REVERT: E 81 ILE cc_start: 0.8807 (mp) cc_final: 0.8384 (tp) REVERT: E 456 MET cc_start: 0.9263 (mmm) cc_final: 0.8665 (tmm) REVERT: G 311 MET cc_start: 0.8305 (tpt) cc_final: 0.7937 (tpt) REVERT: G 319 ASP cc_start: 0.8345 (p0) cc_final: 0.8049 (p0) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.3052 time to fit residues: 44.7479 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 : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 229 optimal weight: 4.9990 chunk 259 optimal weight: 10.0000 chunk 224 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 167 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- 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 ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 GLN G 541 HIS ** G 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.070120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.053237 restraints weight = 181912.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.051225 restraints weight = 141279.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.051674 restraints weight = 120641.605| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23132 Z= 0.219 Angle : 0.652 9.957 31459 Z= 0.328 Chirality : 0.041 0.185 3677 Planarity : 0.005 0.069 4026 Dihedral : 4.594 22.687 3141 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.04 % Allowed : 5.03 % Favored : 94.93 % 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: 0.11 (0.15), residues: 2918 helix: 1.18 (0.14), residues: 1380 sheet: -0.26 (0.28), residues: 334 loop : -1.12 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 89 HIS 0.011 0.002 HIS G 350 PHE 0.022 0.002 PHE E 181 TYR 0.020 0.002 TYR E 167 ARG 0.011 0.001 ARG E 287 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 1067) hydrogen bonds : angle 4.56321 ( 3102) covalent geometry : bond 0.00457 (23132) covalent geometry : angle 0.65177 (31459) *********************** 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 to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 2.853 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.1316 (ttt) cc_final: 0.0953 (ttt) REVERT: A 66 MET cc_start: 0.4250 (tmm) cc_final: 0.3813 (ptm) REVERT: A 76 MET cc_start: 0.8599 (tpt) cc_final: 0.8280 (tpp) REVERT: A 559 MET cc_start: 0.4374 (ttp) cc_final: 0.3304 (tmm) REVERT: A 587 MET cc_start: 0.8527 (mmp) cc_final: 0.8116 (mmp) REVERT: A 776 MET cc_start: 0.6112 (mmp) cc_final: 0.5729 (mtt) REVERT: B 317 CYS cc_start: 0.8599 (m) cc_final: 0.7593 (p) REVERT: B 435 MET cc_start: 0.4592 (mmm) cc_final: 0.4228 (mmm) REVERT: B 559 MET cc_start: 0.2491 (mmt) cc_final: 0.0806 (tpt) REVERT: B 696 MET cc_start: 0.2027 (mtp) cc_final: 0.1529 (mtp) REVERT: B 776 MET cc_start: 0.8303 (tpp) cc_final: 0.7976 (tpp) REVERT: E 456 MET cc_start: 0.9265 (mmm) cc_final: 0.8689 (tmm) REVERT: G 485 MET cc_start: 0.8646 (mmp) cc_final: 0.8162 (mmm) outliers start: 1 outliers final: 1 residues processed: 83 average time/residue: 0.3012 time to fit residues: 45.3803 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 : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 238 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 274 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 33 optimal weight: 30.0000 chunk 288 optimal weight: 9.9990 chunk 36 optimal weight: 30.0000 chunk 39 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 191 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 GLN ** E 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 500 HIS E 589 HIS ** G 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 ASN G 351 HIS G 504 HIS G 574 HIS ** G 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 ASN G 614 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.067430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.045970 restraints weight = 186625.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.044421 restraints weight = 131979.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.044674 restraints weight = 109214.631| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 23132 Z= 0.396 Angle : 0.903 14.535 31459 Z= 0.456 Chirality : 0.047 0.306 3677 Planarity : 0.007 0.086 4026 Dihedral : 5.558 31.865 3141 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.21 % Allowed : 5.58 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.61 (0.15), residues: 2918 helix: 0.46 (0.13), residues: 1405 sheet: -0.92 (0.27), residues: 345 loop : -1.22 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 179 HIS 0.020 0.003 HIS G 350 PHE 0.031 0.003 PHE E 134 TYR 0.032 0.002 TYR E 637 ARG 0.016 0.001 ARG E 287 Details of bonding type rmsd hydrogen bonds : bond 0.05296 ( 1067) hydrogen bonds : angle 5.30150 ( 3102) covalent geometry : bond 0.00825 (23132) covalent geometry : angle 0.90287 (31459) *********************** 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: 5 poor density : 74 time to evaluate : 2.670 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.1794 (ttt) cc_final: 0.1184 (tpp) REVERT: A 66 MET cc_start: 0.5738 (tmm) cc_final: 0.5159 (tmm) REVERT: A 76 MET cc_start: 0.8990 (tpt) cc_final: 0.8728 (tpp) REVERT: A 559 MET cc_start: 0.4837 (ttp) cc_final: 0.3728 (tmm) REVERT: A 586 MET cc_start: 0.7029 (mmm) cc_final: 0.6454 (mmm) REVERT: A 587 MET cc_start: 0.8654 (mmp) cc_final: 0.8240 (mmp) REVERT: B 317 CYS cc_start: 0.8961 (m) cc_final: 0.8320 (t) REVERT: B 435 MET cc_start: 0.4855 (mmm) cc_final: 0.4527 (mmm) REVERT: B 696 MET cc_start: 0.2654 (mtp) cc_final: 0.2202 (mtp) REVERT: E 456 MET cc_start: 0.9357 (mmm) cc_final: 0.8617 (tmm) REVERT: G 311 MET cc_start: 0.8630 (tpt) cc_final: 0.8307 (tpt) outliers start: 5 outliers final: 5 residues processed: 79 average time/residue: 0.3074 time to fit residues: 43.3540 Evaluate side-chains 72 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 98 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 198 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 164 optimal weight: 20.0000 chunk 46 optimal weight: 30.0000 chunk 247 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 161 HIS ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.070557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.048387 restraints weight = 181518.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.047455 restraints weight = 121805.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.047634 restraints weight = 96548.231| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23132 Z= 0.114 Angle : 0.560 9.400 31459 Z= 0.281 Chirality : 0.040 0.196 3677 Planarity : 0.004 0.049 4026 Dihedral : 4.637 21.436 3141 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.10 (0.15), residues: 2918 helix: 1.12 (0.14), residues: 1405 sheet: -0.56 (0.27), residues: 335 loop : -0.98 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 662 HIS 0.005 0.001 HIS A 47 PHE 0.013 0.001 PHE E 292 TYR 0.015 0.002 TYR A 390 ARG 0.010 0.001 ARG E 155 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 1067) hydrogen bonds : angle 4.40411 ( 3102) covalent geometry : bond 0.00242 (23132) covalent geometry : angle 0.56027 (31459) *********************** 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 90 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.0910 (ttt) cc_final: -0.0023 (tpp) REVERT: A 66 MET cc_start: 0.5367 (tmm) cc_final: 0.4868 (tmm) REVERT: A 559 MET cc_start: 0.4792 (ttp) cc_final: 0.3640 (tmm) REVERT: A 586 MET cc_start: 0.6827 (mmm) cc_final: 0.6207 (mmm) REVERT: A 587 MET cc_start: 0.8670 (mmp) cc_final: 0.8224 (mmp) REVERT: A 776 MET cc_start: 0.5625 (mmp) cc_final: 0.5188 (ptp) REVERT: B 317 CYS cc_start: 0.8902 (m) cc_final: 0.8009 (p) REVERT: B 435 MET cc_start: 0.4694 (mmm) cc_final: 0.4464 (mmm) REVERT: B 696 MET cc_start: 0.3377 (mtp) cc_final: 0.2870 (mtp) REVERT: G 311 MET cc_start: 0.8623 (tpt) cc_final: 0.8192 (tpt) REVERT: G 319 ASP cc_start: 0.8712 (p0) cc_final: 0.8477 (p0) REVERT: G 485 MET cc_start: 0.8803 (mmp) cc_final: 0.8516 (mmm) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2997 time to fit residues: 47.6925 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 : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 249 optimal weight: 0.0050 chunk 110 optimal weight: 6.9990 chunk 288 optimal weight: 6.9990 chunk 209 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 overall best weight: 4.2002 ------------------------------------------------------------------------------- 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 186 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 HIS ** E 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 579 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.069034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.047164 restraints weight = 182178.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.045716 restraints weight = 134109.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.045781 restraints weight = 114299.422| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23132 Z= 0.238 Angle : 0.656 10.713 31459 Z= 0.331 Chirality : 0.041 0.148 3677 Planarity : 0.005 0.052 4026 Dihedral : 4.729 22.654 3141 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % 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: 0.11 (0.16), residues: 2918 helix: 1.10 (0.14), residues: 1407 sheet: -0.68 (0.27), residues: 342 loop : -0.90 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 662 HIS 0.011 0.001 HIS G 350 PHE 0.017 0.001 PHE E 134 TYR 0.017 0.002 TYR E 167 ARG 0.007 0.001 ARG E 287 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 1067) hydrogen bonds : angle 4.65033 ( 3102) covalent geometry : bond 0.00498 (23132) covalent geometry : angle 0.65626 (31459) *********************** 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 : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.1231 (ttt) cc_final: 0.0201 (tpp) REVERT: A 76 MET cc_start: 0.9147 (tpt) cc_final: 0.8799 (tpp) REVERT: A 559 MET cc_start: 0.5043 (ttp) cc_final: 0.3901 (tmm) REVERT: A 578 MET cc_start: 0.8219 (mpp) cc_final: 0.7971 (mpp) REVERT: A 587 MET cc_start: 0.8701 (mmp) cc_final: 0.8265 (mmp) REVERT: B 317 CYS cc_start: 0.8981 (m) cc_final: 0.8429 (t) REVERT: B 696 MET cc_start: 0.3997 (mtp) cc_final: 0.3397 (mtp) REVERT: E 456 MET cc_start: 0.9274 (mmm) cc_final: 0.8597 (tmm) REVERT: G 311 MET cc_start: 0.8655 (tpt) cc_final: 0.8252 (tpt) REVERT: G 443 MET cc_start: 0.8918 (tpt) cc_final: 0.8715 (tpp) REVERT: G 485 MET cc_start: 0.8705 (mmp) cc_final: 0.8444 (mmm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.3195 time to fit residues: 46.0011 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 : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 235 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 205 optimal weight: 0.7980 chunk 118 optimal weight: 20.0000 chunk 266 optimal weight: 0.1980 chunk 49 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 265 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** ** E 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 215 HIS ** G 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 579 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.070723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.048657 restraints weight = 181122.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.047796 restraints weight = 102836.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.048061 restraints weight = 83642.767| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3423 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= 0.107 Angle : 0.543 7.826 31459 Z= 0.268 Chirality : 0.039 0.145 3677 Planarity : 0.004 0.048 4026 Dihedral : 4.346 20.650 3141 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.48 (0.16), residues: 2918 helix: 1.43 (0.14), residues: 1400 sheet: -0.39 (0.28), residues: 333 loop : -0.77 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 662 HIS 0.004 0.001 HIS G 647 PHE 0.015 0.001 PHE B 264 TYR 0.013 0.001 TYR E 167 ARG 0.007 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 1067) hydrogen bonds : angle 4.23303 ( 3102) covalent geometry : bond 0.00228 (23132) covalent geometry : angle 0.54257 (31459) *********************** 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 89 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.1069 (ttt) cc_final: 0.0166 (tpp) REVERT: A 76 MET cc_start: 0.8939 (tpt) cc_final: 0.8664 (tpp) REVERT: A 559 MET cc_start: 0.5049 (ttp) cc_final: 0.4185 (tpp) REVERT: A 586 MET cc_start: 0.6983 (mmm) cc_final: 0.6393 (mmm) REVERT: A 587 MET cc_start: 0.8648 (mmp) cc_final: 0.8169 (mmp) REVERT: B 265 LEU cc_start: 0.9216 (tp) cc_final: 0.8872 (pt) REVERT: B 317 CYS cc_start: 0.8820 (m) cc_final: 0.7939 (p) REVERT: B 696 MET cc_start: 0.3221 (mtp) cc_final: 0.2620 (mtp) REVERT: B 712 MET cc_start: 0.4166 (ttp) cc_final: 0.3815 (ppp) REVERT: E 456 MET cc_start: 0.9261 (mmm) cc_final: 0.8561 (tmm) REVERT: G 319 ASP cc_start: 0.8813 (p0) cc_final: 0.8584 (p0) REVERT: G 443 MET cc_start: 0.8850 (tpt) cc_final: 0.8629 (tpp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.3253 time to fit residues: 49.8894 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 : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 91 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 210 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 40.0000 chunk 151 optimal weight: 30.0000 chunk 61 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 347 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.070095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.048535 restraints weight = 181236.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.046287 restraints weight = 139523.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.046759 restraints weight = 113944.691| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3611 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= 0.149 Angle : 0.566 7.829 31459 Z= 0.282 Chirality : 0.040 0.176 3677 Planarity : 0.004 0.046 4026 Dihedral : 4.277 20.465 3141 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: 0.58 (0.16), residues: 2918 helix: 1.49 (0.14), residues: 1403 sheet: -0.40 (0.28), residues: 338 loop : -0.69 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 723 HIS 0.007 0.001 HIS E 632 PHE 0.010 0.001 PHE E 134 TYR 0.014 0.001 TYR E 167 ARG 0.005 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 1067) hydrogen bonds : angle 4.24284 ( 3102) covalent geometry : bond 0.00315 (23132) covalent geometry : angle 0.56608 (31459) *********************** 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 81 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.0643 (ttt) cc_final: 0.0217 (tpp) REVERT: A 76 MET cc_start: 0.8979 (tpt) cc_final: 0.8705 (tpp) REVERT: A 435 MET cc_start: 0.5923 (ttm) cc_final: 0.4627 (tpt) REVERT: A 559 MET cc_start: 0.5050 (ttp) cc_final: 0.4245 (mmt) REVERT: A 586 MET cc_start: 0.7004 (mmm) cc_final: 0.5564 (tpt) REVERT: A 587 MET cc_start: 0.8711 (mmp) cc_final: 0.8118 (mmp) REVERT: B 265 LEU cc_start: 0.9157 (tp) cc_final: 0.8807 (pt) REVERT: B 317 CYS cc_start: 0.8910 (m) cc_final: 0.8082 (p) REVERT: B 696 MET cc_start: 0.3628 (mtp) cc_final: 0.2931 (mtp) REVERT: B 712 MET cc_start: 0.4035 (ttp) cc_final: 0.3550 (tmm) REVERT: B 741 MET cc_start: -0.0310 (ptt) cc_final: -0.0560 (ptt) REVERT: E 456 MET cc_start: 0.9255 (mmm) cc_final: 0.8594 (tmm) REVERT: G 311 MET cc_start: 0.8513 (tpt) cc_final: 0.8018 (tpt) REVERT: G 485 MET cc_start: 0.8807 (mmp) cc_final: 0.8348 (mmm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2978 time to fit residues: 42.6457 Evaluate side-chains 72 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 248 optimal weight: 0.8980 chunk 274 optimal weight: 7.9990 chunk 281 optimal weight: 9.9990 chunk 264 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 245 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 100 optimal weight: 8.9990 chunk 138 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 482 ASN E 13 GLN ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 579 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.069873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.047529 restraints weight = 181463.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.046450 restraints weight = 131022.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.046539 restraints weight = 110882.866| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23132 Z= 0.160 Angle : 0.580 7.684 31459 Z= 0.289 Chirality : 0.040 0.157 3677 Planarity : 0.004 0.043 4026 Dihedral : 4.299 20.732 3141 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % 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: 0.58 (0.16), residues: 2918 helix: 1.49 (0.14), residues: 1398 sheet: -0.40 (0.28), residues: 334 loop : -0.68 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 662 HIS 0.008 0.001 HIS G 442 PHE 0.012 0.001 PHE G 413 TYR 0.014 0.001 TYR E 167 ARG 0.006 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 1067) hydrogen bonds : angle 4.27637 ( 3102) covalent geometry : bond 0.00340 (23132) covalent geometry : angle 0.57973 (31459) *********************** 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 81 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.0614 (ttt) cc_final: 0.0087 (tpp) REVERT: A 76 MET cc_start: 0.8933 (tpt) cc_final: 0.8666 (tpp) REVERT: A 435 MET cc_start: 0.6081 (ttm) cc_final: 0.4797 (tpt) REVERT: A 559 MET cc_start: 0.5057 (ttp) cc_final: 0.4295 (mmt) REVERT: A 586 MET cc_start: 0.7007 (mmm) cc_final: 0.6427 (mmm) REVERT: A 587 MET cc_start: 0.8637 (mmp) cc_final: 0.8147 (mmp) REVERT: B 265 LEU cc_start: 0.9120 (tp) cc_final: 0.8754 (pt) REVERT: B 317 CYS cc_start: 0.8882 (m) cc_final: 0.8116 (p) REVERT: B 696 MET cc_start: 0.3445 (mtp) cc_final: 0.2738 (mtp) REVERT: B 712 MET cc_start: 0.3997 (ttp) cc_final: 0.3547 (tmm) REVERT: B 741 MET cc_start: -0.0379 (ptt) cc_final: -0.0604 (ptt) REVERT: E 456 MET cc_start: 0.9253 (mmm) cc_final: 0.8595 (tmm) REVERT: G 485 MET cc_start: 0.8688 (mmp) cc_final: 0.8408 (mmm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2993 time to fit residues: 42.9538 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 : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 124 optimal weight: 30.0000 chunk 250 optimal weight: 1.9990 chunk 37 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 chunk 139 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 96 optimal weight: 0.0070 chunk 147 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 overall best weight: 5.8008 ------------------------------------------------------------------------------- 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 302 GLN ** 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 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 579 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.067922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.046313 restraints weight = 184066.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.044899 restraints weight = 121848.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.044755 restraints weight = 112291.743| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 23132 Z= 0.330 Angle : 0.799 13.037 31459 Z= 0.406 Chirality : 0.045 0.221 3677 Planarity : 0.005 0.058 4026 Dihedral : 5.052 24.628 3141 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -0.02 (0.15), residues: 2918 helix: 0.99 (0.14), residues: 1397 sheet: -0.95 (0.27), residues: 345 loop : -0.85 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 269 HIS 0.014 0.002 HIS E 632 PHE 0.021 0.002 PHE E 79 TYR 0.024 0.002 TYR E 637 ARG 0.010 0.001 ARG E 287 Details of bonding type rmsd hydrogen bonds : bond 0.04668 ( 1067) hydrogen bonds : angle 4.93004 ( 3102) covalent geometry : bond 0.00685 (23132) covalent geometry : angle 0.79851 (31459) ********************** 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 77 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.1041 (ttt) cc_final: 0.0579 (tpp) REVERT: A 76 MET cc_start: 0.8869 (tpt) cc_final: 0.8610 (tpp) REVERT: A 435 MET cc_start: 0.6441 (ttm) cc_final: 0.5133 (mmp) REVERT: A 559 MET cc_start: 0.5258 (ttp) cc_final: 0.4108 (tmm) REVERT: A 586 MET cc_start: 0.6952 (mmm) cc_final: 0.5442 (tpt) REVERT: A 587 MET cc_start: 0.8660 (mmp) cc_final: 0.8060 (mmp) REVERT: B 317 CYS cc_start: 0.8879 (m) cc_final: 0.8212 (p) REVERT: B 696 MET cc_start: 0.3482 (mtp) cc_final: 0.3012 (mtp) REVERT: B 712 MET cc_start: 0.4291 (ttp) cc_final: 0.3739 (tmm) REVERT: E 456 MET cc_start: 0.9305 (mmm) cc_final: 0.9014 (mmm) REVERT: G 311 MET cc_start: 0.8615 (tpt) cc_final: 0.8134 (tpt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.3001 time to fit residues: 41.7982 Evaluate side-chains 67 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 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 206 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 274 optimal weight: 8.9990 chunk 230 optimal weight: 0.0970 chunk 217 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 115 optimal weight: 30.0000 chunk 255 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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 A 373 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 HIS B 62 GLN ** E 410 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.070593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.049850 restraints weight = 180511.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.047634 restraints weight = 133563.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.047903 restraints weight = 120534.173| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 23132 Z= 0.106 Angle : 0.572 8.202 31459 Z= 0.283 Chirality : 0.040 0.228 3677 Planarity : 0.004 0.043 4026 Dihedral : 4.366 21.217 3141 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: 0.57 (0.16), residues: 2918 helix: 1.49 (0.14), residues: 1399 sheet: -0.53 (0.28), residues: 342 loop : -0.64 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 662 HIS 0.004 0.001 HIS G 647 PHE 0.058 0.001 PHE B 583 TYR 0.018 0.001 TYR E 518 ARG 0.006 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 1067) hydrogen bonds : angle 4.23970 ( 3102) covalent geometry : bond 0.00227 (23132) covalent geometry : angle 0.57249 (31459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6482.35 seconds wall clock time: 113 minutes 56.98 seconds (6836.98 seconds total)