Starting phenix.real_space_refine on Wed Jun 26 20:40:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zjf_60143/06_2024/8zjf_60143.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zjf_60143/06_2024/8zjf_60143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zjf_60143/06_2024/8zjf_60143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zjf_60143/06_2024/8zjf_60143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zjf_60143/06_2024/8zjf_60143.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zjf_60143/06_2024/8zjf_60143.pdb" } resolution = 2.7 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= 0.001 sd= 0.027 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Mg 1 5.21 5 S 73 5.16 5 C 6800 2.51 5 N 1931 2.21 5 O 2110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 104": "OE1" <-> "OE2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A GLU 795": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 10917 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3882 Classifications: {'peptide': 510} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 478} Chain breaks: 1 Chain: "A" Number of atoms: 6993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 909, 6993 Classifications: {'peptide': 909} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 864} Chain breaks: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.76, per 1000 atoms: 0.53 Number of scatterers: 10917 At special positions: 0 Unit cell: (87.69, 97.68, 172.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 73 16.00 Mg 1 11.99 O 2110 8.00 N 1931 7.00 C 6800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 61 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 91 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 271 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 412 " - pdb=" SG CYS B 428 " distance=2.03 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 488 " - pdb=" SG CYS B 500 " distance=2.03 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 543 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 550 " - pdb=" SG CYS B 559 " distance=2.03 Simple disulfide: pdb=" SG CYS A 70 " - pdb=" SG CYS A 79 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 706 " - pdb=" SG CYS A 762 " distance=2.03 Simple disulfide: pdb=" SG CYS A 742 " - pdb=" SG CYS A 748 " distance=2.03 Simple disulfide: pdb=" SG CYS A 775 " - pdb=" SG CYS A 779 " distance=2.03 Simple disulfide: pdb=" SG CYS A 823 " - pdb=" SG CYS A 829 " distance=2.03 Simple disulfide: pdb=" SG CYS A 893 " - pdb=" SG CYS A 907 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN A 444 " Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 2.1 seconds 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2610 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 24 sheets defined 19.1% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'B' and resid 50 through 58 removed outlier: 3.736A pdb=" N HIS B 58 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 174 through 183 Processing helix chain 'B' and resid 208 through 214 Processing helix chain 'B' and resid 238 through 249 removed outlier: 3.964A pdb=" N PHE B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 271 removed outlier: 3.816A pdb=" N ALA B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 294 through 302 removed outlier: 4.155A pdb=" N GLY B 298 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 299 " --> pdb=" O GLY B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.560A pdb=" N SER B 322 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 319 through 323' Processing helix chain 'B' and resid 329 through 340 Processing helix chain 'B' and resid 352 through 362 removed outlier: 3.580A pdb=" N TYR B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 391 Processing helix chain 'B' and resid 515 through 520 removed outlier: 3.591A pdb=" N SER B 520 " --> pdb=" O ALA B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 3.528A pdb=" N SER B 525 " --> pdb=" O PRO B 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 214 through 236 Processing helix chain 'A' and resid 257 through 260 removed outlier: 3.818A pdb=" N GLN A 260 " --> pdb=" O ARG A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 294 through 298 removed outlier: 4.022A pdb=" N HIS A 297 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 327 removed outlier: 3.511A pdb=" N ILE A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.674A pdb=" N GLN A 332 " --> pdb=" O PRO A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 348 removed outlier: 3.925A pdb=" N LYS A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 358 removed outlier: 3.657A pdb=" N GLU A 353 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 374 through 385 removed outlier: 4.465A pdb=" N SER A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYS A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'A' and resid 482 through 486 Processing helix chain 'A' and resid 606 through 610 removed outlier: 3.895A pdb=" N GLY A 609 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 744 through 748 removed outlier: 3.502A pdb=" N SER A 747 " --> pdb=" O ASP A 744 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS A 748 " --> pdb=" O VAL A 745 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 744 through 748' Processing sheet with id=AA1, first strand: chain 'B' and resid 102 through 107 removed outlier: 7.022A pdb=" N ARG B 127 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL B 128 " --> pdb=" O GLU B 469 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N HIS B 471 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 130 " --> pdb=" O HIS B 471 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS B 453 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AA3, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AA4, first strand: chain 'B' and resid 230 through 236 removed outlier: 5.246A pdb=" N HIS B 231 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER B 195 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU B 235 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE B 191 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 152 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLY B 192 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 154 " --> pdb=" O GLY B 192 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLY B 194 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR B 156 " --> pdb=" O GLY B 194 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE B 196 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N MET B 158 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASP B 153 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL B 285 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TYR B 155 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N THR B 287 " --> pdb=" O TYR B 155 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU B 157 " --> pdb=" O THR B 287 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 543 through 544 Processing sheet with id=AA6, first strand: chain 'A' and resid 21 through 28 removed outlier: 4.585A pdb=" N ARG A 675 " --> pdb=" O ASP A 22 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA A 24 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 10.924A pdb=" N VAL A 673 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 10.765A pdb=" N ALA A 671 " --> pdb=" O PRO A 26 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ASP A 662 " --> pdb=" O GLY A 652 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 652 " --> pdb=" O ASP A 662 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.629A pdb=" N SER A 39 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA9, first strand: chain 'A' and resid 95 through 100 Processing sheet with id=AB1, first strand: chain 'A' and resid 251 through 252 removed outlier: 4.311A pdb=" N GLN A 251 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 201 " --> pdb=" O ASN A 240 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ALA A 242 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE A 203 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N VAL A 244 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE A 205 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR A 246 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU A 207 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS A 305 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N PHE A 337 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N MET A 307 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 339 " --> pdb=" O MET A 307 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 309 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N PHE A 367 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA A 338 " --> pdb=" O PHE A 367 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 404 through 410 removed outlier: 4.227A pdb=" N SER A 407 " --> pdb=" O GLY A 419 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 465 through 469 removed outlier: 11.942A pdb=" N LEU A 474 " --> pdb=" O LYS A 494 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LYS A 494 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N TYR A 476 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 489 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 500 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 518 through 521 removed outlier: 6.280A pdb=" N ARG A 552 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU A 562 " --> pdb=" O ARG A 552 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 518 through 521 removed outlier: 7.185A pdb=" N GLU A 545 " --> pdb=" O PHE A 577 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 580 through 583 removed outlier: 4.050A pdb=" N ALA A 580 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 631 " --> pdb=" O ILE A 617 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 679 through 680 Processing sheet with id=AB8, first strand: chain 'A' and resid 682 through 683 Processing sheet with id=AB9, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AC1, first strand: chain 'A' and resid 751 through 754 Processing sheet with id=AC2, first strand: chain 'A' and resid 729 through 731 Processing sheet with id=AC3, first strand: chain 'A' and resid 833 through 835 Processing sheet with id=AC4, first strand: chain 'A' and resid 838 through 839 removed outlier: 7.319A pdb=" N SER A 922 " --> pdb=" O MET A 883 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N MET A 883 " --> pdb=" O SER A 922 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N VAL A 924 " --> pdb=" O LYS A 881 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 881 " --> pdb=" O VAL A 924 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 868 through 869 Processing sheet with id=AC6, first strand: chain 'A' and resid 868 through 869 removed outlier: 3.654A pdb=" N GLU A 955 " --> pdb=" O VAL A 941 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 943 " --> pdb=" O ALA A 953 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A 953 " --> pdb=" O VAL A 943 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 873 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: 3.95 Time building geometry restraints manager: 4.66 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: 3741 1.34 - 1.46: 2390 1.46 - 1.58: 4908 1.58 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 11136 Sorted by residual: bond pdb=" CB CYS A 236 " pdb=" SG CYS A 236 " ideal model delta sigma weight residual 1.808 1.756 0.052 3.30e-02 9.18e+02 2.48e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.546 -0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" N PRO A 811 " pdb=" CA PRO A 811 " ideal model delta sigma weight residual 1.468 1.478 -0.011 7.90e-03 1.60e+04 1.80e+00 bond pdb=" N MET A 867 " pdb=" CA MET A 867 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.29e+00 bond pdb=" CB CYS A 239 " pdb=" SG CYS A 239 " ideal model delta sigma weight residual 1.808 1.771 0.037 3.30e-02 9.18e+02 1.26e+00 ... (remaining 11131 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.52: 347 106.52 - 113.38: 6052 113.38 - 120.25: 3714 120.25 - 127.11: 4867 127.11 - 133.98: 123 Bond angle restraints: 15103 Sorted by residual: angle pdb=" CA MET A 867 " pdb=" CB MET A 867 " pdb=" CG MET A 867 " ideal model delta sigma weight residual 114.10 122.82 -8.72 2.00e+00 2.50e-01 1.90e+01 angle pdb=" C THR A 936 " pdb=" N ALA A 937 " pdb=" CA ALA A 937 " ideal model delta sigma weight residual 121.54 128.44 -6.90 1.91e+00 2.74e-01 1.30e+01 angle pdb=" CB MET A 867 " pdb=" CG MET A 867 " pdb=" SD MET A 867 " ideal model delta sigma weight residual 112.70 123.29 -10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CB MET A 883 " pdb=" CG MET A 883 " pdb=" SD MET A 883 " ideal model delta sigma weight residual 112.70 123.08 -10.38 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CB MET A 768 " pdb=" CG MET A 768 " pdb=" SD MET A 768 " ideal model delta sigma weight residual 112.70 121.84 -9.14 3.00e+00 1.11e-01 9.29e+00 ... (remaining 15098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 6132 21.43 - 42.86: 531 42.86 - 64.29: 119 64.29 - 85.72: 26 85.72 - 107.14: 8 Dihedral angle restraints: 6816 sinusoidal: 2759 harmonic: 4057 Sorted by residual: dihedral pdb=" CB CYS A 775 " pdb=" SG CYS A 775 " pdb=" SG CYS A 779 " pdb=" CB CYS A 779 " ideal model delta sinusoidal sigma weight residual 93.00 176.62 -83.62 1 1.00e+01 1.00e-02 8.53e+01 dihedral pdb=" CB CYS B 488 " pdb=" SG CYS B 488 " pdb=" SG CYS B 500 " pdb=" CB CYS B 500 " ideal model delta sinusoidal sigma weight residual -86.00 -9.12 -76.88 1 1.00e+01 1.00e-02 7.42e+01 dihedral pdb=" CB CYS B 527 " pdb=" SG CYS B 527 " pdb=" SG CYS B 543 " pdb=" CB CYS B 543 " ideal model delta sinusoidal sigma weight residual -86.00 -154.74 68.74 1 1.00e+01 1.00e-02 6.12e+01 ... (remaining 6813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1373 0.053 - 0.106: 282 0.106 - 0.159: 37 0.159 - 0.212: 3 0.212 - 0.265: 1 Chirality restraints: 1696 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.65e+00 chirality pdb=" CG LEU B 523 " pdb=" CB LEU B 523 " pdb=" CD1 LEU B 523 " pdb=" CD2 LEU B 523 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1693 not shown) Planarity restraints: 2003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 136 " 0.052 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO B 137 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 137 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 137 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 911 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO A 912 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 912 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 912 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 133 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO B 134 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 134 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 134 " -0.028 5.00e-02 4.00e+02 ... (remaining 2000 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 227 2.68 - 3.24: 10174 3.24 - 3.79: 17112 3.79 - 4.35: 23761 4.35 - 4.90: 38453 Nonbonded interactions: 89727 Sorted by model distance: nonbonded pdb=" OD2 ASP B 198 " pdb="CA CA B 902 " model vdw 2.127 2.510 nonbonded pdb=" OD1 ASP B 297 " pdb=" OH TYR A 513 " model vdw 2.141 2.440 nonbonded pdb=" OD1 ASP B 256 " pdb="CA CA B 902 " model vdw 2.162 2.510 nonbonded pdb=" O PRO B 258 " pdb="CA CA B 902 " model vdw 2.181 2.510 nonbonded pdb=" ND2 ASN B 254 " pdb="CA CA B 902 " model vdw 2.218 2.590 ... (remaining 89722 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 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: 0.010 Extract box with map and model: 2.190 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 32.080 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:10.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 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 : 0.003 0.052 11136 Z= 0.195 Angle : 0.652 10.588 15103 Z= 0.337 Chirality : 0.044 0.265 1696 Planarity : 0.005 0.080 2002 Dihedral : 16.727 107.144 4149 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.50 % Allowed : 19.58 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.43 (0.22), residues: 1411 helix: 0.26 (0.39), residues: 203 sheet: -0.50 (0.26), residues: 413 loop : -1.55 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 925 HIS 0.012 0.001 HIS B 453 PHE 0.013 0.001 PHE A 688 TYR 0.012 0.001 TYR B 162 ARG 0.006 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 GLU cc_start: 0.7223 (tt0) cc_final: 0.7023 (tt0) REVERT: B 164 MET cc_start: 0.7521 (mmm) cc_final: 0.7030 (mmm) REVERT: B 314 ASP cc_start: 0.7108 (p0) cc_final: 0.6790 (p0) REVERT: B 326 ASP cc_start: 0.7204 (t0) cc_final: 0.6969 (t0) REVERT: B 383 MET cc_start: 0.8268 (mmm) cc_final: 0.8063 (mmm) REVERT: B 421 LYS cc_start: 0.6005 (ptpp) cc_final: 0.5675 (ttmt) REVERT: B 500 CYS cc_start: 0.4210 (m) cc_final: 0.3877 (m) REVERT: B 543 CYS cc_start: 0.3093 (OUTLIER) cc_final: 0.2542 (t) REVERT: A 76 GLU cc_start: 0.6026 (tp30) cc_final: 0.5344 (tm-30) REVERT: A 146 ASN cc_start: 0.8029 (m-40) cc_final: 0.7674 (m-40) REVERT: A 228 MET cc_start: 0.8809 (ttp) cc_final: 0.8014 (tpt) REVERT: A 574 ASN cc_start: 0.6992 (m-40) cc_final: 0.6696 (m110) REVERT: A 594 ASP cc_start: 0.7196 (p0) cc_final: 0.6723 (p0) REVERT: A 686 MET cc_start: 0.8311 (mmt) cc_final: 0.8063 (mmt) REVERT: A 870 MET cc_start: 0.5572 (tpt) cc_final: 0.5175 (mtm) outliers start: 30 outliers final: 16 residues processed: 154 average time/residue: 0.9243 time to fit residues: 157.0294 Evaluate side-chains 98 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 57 optimal weight: 0.0060 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 82 optimal weight: 50.0000 chunk 128 optimal weight: 20.0000 overall best weight: 2.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN B 272 GLN B 274 GLN B 453 HIS B 471 HIS ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 569 HIS A 797 GLN A 802 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 11136 Z= 0.424 Angle : 0.759 9.260 15103 Z= 0.384 Chirality : 0.050 0.218 1696 Planarity : 0.006 0.055 2002 Dihedral : 7.757 59.956 1622 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 5.17 % Allowed : 19.33 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.52 (0.22), residues: 1411 helix: 0.25 (0.38), residues: 204 sheet: -0.55 (0.25), residues: 425 loop : -1.64 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 277 HIS 0.008 0.001 HIS B 187 PHE 0.019 0.003 PHE A 406 TYR 0.019 0.003 TYR B 162 ARG 0.008 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 81 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7476 (t0) REVERT: B 387 ASN cc_start: 0.7942 (t0) cc_final: 0.7557 (m110) REVERT: B 409 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: A 72 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8662 (mp) REVERT: A 84 HIS cc_start: 0.8616 (m170) cc_final: 0.8402 (m170) REVERT: A 136 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: A 198 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.6037 (tt0) REVERT: A 228 MET cc_start: 0.8812 (ttp) cc_final: 0.8078 (tpt) REVERT: A 285 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6379 (mpp) REVERT: A 594 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7463 (OUTLIER) REVERT: A 708 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7344 (tt0) REVERT: A 720 LEU cc_start: 0.2063 (OUTLIER) cc_final: 0.1473 (pp) outliers start: 62 outliers final: 20 residues processed: 136 average time/residue: 0.9055 time to fit residues: 136.4758 Evaluate side-chains 101 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 73 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 128 optimal weight: 40.0000 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 43 optimal weight: 40.0000 chunk 102 optimal weight: 0.0170 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 HIS ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN B 427 GLN B 453 HIS ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 892 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11136 Z= 0.356 Angle : 0.694 9.266 15103 Z= 0.347 Chirality : 0.048 0.224 1696 Planarity : 0.005 0.046 2002 Dihedral : 6.737 51.803 1617 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.92 % Allowed : 20.33 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.51 (0.22), residues: 1411 helix: 0.47 (0.39), residues: 199 sheet: -0.54 (0.26), residues: 426 loop : -1.69 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 277 HIS 0.009 0.001 HIS B 293 PHE 0.020 0.002 PHE A 812 TYR 0.018 0.002 TYR B 162 ARG 0.005 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 77 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7381 (t0) REVERT: B 387 ASN cc_start: 0.7846 (t0) cc_final: 0.7606 (m110) REVERT: B 444 GLN cc_start: 0.7258 (tp40) cc_final: 0.6882 (tp40) REVERT: A 72 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8748 (mp) REVERT: A 113 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8176 (ttm170) REVERT: A 136 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: A 228 MET cc_start: 0.8808 (ttp) cc_final: 0.8106 (tpt) REVERT: A 285 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.6550 (mmm) REVERT: A 468 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8694 (mp) REVERT: A 498 GLU cc_start: 0.6166 (mm-30) cc_final: 0.5715 (mp0) REVERT: A 584 MET cc_start: 0.8542 (mmm) cc_final: 0.8135 (mmm) REVERT: A 594 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7549 (p0) REVERT: A 622 TRP cc_start: 0.6450 (m100) cc_final: 0.6193 (m100) REVERT: A 662 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7150 (p0) REVERT: A 708 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: A 720 LEU cc_start: 0.2319 (OUTLIER) cc_final: 0.1804 (pp) REVERT: A 727 PHE cc_start: 0.6753 (OUTLIER) cc_final: 0.6379 (m-80) REVERT: A 791 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7947 (mp) REVERT: A 798 THR cc_start: 0.7513 (OUTLIER) cc_final: 0.7048 (p) outliers start: 59 outliers final: 27 residues processed: 132 average time/residue: 1.0593 time to fit residues: 152.5152 Evaluate side-chains 113 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 73 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 941 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 128 optimal weight: 20.0000 chunk 136 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 HIS ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN ** B 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 260 GLN A 486 HIS A 556 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11136 Z= 0.324 Angle : 0.660 10.044 15103 Z= 0.329 Chirality : 0.047 0.220 1696 Planarity : 0.005 0.045 2002 Dihedral : 6.351 53.167 1615 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 5.33 % Allowed : 20.83 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.37 (0.22), residues: 1411 helix: 0.39 (0.38), residues: 205 sheet: -0.38 (0.26), residues: 426 loop : -1.61 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 277 HIS 0.007 0.001 HIS B 293 PHE 0.018 0.002 PHE A 812 TYR 0.018 0.002 TYR B 162 ARG 0.007 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 76 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7364 (t0) REVERT: B 387 ASN cc_start: 0.7823 (t0) cc_final: 0.7579 (m110) REVERT: B 444 GLN cc_start: 0.7420 (tp40) cc_final: 0.6684 (tp40) REVERT: B 523 LEU cc_start: 0.4622 (OUTLIER) cc_final: 0.4097 (mp) REVERT: A 72 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8782 (mp) REVERT: A 99 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8391 (ppp-140) REVERT: A 113 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.8037 (ttm170) REVERT: A 136 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: A 214 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8121 (p0) REVERT: A 228 MET cc_start: 0.8807 (ttp) cc_final: 0.8014 (tpt) REVERT: A 285 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.6631 (mmm) REVERT: A 498 GLU cc_start: 0.6169 (mm-30) cc_final: 0.5457 (tp30) REVERT: A 584 MET cc_start: 0.8544 (mmm) cc_final: 0.8249 (mmm) REVERT: A 622 TRP cc_start: 0.6516 (m100) cc_final: 0.6274 (m100) REVERT: A 720 LEU cc_start: 0.2465 (OUTLIER) cc_final: 0.2035 (pp) REVERT: A 722 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7133 (mp0) outliers start: 64 outliers final: 29 residues processed: 136 average time/residue: 1.0447 time to fit residues: 155.4487 Evaluate side-chains 109 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 70 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 941 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 122 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN B 316 ASN B 427 GLN ** B 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 260 GLN A 486 HIS A 556 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 11136 Z= 0.418 Angle : 0.715 10.787 15103 Z= 0.355 Chirality : 0.049 0.268 1696 Planarity : 0.005 0.055 2002 Dihedral : 6.211 52.892 1611 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 6.25 % Allowed : 20.58 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.37 (0.22), residues: 1411 helix: 0.37 (0.38), residues: 205 sheet: -0.31 (0.26), residues: 415 loop : -1.63 (0.20), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 277 HIS 0.008 0.001 HIS A 486 PHE 0.018 0.003 PHE A 19 TYR 0.018 0.003 TYR B 162 ARG 0.005 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 70 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7216 (t70) REVERT: B 321 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8117 (ptm-80) REVERT: B 387 ASN cc_start: 0.7827 (t0) cc_final: 0.7615 (m110) REVERT: B 444 GLN cc_start: 0.7616 (tp40) cc_final: 0.6932 (tp40) REVERT: B 523 LEU cc_start: 0.4744 (OUTLIER) cc_final: 0.4303 (mp) REVERT: A 72 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8806 (mp) REVERT: A 99 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8401 (ppp-140) REVERT: A 113 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8019 (ttm170) REVERT: A 136 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: A 198 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6409 (tt0) REVERT: A 214 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8130 (p0) REVERT: A 228 MET cc_start: 0.8838 (ttp) cc_final: 0.8000 (tpt) REVERT: A 493 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8165 (mp10) REVERT: A 498 GLU cc_start: 0.6161 (mm-30) cc_final: 0.5479 (tp30) REVERT: A 594 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7618 (OUTLIER) REVERT: A 622 TRP cc_start: 0.6619 (m100) cc_final: 0.6362 (m100) REVERT: A 707 PHE cc_start: 0.8631 (m-80) cc_final: 0.8268 (m-80) REVERT: A 720 LEU cc_start: 0.2717 (OUTLIER) cc_final: 0.2337 (pp) REVERT: A 727 PHE cc_start: 0.6973 (OUTLIER) cc_final: 0.6054 (m-80) REVERT: A 791 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7998 (mp) outliers start: 75 outliers final: 32 residues processed: 140 average time/residue: 0.9532 time to fit residues: 147.4517 Evaluate side-chains 111 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 67 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 941 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 20.0000 chunk 122 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 30.0000 chunk 33 optimal weight: 3.9990 chunk 136 optimal weight: 40.0000 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 131 optimal weight: 50.0000 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 HIS B 274 GLN B 316 ASN B 453 HIS ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 260 GLN A 556 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 11136 Z= 0.251 Angle : 0.633 11.174 15103 Z= 0.314 Chirality : 0.045 0.247 1696 Planarity : 0.004 0.048 2002 Dihedral : 5.840 51.571 1610 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 5.33 % Allowed : 21.58 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.30 (0.22), residues: 1411 helix: 0.41 (0.38), residues: 208 sheet: -0.33 (0.26), residues: 413 loop : -1.54 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 277 HIS 0.006 0.001 HIS B 293 PHE 0.013 0.002 PHE A 406 TYR 0.016 0.002 TYR A 789 ARG 0.005 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 66 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7343 (t0) REVERT: B 387 ASN cc_start: 0.7820 (t0) cc_final: 0.7599 (m110) REVERT: B 444 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6973 (tp-100) REVERT: B 523 LEU cc_start: 0.4642 (OUTLIER) cc_final: 0.4233 (mp) REVERT: A 99 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8580 (ppp-140) REVERT: A 113 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7972 (ttm170) REVERT: A 214 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8167 (p0) REVERT: A 228 MET cc_start: 0.8841 (ttp) cc_final: 0.7986 (tpt) REVERT: A 493 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8158 (mp10) REVERT: A 498 GLU cc_start: 0.6084 (mm-30) cc_final: 0.5444 (tp30) REVERT: A 513 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.8520 (m-80) REVERT: A 622 TRP cc_start: 0.6631 (m100) cc_final: 0.6361 (m100) REVERT: A 720 LEU cc_start: 0.2742 (OUTLIER) cc_final: 0.2297 (pp) REVERT: A 727 PHE cc_start: 0.6740 (OUTLIER) cc_final: 0.5997 (m-80) REVERT: A 798 THR cc_start: 0.7910 (OUTLIER) cc_final: 0.7689 (p) outliers start: 64 outliers final: 29 residues processed: 125 average time/residue: 0.9844 time to fit residues: 135.4544 Evaluate side-chains 106 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 66 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 444 GLN Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 941 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 0.8980 chunk 77 optimal weight: 50.0000 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 135 optimal weight: 30.0000 chunk 85 optimal weight: 2.9990 chunk 82 optimal weight: 50.0000 chunk 62 optimal weight: 0.0970 chunk 84 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 HIS B 274 GLN B 316 ASN B 453 HIS A 231 ASN A 260 GLN A 556 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 11136 Z= 0.252 Angle : 0.628 11.008 15103 Z= 0.310 Chirality : 0.045 0.239 1696 Planarity : 0.005 0.055 2002 Dihedral : 5.727 49.201 1610 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 5.08 % Allowed : 22.33 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.18 (0.22), residues: 1411 helix: 0.51 (0.38), residues: 208 sheet: -0.23 (0.26), residues: 421 loop : -1.49 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 277 HIS 0.005 0.001 HIS B 293 PHE 0.014 0.002 PHE A 406 TYR 0.018 0.002 TYR A 789 ARG 0.005 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 68 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7332 (t0) REVERT: B 387 ASN cc_start: 0.7826 (t0) cc_final: 0.7603 (m110) REVERT: B 444 GLN cc_start: 0.7578 (tp40) cc_final: 0.6919 (tp40) REVERT: B 523 LEU cc_start: 0.4614 (OUTLIER) cc_final: 0.4327 (mp) REVERT: A 99 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8615 (ppp-140) REVERT: A 113 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7982 (ttm170) REVERT: A 136 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: A 214 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8163 (p0) REVERT: A 228 MET cc_start: 0.8820 (ttp) cc_final: 0.7928 (tpt) REVERT: A 493 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8159 (mp10) REVERT: A 498 GLU cc_start: 0.5993 (mm-30) cc_final: 0.5359 (tp30) REVERT: A 594 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7560 (p0) REVERT: A 622 TRP cc_start: 0.6559 (m100) cc_final: 0.6340 (m100) REVERT: A 720 LEU cc_start: 0.2848 (OUTLIER) cc_final: 0.2449 (pp) REVERT: A 727 PHE cc_start: 0.6885 (OUTLIER) cc_final: 0.6109 (m-80) REVERT: A 798 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7765 (p) outliers start: 61 outliers final: 33 residues processed: 125 average time/residue: 0.9692 time to fit residues: 133.6600 Evaluate side-chains 110 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 66 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 130 optimal weight: 40.0000 chunk 118 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 HIS B 274 GLN B 316 ASN B 427 GLN B 453 HIS A 231 ASN A 260 GLN A 556 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 11136 Z= 0.370 Angle : 0.704 15.169 15103 Z= 0.345 Chirality : 0.048 0.267 1696 Planarity : 0.005 0.051 2002 Dihedral : 5.689 49.161 1604 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 4.50 % Allowed : 23.25 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.27 (0.22), residues: 1411 helix: 0.43 (0.38), residues: 208 sheet: -0.35 (0.26), residues: 429 loop : -1.51 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 277 HIS 0.007 0.001 HIS B 293 PHE 0.017 0.002 PHE A 406 TYR 0.019 0.002 TYR A 789 ARG 0.005 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 67 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 VAL cc_start: 0.7495 (t) cc_final: 0.7282 (t) REVERT: B 290 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7206 (t0) REVERT: B 387 ASN cc_start: 0.7819 (t0) cc_final: 0.7615 (m110) REVERT: B 396 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7004 (mm-30) REVERT: B 444 GLN cc_start: 0.7591 (tp40) cc_final: 0.6926 (tp40) REVERT: B 523 LEU cc_start: 0.4637 (OUTLIER) cc_final: 0.4283 (mp) REVERT: A 99 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8710 (ppp-140) REVERT: A 113 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7980 (ttm170) REVERT: A 149 ASP cc_start: 0.5994 (m-30) cc_final: 0.5485 (p0) REVERT: A 214 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8185 (p0) REVERT: A 228 MET cc_start: 0.8819 (ttp) cc_final: 0.7903 (tpt) REVERT: A 331 MET cc_start: 0.3994 (mpp) cc_final: 0.3455 (mtp) REVERT: A 493 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8163 (mp10) REVERT: A 498 GLU cc_start: 0.6017 (mm-30) cc_final: 0.5355 (tp30) REVERT: A 594 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7693 (OUTLIER) REVERT: A 622 TRP cc_start: 0.6627 (m100) cc_final: 0.6399 (m100) REVERT: A 662 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7328 (p0) REVERT: A 720 LEU cc_start: 0.3067 (OUTLIER) cc_final: 0.2804 (pp) REVERT: A 727 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.6134 (m-80) REVERT: A 730 ASP cc_start: 0.7745 (t0) cc_final: 0.7445 (t0) outliers start: 54 outliers final: 30 residues processed: 118 average time/residue: 1.0413 time to fit residues: 135.0347 Evaluate side-chains 104 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 65 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 941 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 1.9990 chunk 130 optimal weight: 40.0000 chunk 76 optimal weight: 30.0000 chunk 55 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 114 optimal weight: 0.0870 chunk 119 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 81 optimal weight: 50.0000 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 HIS B 274 GLN B 316 ASN A 231 ASN A 260 GLN A 556 GLN A 574 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 11136 Z= 0.226 Angle : 0.626 14.781 15103 Z= 0.307 Chirality : 0.044 0.214 1696 Planarity : 0.004 0.047 2002 Dihedral : 5.337 48.903 1604 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.92 % Allowed : 23.67 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.16 (0.22), residues: 1411 helix: 0.49 (0.38), residues: 210 sheet: -0.23 (0.26), residues: 426 loop : -1.47 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 277 HIS 0.005 0.001 HIS B 293 PHE 0.013 0.002 PHE A 406 TYR 0.017 0.002 TYR A 789 ARG 0.004 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 69 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7356 (mm) REVERT: B 290 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7335 (t0) REVERT: B 387 ASN cc_start: 0.7812 (t0) cc_final: 0.7597 (m110) REVERT: B 396 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7039 (mm-30) REVERT: B 444 GLN cc_start: 0.7619 (tp40) cc_final: 0.6957 (tp40) REVERT: B 523 LEU cc_start: 0.4356 (OUTLIER) cc_final: 0.4096 (mp) REVERT: A 20 ASN cc_start: 0.6807 (m110) cc_final: 0.6029 (m110) REVERT: A 99 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8556 (ppp-140) REVERT: A 113 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7922 (ttm170) REVERT: A 149 ASP cc_start: 0.5939 (m-30) cc_final: 0.5417 (p0) REVERT: A 214 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8254 (p0) REVERT: A 228 MET cc_start: 0.8820 (ttp) cc_final: 0.7896 (tpt) REVERT: A 498 GLU cc_start: 0.6042 (mm-30) cc_final: 0.5424 (tp30) REVERT: A 594 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8145 (p0) REVERT: A 662 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7371 (p0) REVERT: A 720 LEU cc_start: 0.2955 (OUTLIER) cc_final: 0.2649 (pp) REVERT: A 727 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.6108 (m-80) REVERT: A 730 ASP cc_start: 0.7726 (t0) cc_final: 0.7421 (t0) outliers start: 47 outliers final: 29 residues processed: 112 average time/residue: 1.0282 time to fit residues: 126.7317 Evaluate side-chains 107 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 68 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN B 138 GLN B 176 HIS B 274 GLN B 316 ASN B 453 HIS A 231 ASN A 260 GLN A 556 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 11136 Z= 0.174 Angle : 0.613 14.168 15103 Z= 0.296 Chirality : 0.044 0.199 1696 Planarity : 0.004 0.048 2002 Dihedral : 5.112 48.762 1604 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.50 % Allowed : 24.25 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.06 (0.22), residues: 1411 helix: 0.58 (0.38), residues: 210 sheet: -0.22 (0.26), residues: 426 loop : -1.37 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 426 HIS 0.003 0.001 HIS B 293 PHE 0.012 0.001 PHE A 812 TYR 0.017 0.001 TYR A 789 ARG 0.004 0.000 ARG A 753 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 71 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7320 (mm) REVERT: B 290 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7393 (t0) REVERT: B 396 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6964 (mm-30) REVERT: B 444 GLN cc_start: 0.7618 (tp40) cc_final: 0.6958 (tp40) REVERT: B 523 LEU cc_start: 0.4299 (OUTLIER) cc_final: 0.4045 (mp) REVERT: A 99 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8455 (ppp-140) REVERT: A 113 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7912 (ttm170) REVERT: A 214 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8289 (p0) REVERT: A 228 MET cc_start: 0.8816 (ttp) cc_final: 0.7895 (tpt) REVERT: A 331 MET cc_start: 0.4016 (mpp) cc_final: 0.3500 (mtp) REVERT: A 439 ARG cc_start: 0.7904 (mtp85) cc_final: 0.7686 (mmm160) REVERT: A 498 GLU cc_start: 0.5993 (mm-30) cc_final: 0.5400 (tp30) REVERT: A 594 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.8059 (p0) REVERT: A 662 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7395 (p0) REVERT: A 720 LEU cc_start: 0.2888 (OUTLIER) cc_final: 0.2535 (pp) REVERT: A 730 ASP cc_start: 0.7702 (t0) cc_final: 0.7438 (t0) outliers start: 42 outliers final: 24 residues processed: 111 average time/residue: 1.0078 time to fit residues: 122.5922 Evaluate side-chains 103 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 70 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 chunk 115 optimal weight: 0.0970 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN B 176 HIS B 274 GLN B 316 ASN B 453 HIS A 231 ASN A 556 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.236821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.156322 restraints weight = 9974.250| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 6.00 r_work: 0.2982 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11136 Z= 0.170 Angle : 0.604 13.707 15103 Z= 0.293 Chirality : 0.043 0.175 1696 Planarity : 0.004 0.049 2002 Dihedral : 5.010 48.607 1604 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.08 % Allowed : 24.58 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.99 (0.22), residues: 1411 helix: 0.65 (0.38), residues: 210 sheet: -0.16 (0.26), residues: 422 loop : -1.33 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 426 HIS 0.003 0.001 HIS B 293 PHE 0.012 0.001 PHE A 812 TYR 0.017 0.001 TYR A 789 ARG 0.004 0.000 ARG A 753 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3290.02 seconds wall clock time: 58 minutes 26.72 seconds (3506.72 seconds total)