Starting phenix.real_space_refine on Mon Apr 6 22:17:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9clm_45682/04_2026/9clm_45682.cif Found real_map, /net/cci-nas-00/data/ceres_data/9clm_45682/04_2026/9clm_45682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9clm_45682/04_2026/9clm_45682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9clm_45682/04_2026/9clm_45682.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9clm_45682/04_2026/9clm_45682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9clm_45682/04_2026/9clm_45682.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.018 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: 5 Type Number sf(0) Gaussians Fe 3 7.16 5 S 111 5.16 5 C 13750 2.51 5 N 3873 2.21 5 O 4235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21972 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 870, 6869 Classifications: {'peptide': 870} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 845} Chain: "B" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4720 Classifications: {'peptide': 600} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 572} Chain breaks: 4 Chain: "F" Number of atoms: 5176 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 675, 5171 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 28, 'TRANS': 643} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 675, 5171 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 28, 'TRANS': 643} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 5282 Chain: "G" Number of atoms: 5192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5192 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 28, 'TRANS': 642} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' FE': 1, 'BCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 10 Unusual residues: {' FE': 2, 'BCT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA F 353 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA F 353 " occ=0.50 Time building chain proxies: 5.86, per 1000 atoms: 0.27 Number of scatterers: 21972 At special positions: 0 Unit cell: (132.594, 151.998, 218.834, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 3 26.01 S 111 16.00 O 4235 8.00 N 3873 7.00 C 13750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 272 " distance=2.03 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 572 " distance=2.04 Simple disulfide: pdb=" SG CYS B 506 " - pdb=" SG CYS B 507 " distance=2.03 Simple disulfide: pdb=" SG CYS F 28 " - pdb=" SG CYS F 67 " distance=2.03 Simple disulfide: pdb=" SG CYS F 38 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS F 213 " distance=2.03 Simple disulfide: pdb=" SG CYS F 156 " - pdb=" SG CYS F 350 " distance=2.03 Simple disulfide: pdb=" SG CYS F 177 " - pdb=" SG CYS F 193 " distance=2.03 Simple disulfide: pdb=" SG CYS F 180 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 190 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 246 " - pdb=" SG CYS F 260 " distance=2.03 Simple disulfide: pdb=" SG CYS F 358 " - pdb=" SG CYS F 615 " distance=2.03 Simple disulfide: pdb=" SG CYS F 364 " - pdb=" SG CYS F 396 " distance=2.04 Simple disulfide: pdb=" SG CYS F 374 " - pdb=" SG CYS F 387 " distance=2.03 Simple disulfide: pdb=" SG CYS F 421 " - pdb=" SG CYS F 693 " distance=2.03 Simple disulfide: pdb=" SG CYS F 437 " - pdb=" SG CYS F 656 " distance=2.03 Simple disulfide: pdb=" SG CYS F 469 " - pdb=" SG CYS F 542 " distance=2.04 Simple disulfide: pdb=" SG CYS F 493 " - pdb=" SG CYS F 684 " distance=2.03 Simple disulfide: pdb=" SG CYS F 503 " - pdb=" SG CYS F 517 " distance=2.03 Simple disulfide: pdb=" SG CYS F 514 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 582 " - pdb=" SG CYS F 596 " distance=2.03 Simple disulfide: pdb=" SG CYS F 634 " - pdb=" SG CYS F 639 " distance=2.03 Simple disulfide: pdb=" SG CYS G 28 " - pdb=" SG CYS G 67 " distance=2.03 Simple disulfide: pdb=" SG CYS G 38 " - pdb=" SG CYS G 58 " distance=2.03 Simple disulfide: pdb=" SG CYS G 137 " - pdb=" SG CYS G 213 " distance=2.03 Simple disulfide: pdb=" SG CYS G 156 " - pdb=" SG CYS G 350 " distance=2.03 Simple disulfide: pdb=" SG CYS G 177 " - pdb=" SG CYS G 193 " distance=2.03 Simple disulfide: pdb=" SG CYS G 180 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 190 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 246 " - pdb=" SG CYS G 260 " distance=2.03 Simple disulfide: pdb=" SG CYS G 358 " - pdb=" SG CYS G 615 " distance=2.03 Simple disulfide: pdb=" SG CYS G 364 " - pdb=" SG CYS G 396 " distance=2.04 Simple disulfide: pdb=" SG CYS G 374 " - pdb=" SG CYS G 387 " distance=2.04 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 693 " distance=2.03 Simple disulfide: pdb=" SG CYS G 437 " - pdb=" SG CYS G 656 " distance=2.03 Simple disulfide: pdb=" SG CYS G 469 " - pdb=" SG CYS G 542 " distance=2.03 Simple disulfide: pdb=" SG CYS G 493 " - pdb=" SG CYS G 684 " distance=2.03 Simple disulfide: pdb=" SG CYS G 503 " - pdb=" SG CYS G 517 " distance=2.03 Simple disulfide: pdb=" SG CYS G 514 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 582 " - pdb=" SG CYS G 596 " distance=2.03 Simple disulfide: pdb=" SG CYS G 634 " - pdb=" SG CYS G 639 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 1.3 seconds 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5154 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 29 sheets defined 22.4% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 64 through 72 Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.639A pdb=" N THR A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.745A pdb=" N VAL A 109 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 253 through 256 Processing helix chain 'A' and resid 268 through 274 removed outlier: 3.675A pdb=" N CYS A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 362 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 531 through 535 removed outlier: 3.728A pdb=" N GLY A 534 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 535 " --> pdb=" O ASN A 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 531 through 535' Processing helix chain 'A' and resid 652 through 658 removed outlier: 3.588A pdb=" N MET A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 748 Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 828 through 830 No H-bonds generated for 'chain 'A' and resid 828 through 830' Processing helix chain 'A' and resid 876 through 882 removed outlier: 3.930A pdb=" N VAL A 880 " --> pdb=" O THR A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 901 removed outlier: 4.012A pdb=" N ARG A 899 " --> pdb=" O VAL A 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 110 Processing helix chain 'B' and resid 555 through 559 removed outlier: 3.531A pdb=" N ILE B 559 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 48 removed outlier: 3.796A pdb=" N GLU F 34 " --> pdb=" O VAL F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 73 Processing helix chain 'F' and resid 85 through 91 removed outlier: 3.546A pdb=" N LEU F 91 " --> pdb=" O TYR F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 131 removed outlier: 3.584A pdb=" N LEU F 131 " --> pdb=" O MET F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 155 Processing helix chain 'F' and resid 164 through 173 removed outlier: 4.478A pdb=" N PHE F 173 " --> pdb=" O VAL F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 191 removed outlier: 4.124A pdb=" N LEU F 189 " --> pdb=" O PHE F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 206 No H-bonds generated for 'chain 'F' and resid 205 through 206' Processing helix chain 'F' and resid 208 through 216 Processing helix chain 'F' and resid 226 through 232 removed outlier: 3.582A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 241 removed outlier: 4.085A pdb=" N ARG F 239 " --> pdb=" O ASN F 235 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN F 241 " --> pdb=" O ALA F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 261 removed outlier: 3.996A pdb=" N HIS F 261 " --> pdb=" O LYS F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 294 Processing helix chain 'F' and resid 329 through 335 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 367 through 380 Processing helix chain 'F' and resid 392 through 402 Processing helix chain 'F' and resid 411 through 421 removed outlier: 4.205A pdb=" N ILE F 417 " --> pdb=" O GLY F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 440 removed outlier: 4.139A pdb=" N ASP F 439 " --> pdb=" O ASN F 436 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR F 440 " --> pdb=" O CYS F 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 436 through 440' Processing helix chain 'F' and resid 479 through 487 removed outlier: 3.887A pdb=" N MET F 483 " --> pdb=" O TRP F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 499 removed outlier: 3.659A pdb=" N PHE F 498 " --> pdb=" O ARG F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 520 through 524 Processing helix chain 'F' and resid 535 through 547 Processing helix chain 'F' and resid 555 through 562 removed outlier: 3.733A pdb=" N GLN F 559 " --> pdb=" O GLN F 555 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR F 561 " --> pdb=" O VAL F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 576 No H-bonds generated for 'chain 'F' and resid 574 through 576' Processing helix chain 'F' and resid 589 through 593 Processing helix chain 'F' and resid 612 through 627 removed outlier: 4.252A pdb=" N HIS F 625 " --> pdb=" O ARG F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 665 through 671 removed outlier: 4.531A pdb=" N GLY F 671 " --> pdb=" O GLU F 667 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 681 Processing helix chain 'F' and resid 689 through 694 Processing helix chain 'G' and resid 30 through 49 removed outlier: 3.907A pdb=" N GLU G 34 " --> pdb=" O VAL G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 72 Processing helix chain 'G' and resid 82 through 91 removed outlier: 4.360A pdb=" N ASP G 88 " --> pdb=" O GLY G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 131 removed outlier: 3.510A pdb=" N LEU G 131 " --> pdb=" O MET G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 155 removed outlier: 3.699A pdb=" N ILE G 151 " --> pdb=" O TRP G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 173 removed outlier: 3.739A pdb=" N ALA G 168 " --> pdb=" O PRO G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 191 Processing helix chain 'G' and resid 205 through 216 Processing helix chain 'G' and resid 227 through 233 Processing helix chain 'G' and resid 235 through 240 Processing helix chain 'G' and resid 255 through 259 removed outlier: 4.325A pdb=" N LYS G 258 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 291 Processing helix chain 'G' and resid 329 through 335 Processing helix chain 'G' and resid 335 through 347 Processing helix chain 'G' and resid 367 through 381 removed outlier: 3.602A pdb=" N LEU G 372 " --> pdb=" O HIS G 368 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LYS G 373 " --> pdb=" O HIS G 369 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU G 376 " --> pdb=" O LEU G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 392 through 399 removed outlier: 3.681A pdb=" N LYS G 399 " --> pdb=" O ASP G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 421 removed outlier: 4.212A pdb=" N TYR G 416 " --> pdb=" O GLY G 412 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ILE G 417 " --> pdb=" O GLY G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 479 through 491 removed outlier: 3.528A pdb=" N ASN G 488 " --> pdb=" O GLY G 484 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 499 Processing helix chain 'G' and resid 511 through 515 removed outlier: 3.542A pdb=" N CYS G 514 " --> pdb=" O SER G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 520 through 524 Processing helix chain 'G' and resid 534 through 546 Processing helix chain 'G' and resid 591 through 595 removed outlier: 4.553A pdb=" N ALA G 594 " --> pdb=" O GLU G 591 " (cutoff:3.500A) Processing helix chain 'G' and resid 612 through 628 removed outlier: 3.599A pdb=" N VAL G 616 " --> pdb=" O LYS G 612 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG G 621 " --> pdb=" O HIS G 617 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN G 622 " --> pdb=" O LYS G 618 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY G 628 " --> pdb=" O GLN G 624 " (cutoff:3.500A) Processing helix chain 'G' and resid 666 through 671 Processing helix chain 'G' and resid 671 through 680 Processing helix chain 'G' and resid 687 through 693 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 removed outlier: 7.190A pdb=" N GLN A 174 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL A 151 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ALA A 172 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ILE A 153 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER A 170 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER A 110 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N PHE A 173 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90 removed outlier: 4.461A pdb=" N GLY A 98 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 193 through 197 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 193 through 197 current: chain 'A' and resid 218 through 227 removed outlier: 3.807A pdb=" N GLY A 328 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 411 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 401 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR A 340 " --> pdb=" O TYR A 399 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL A 397 " --> pdb=" O ASP A 342 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 425 through 432 current: chain 'A' and resid 465 through 482 removed outlier: 4.305A pdb=" N ARG A 470 " --> pdb=" O ASP A 514 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASP A 514 " --> pdb=" O ARG A 470 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE A 472 " --> pdb=" O HIS A 512 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N HIS A 512 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLY A 474 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU A 510 " --> pdb=" O GLY A 474 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER A 476 " --> pdb=" O SER A 508 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER A 508 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYS A 478 " --> pdb=" O PHE A 506 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N PHE A 506 " --> pdb=" O LYS A 478 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU A 480 " --> pdb=" O ASP A 504 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASP A 504 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ALA A 482 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLY A 502 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN A 521 " --> pdb=" O ASN A 555 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN A 555 " --> pdb=" O ASN A 521 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 555 through 560 current: chain 'A' and resid 596 through 610 removed outlier: 3.999A pdb=" N ASP A 597 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 631 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY A 599 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 629 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR A 609 " --> pdb=" O GLY A 619 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLY A 619 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLY A 689 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 742 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 691 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY A 740 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA A 693 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 738 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TRP A 695 " --> pdb=" O ILE A 736 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 736 " --> pdb=" O TRP A 695 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN A 697 " --> pdb=" O THR A 734 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR A 734 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA A 699 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARG A 732 " --> pdb=" O ALA A 699 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG A 701 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER A 730 " --> pdb=" O ARG A 701 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A 703 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 724 " --> pdb=" O GLY A 707 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU A 709 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASN A 722 " --> pdb=" O GLU A 709 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN A 711 " --> pdb=" O LYS A 720 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS A 720 " --> pdb=" O GLN A 711 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LYS A 713 " --> pdb=" O GLN A 718 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN A 718 " --> pdb=" O LYS A 713 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP A 768 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N THR A 734 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL A 766 " --> pdb=" O THR A 734 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE A 736 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL A 764 " --> pdb=" O ILE A 736 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE A 738 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN A 762 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLY A 740 " --> pdb=" O ALA A 760 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ALA A 760 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE A 742 " --> pdb=" O THR A 758 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N THR A 758 " --> pdb=" O ILE A 742 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 755 through 771 current: chain 'A' and resid 804 through 813 removed outlier: 3.833A pdb=" N TYR A 854 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 862 " --> pdb=" O TYR A 854 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 856 " --> pdb=" O PHE A 860 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE A 860 " --> pdb=" O VAL A 856 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR A 861 " --> pdb=" O GLU A 912 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A 912 " --> pdb=" O THR A 861 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 244 through 250 Processing sheet with id=AA5, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.796A pdb=" N ILE A 259 " --> pdb=" O TYR A 547 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 380 through 381 Processing sheet with id=AA7, first strand: chain 'A' and resid 822 through 826 Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 90 Processing sheet with id=AA9, first strand: chain 'B' and resid 167 through 169 Processing sheet with id=AB1, first strand: chain 'B' and resid 195 through 196 Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 212 removed outlier: 4.443A pdb=" N PHE B 262 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG B 281 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLN B 295 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE B 308 " --> pdb=" O SER B 337 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER B 337 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY B 310 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER B 335 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER B 335 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU B 353 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 417 through 419 Processing sheet with id=AB4, first strand: chain 'B' and resid 428 through 431 Processing sheet with id=AB5, first strand: chain 'B' and resid 582 through 585 removed outlier: 4.083A pdb=" N ALA B 680 " --> pdb=" O LYS B 662 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS B 662 " --> pdb=" O ALA B 680 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 25 through 28 Processing sheet with id=AB7, first strand: chain 'F' and resid 78 through 81 removed outlier: 6.614A pdb=" N VAL F 270 " --> pdb=" O VAL F 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 114 through 121 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 221 through 225 current: chain 'F' and resid 251 through 253 Processing sheet with id=AB9, first strand: chain 'F' and resid 361 through 365 removed outlier: 6.880A pdb=" N VAL F 361 " --> pdb=" O GLU F 386 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL F 388 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TRP F 363 " --> pdb=" O VAL F 388 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 408 through 410 removed outlier: 3.662A pdb=" N MET F 408 " --> pdb=" O VAL F 607 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL F 606 " --> pdb=" O VAL F 426 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 444 through 446 Processing sheet with id=AC3, first strand: chain 'F' and resid 450 through 452 Processing sheet with id=AC4, first strand: chain 'G' and resid 24 through 27 removed outlier: 5.631A pdb=" N VAL G 25 " --> pdb=" O ALA G 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'G' and resid 78 through 81 removed outlier: 3.615A pdb=" N VAL G 79 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL G 270 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 104 through 105 Processing sheet with id=AC7, first strand: chain 'G' and resid 113 through 121 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 113 through 121 current: chain 'G' and resid 176 through 177 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 176 through 177 current: chain 'G' and resid 251 through 253 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'G' and resid 361 through 363 removed outlier: 6.061A pdb=" N VAL G 361 " --> pdb=" O GLU G 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 407 through 410 removed outlier: 6.957A pdb=" N VAL G 606 " --> pdb=" O VAL G 426 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL G 424 " --> pdb=" O THR G 608 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS G 656 " --> pdb=" O ASN G 430 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 550 through 553 removed outlier: 4.523A pdb=" N ALA G 449 " --> pdb=" O LEU G 581 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 467 through 469 removed outlier: 7.214A pdb=" N SER G 468 " --> pdb=" O CYS G 503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 658 hydrogen bonds defined for protein. 1779 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.04 Time building geometry restraints manager: 2.51 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: 7356 1.34 - 1.47: 5380 1.47 - 1.59: 9576 1.59 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 22450 Sorted by residual: bond pdb=" CA VAL F 557 " pdb=" CB VAL F 557 " ideal model delta sigma weight residual 1.539 1.533 0.006 5.40e-03 3.43e+04 1.40e+00 bond pdb=" CA GLY B 259 " pdb=" C GLY B 259 " ideal model delta sigma weight residual 1.514 1.498 0.016 1.41e-02 5.03e+03 1.29e+00 bond pdb=" CB TYR A 473 " pdb=" CG TYR A 473 " ideal model delta sigma weight residual 1.512 1.488 0.024 2.20e-02 2.07e+03 1.20e+00 bond pdb=" CA ILE A 230 " pdb=" CB ILE A 230 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.18e+00 bond pdb=" CB TRP F 363 " pdb=" CG TRP F 363 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.08e+00 ... (remaining 22445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 29379 1.59 - 3.18: 811 3.18 - 4.77: 113 4.77 - 6.36: 18 6.36 - 7.96: 6 Bond angle restraints: 30327 Sorted by residual: angle pdb=" C CYS F 358 " pdb=" CA CYS F 358 " pdb=" CB CYS F 358 " ideal model delta sigma weight residual 116.63 110.64 5.99 1.16e+00 7.43e-01 2.67e+01 angle pdb=" C ARG F 346 " pdb=" N GLU F 347 " pdb=" CA GLU F 347 " ideal model delta sigma weight residual 120.72 112.76 7.96 1.67e+00 3.59e-01 2.27e+01 angle pdb=" C SER F 381 " pdb=" N VAL F 382 " pdb=" CA VAL F 382 " ideal model delta sigma weight residual 121.97 129.77 -7.80 1.80e+00 3.09e-01 1.88e+01 angle pdb=" C SER G 298 " pdb=" N LYS G 299 " pdb=" CA LYS G 299 " ideal model delta sigma weight residual 121.70 128.58 -6.88 1.80e+00 3.09e-01 1.46e+01 angle pdb=" C SER F 298 " pdb=" N LYS F 299 " pdb=" CA LYS F 299 " ideal model delta sigma weight residual 121.70 128.23 -6.53 1.80e+00 3.09e-01 1.32e+01 ... (remaining 30322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12224 17.98 - 35.95: 1087 35.95 - 53.93: 166 53.93 - 71.91: 26 71.91 - 89.89: 22 Dihedral angle restraints: 13525 sinusoidal: 5429 harmonic: 8096 Sorted by residual: dihedral pdb=" CB CYS G 374 " pdb=" SG CYS G 374 " pdb=" SG CYS G 387 " pdb=" CB CYS G 387 " ideal model delta sinusoidal sigma weight residual -86.00 -0.09 -85.91 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS F 177 " pdb=" SG CYS F 177 " pdb=" SG CYS F 193 " pdb=" CB CYS F 193 " ideal model delta sinusoidal sigma weight residual -86.00 -168.38 82.38 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS F 634 " pdb=" SG CYS F 634 " pdb=" SG CYS F 639 " pdb=" CB CYS F 639 " ideal model delta sinusoidal sigma weight residual 93.00 175.35 -82.35 1 1.00e+01 1.00e-02 8.32e+01 ... (remaining 13522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2499 0.050 - 0.099: 571 0.099 - 0.149: 110 0.149 - 0.198: 5 0.198 - 0.248: 2 Chirality restraints: 3187 Sorted by residual: chirality pdb=" CB VAL F 382 " pdb=" CA VAL F 382 " pdb=" CG1 VAL F 382 " pdb=" CG2 VAL F 382 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ARG F 346 " pdb=" N ARG F 346 " pdb=" C ARG F 346 " pdb=" CB ARG F 346 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CB THR F 440 " pdb=" CA THR F 440 " pdb=" OG1 THR F 440 " pdb=" CG2 THR F 440 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.09e-01 ... (remaining 3184 not shown) Planarity restraints: 4003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 252 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO F 253 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO F 253 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 253 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 186 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO F 187 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO F 187 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 187 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 92 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO G 93 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO G 93 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 93 " -0.023 5.00e-02 4.00e+02 ... (remaining 4000 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 401 2.56 - 3.15: 19409 3.15 - 3.73: 37422 3.73 - 4.32: 49631 4.32 - 4.90: 77307 Nonbonded interactions: 184170 Sorted by model distance: nonbonded pdb=" OD1 ASP G 82 " pdb="FE FE G 704 " model vdw 1.977 2.260 nonbonded pdb=" OH TYR G 445 " pdb="FE FE G 703 " model vdw 1.996 2.260 nonbonded pdb=" O1 BCT G 702 " pdb="FE FE G 703 " model vdw 2.005 2.260 nonbonded pdb=" NH2 ARG G 143 " pdb="FE FE G 704 " model vdw 2.037 2.340 nonbonded pdb=" NE2 HIS G 268 " pdb="FE FE G 704 " model vdw 2.084 2.340 ... (remaining 184165 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 22 through 352 or resid 354 through 521 or (resid 522 and \ (name N or name CA or name C or name O or name CB )) or resid 523 through 577 or \ (resid 578 and (name CA or name C or name O or name CB or name CG or name CD1 o \ r name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resid 579 through \ 681 or (resid 682 and (name N or name CA or name C or name O or name CB )) or r \ esid 683 through 701)) selection = (chain 'G' and (resid 22 through 352 or resid 354 through 458 or (resid 459 and \ (name N or name CA or name C or name O or name CB )) or resid 460 through 490 or \ (resid 491 and (name N or name CA or name C or name O or name CB )) or resid 49 \ 2 through 583 or (resid 584 and (name N or name CA or name C or name O or name C \ B )) or resid 585 or (resid 586 and (name N or name CA or name C or name O or na \ me CB )) or resid 587 through 630 or (resid 631 through 633 and (name N or name \ CA or name C or name O or name CB )) or resid 634 or (resid 635 and (name N or n \ ame CA or name C or name O or name CB )) or resid 636 through 643 or (resid 644 \ and (name N or name CA or name C or name O or name CB )) or resid 645 through 67 \ 1 or (resid 672 and (name N or name CA or name C or name O or name CB )) or resi \ d 673 through 675 or (resid 676 through 677 and (name N or name CA or name C or \ name O or name CB )) or resid 678 through 695 or (resid 696 and (name N or name \ CA or name C or name O or name CB )) or resid 701)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.640 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22494 Z= 0.171 Angle : 0.646 7.956 30411 Z= 0.356 Chirality : 0.043 0.248 3187 Planarity : 0.004 0.052 4003 Dihedral : 13.502 89.886 8245 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 22.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.96 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.15 % Twisted Proline : 0.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.16), residues: 2803 helix: -1.04 (0.23), residues: 492 sheet: -0.47 (0.19), residues: 762 loop : -0.97 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 346 TYR 0.018 0.002 TYR B 668 PHE 0.017 0.002 PHE B 329 TRP 0.025 0.002 TRP B 571 HIS 0.005 0.001 HIS G 470 Details of bonding type rmsd covalent geometry : bond 0.00354 (22450) covalent geometry : angle 0.64273 (30327) SS BOND : bond 0.00293 ( 42) SS BOND : angle 1.36254 ( 84) hydrogen bonds : bond 0.16515 ( 658) hydrogen bonds : angle 8.00275 ( 1779) Misc. bond : bond 0.00055 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7485 (tptt) cc_final: 0.7132 (tppt) REVERT: A 119 ILE cc_start: 0.8511 (tp) cc_final: 0.7924 (tp) REVERT: A 376 TYR cc_start: 0.7760 (p90) cc_final: 0.7450 (p90) REVERT: B 154 TYR cc_start: 0.8659 (m-80) cc_final: 0.8307 (m-10) REVERT: B 161 TYR cc_start: 0.7471 (p90) cc_final: 0.7006 (p90) REVERT: B 258 GLU cc_start: 0.7861 (tp30) cc_final: 0.7496 (tp30) REVERT: B 410 LEU cc_start: 0.8804 (tp) cc_final: 0.8582 (tp) REVERT: B 464 PHE cc_start: 0.7521 (m-80) cc_final: 0.7077 (m-10) REVERT: B 547 MET cc_start: 0.7884 (ppp) cc_final: 0.7414 (ppp) REVERT: F 128 MET cc_start: 0.9251 (pmm) cc_final: 0.9006 (pmm) REVERT: G 45 MET cc_start: 0.9227 (tmm) cc_final: 0.9017 (tmm) REVERT: G 94 ASN cc_start: 0.9411 (p0) cc_final: 0.9144 (p0) REVERT: G 329 ASP cc_start: 0.9446 (p0) cc_final: 0.9234 (p0) REVERT: G 336 TYR cc_start: 0.8763 (t80) cc_final: 0.8312 (t80) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1504 time to fit residues: 38.9486 Evaluate side-chains 115 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 ASN ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 488 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.067283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.056250 restraints weight = 222238.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.057283 restraints weight = 148256.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.057922 restraints weight = 110362.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.058522 restraints weight = 89490.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.058909 restraints weight = 75649.556| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22494 Z= 0.172 Angle : 0.616 7.587 30411 Z= 0.332 Chirality : 0.042 0.189 3187 Planarity : 0.004 0.048 4003 Dihedral : 5.224 28.393 3079 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.79 % Favored : 92.14 % Rotamer: Outliers : 0.04 % Allowed : 5.83 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.16), residues: 2803 helix: -0.99 (0.22), residues: 497 sheet: -0.44 (0.19), residues: 716 loop : -1.07 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 843 TYR 0.021 0.002 TYR B 668 PHE 0.019 0.002 PHE G 223 TRP 0.021 0.002 TRP B 571 HIS 0.006 0.001 HIS F 617 Details of bonding type rmsd covalent geometry : bond 0.00362 (22450) covalent geometry : angle 0.61460 (30327) SS BOND : bond 0.00260 ( 42) SS BOND : angle 1.06150 ( 84) hydrogen bonds : bond 0.04324 ( 658) hydrogen bonds : angle 7.08199 ( 1779) Misc. bond : bond 0.00062 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 TYR cc_start: 0.7770 (p90) cc_final: 0.7446 (p90) REVERT: A 473 TYR cc_start: 0.6839 (t80) cc_final: 0.6402 (t80) REVERT: A 727 ASN cc_start: 0.8573 (p0) cc_final: 0.7805 (p0) REVERT: A 825 ARG cc_start: 0.7401 (mpt180) cc_final: 0.6418 (mmt90) REVERT: B 154 TYR cc_start: 0.8645 (m-80) cc_final: 0.8266 (m-10) REVERT: B 161 TYR cc_start: 0.7536 (p90) cc_final: 0.7000 (p90) REVERT: B 410 LEU cc_start: 0.8665 (tp) cc_final: 0.8426 (tp) REVERT: B 464 PHE cc_start: 0.7189 (m-80) cc_final: 0.6763 (m-80) REVERT: B 547 MET cc_start: 0.7508 (ppp) cc_final: 0.7159 (ppp) REVERT: F 401 MET cc_start: 0.8257 (tpt) cc_final: 0.7873 (tpt) REVERT: G 45 MET cc_start: 0.9331 (tmm) cc_final: 0.9046 (tmm) REVERT: G 94 ASN cc_start: 0.9334 (p0) cc_final: 0.9084 (p0) REVERT: G 336 TYR cc_start: 0.8849 (t80) cc_final: 0.8509 (t80) REVERT: G 543 LEU cc_start: 0.9374 (tp) cc_final: 0.9153 (tp) REVERT: G 574 ASN cc_start: 0.9135 (t0) cc_final: 0.8897 (t0) outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 0.1475 time to fit residues: 37.9062 Evaluate side-chains 116 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 28 optimal weight: 2.9990 chunk 200 optimal weight: 0.0040 chunk 150 optimal weight: 20.0000 chunk 156 optimal weight: 6.9990 chunk 229 optimal weight: 0.2980 chunk 144 optimal weight: 9.9990 chunk 121 optimal weight: 20.0000 chunk 14 optimal weight: 30.0000 chunk 98 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 272 optimal weight: 7.9990 overall best weight: 3.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 891 HIS ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS ** F 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS G 232 ASN ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.067515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.056301 restraints weight = 214135.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.057365 restraints weight = 147878.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.058079 restraints weight = 109505.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.058631 restraints weight = 87807.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.058957 restraints weight = 74089.681| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22494 Z= 0.156 Angle : 0.606 7.666 30411 Z= 0.324 Chirality : 0.042 0.192 3187 Planarity : 0.004 0.050 4003 Dihedral : 5.210 29.302 3079 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.32 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.16), residues: 2803 helix: -0.94 (0.22), residues: 491 sheet: -0.50 (0.19), residues: 717 loop : -1.11 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 651 TYR 0.019 0.002 TYR B 668 PHE 0.014 0.002 PHE F 551 TRP 0.026 0.002 TRP G 569 HIS 0.005 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00331 (22450) covalent geometry : angle 0.60393 (30327) SS BOND : bond 0.00302 ( 42) SS BOND : angle 1.07257 ( 84) hydrogen bonds : bond 0.03861 ( 658) hydrogen bonds : angle 6.89046 ( 1779) Misc. bond : bond 0.00032 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.7267 (mmp) cc_final: 0.6676 (mmm) REVERT: A 376 TYR cc_start: 0.7757 (p90) cc_final: 0.7425 (p90) REVERT: A 473 TYR cc_start: 0.6957 (t80) cc_final: 0.6558 (t80) REVERT: B 154 TYR cc_start: 0.8641 (m-80) cc_final: 0.8324 (m-80) REVERT: B 161 TYR cc_start: 0.7627 (p90) cc_final: 0.7021 (p90) REVERT: B 410 LEU cc_start: 0.8729 (tp) cc_final: 0.8377 (tp) REVERT: B 464 PHE cc_start: 0.7146 (m-80) cc_final: 0.6802 (m-80) REVERT: B 547 MET cc_start: 0.7550 (ppp) cc_final: 0.7228 (ppp) REVERT: F 128 MET cc_start: 0.9254 (pmm) cc_final: 0.8995 (pmm) REVERT: F 401 MET cc_start: 0.8150 (tpt) cc_final: 0.7908 (tpt) REVERT: G 45 MET cc_start: 0.9309 (tmm) cc_final: 0.9026 (ppp) REVERT: G 94 ASN cc_start: 0.9352 (p0) cc_final: 0.9093 (p0) REVERT: G 336 TYR cc_start: 0.8813 (t80) cc_final: 0.8361 (t80) REVERT: G 406 ASP cc_start: 0.9155 (m-30) cc_final: 0.8460 (p0) REVERT: G 543 LEU cc_start: 0.9335 (tp) cc_final: 0.9107 (tp) REVERT: G 574 ASN cc_start: 0.9223 (t0) cc_final: 0.8990 (t0) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1512 time to fit residues: 39.0198 Evaluate side-chains 118 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 121 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 151 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 470 HIS ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.067507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.056454 restraints weight = 212837.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.057496 restraints weight = 143364.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.058262 restraints weight = 106213.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.058819 restraints weight = 85213.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.059167 restraints weight = 71659.298| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22494 Z= 0.147 Angle : 0.597 7.024 30411 Z= 0.318 Chirality : 0.042 0.183 3187 Planarity : 0.004 0.064 4003 Dihedral : 5.151 27.242 3079 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.54 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.16), residues: 2803 helix: -0.86 (0.22), residues: 486 sheet: -0.56 (0.19), residues: 721 loop : -1.09 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 346 TYR 0.020 0.002 TYR F 445 PHE 0.014 0.002 PHE B 329 TRP 0.016 0.001 TRP B 571 HIS 0.004 0.001 HIS G 470 Details of bonding type rmsd covalent geometry : bond 0.00314 (22450) covalent geometry : angle 0.59467 (30327) SS BOND : bond 0.00264 ( 42) SS BOND : angle 1.14459 ( 84) hydrogen bonds : bond 0.03633 ( 658) hydrogen bonds : angle 6.76714 ( 1779) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.7453 (mmp) cc_final: 0.7112 (mmm) REVERT: A 292 ARG cc_start: 0.8876 (pmt-80) cc_final: 0.8633 (pmt-80) REVERT: A 376 TYR cc_start: 0.7719 (p90) cc_final: 0.7382 (p90) REVERT: B 154 TYR cc_start: 0.8663 (m-80) cc_final: 0.8315 (m-80) REVERT: B 161 TYR cc_start: 0.7650 (p90) cc_final: 0.7015 (p90) REVERT: B 410 LEU cc_start: 0.8709 (tp) cc_final: 0.8392 (tp) REVERT: B 464 PHE cc_start: 0.7146 (m-80) cc_final: 0.6807 (m-80) REVERT: B 547 MET cc_start: 0.7488 (ppp) cc_final: 0.7048 (ppp) REVERT: F 128 MET cc_start: 0.9246 (pmm) cc_final: 0.8999 (pmm) REVERT: F 342 ILE cc_start: 0.9665 (pt) cc_final: 0.9344 (pt) REVERT: F 401 MET cc_start: 0.8132 (tpt) cc_final: 0.7896 (tpt) REVERT: G 45 MET cc_start: 0.9290 (tmm) cc_final: 0.8986 (tmm) REVERT: G 94 ASN cc_start: 0.9354 (p0) cc_final: 0.9095 (p0) REVERT: G 336 TYR cc_start: 0.8777 (t80) cc_final: 0.8339 (t80) REVERT: G 406 ASP cc_start: 0.9192 (m-30) cc_final: 0.8497 (p0) REVERT: G 543 LEU cc_start: 0.9340 (tp) cc_final: 0.9106 (tp) REVERT: G 574 ASN cc_start: 0.9251 (t0) cc_final: 0.9006 (t0) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1498 time to fit residues: 37.7343 Evaluate side-chains 120 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 259 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 239 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 152 optimal weight: 40.0000 chunk 228 optimal weight: 8.9990 chunk 217 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.065476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.054519 restraints weight = 228929.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.055551 restraints weight = 154457.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.056170 restraints weight = 114316.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.056705 restraints weight = 92582.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.057031 restraints weight = 79128.565| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 22494 Z= 0.240 Angle : 0.697 7.778 30411 Z= 0.373 Chirality : 0.044 0.249 3187 Planarity : 0.005 0.077 4003 Dihedral : 5.649 30.639 3079 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.18 % Favored : 90.75 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.15 % Twisted Proline : 0.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.16), residues: 2803 helix: -1.09 (0.22), residues: 497 sheet: -0.81 (0.19), residues: 731 loop : -1.26 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 351 TYR 0.027 0.002 TYR B 297 PHE 0.021 0.002 PHE F 551 TRP 0.020 0.002 TRP B 571 HIS 0.008 0.002 HIS F 625 Details of bonding type rmsd covalent geometry : bond 0.00507 (22450) covalent geometry : angle 0.69468 (30327) SS BOND : bond 0.00299 ( 42) SS BOND : angle 1.34624 ( 84) hydrogen bonds : bond 0.04146 ( 658) hydrogen bonds : angle 7.15009 ( 1779) Misc. bond : bond 0.00042 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 TYR cc_start: 0.7949 (p90) cc_final: 0.7570 (p90) REVERT: B 67 LEU cc_start: 0.9193 (mt) cc_final: 0.8943 (tt) REVERT: B 154 TYR cc_start: 0.8646 (m-80) cc_final: 0.8366 (m-80) REVERT: B 161 TYR cc_start: 0.8124 (p90) cc_final: 0.7306 (p90) REVERT: B 258 GLU cc_start: 0.7605 (tp30) cc_final: 0.7326 (tp30) REVERT: B 410 LEU cc_start: 0.8767 (tp) cc_final: 0.8315 (tp) REVERT: B 464 PHE cc_start: 0.7195 (m-80) cc_final: 0.6859 (m-10) REVERT: B 517 MET cc_start: 0.8532 (ppp) cc_final: 0.8104 (ppp) REVERT: F 26 ARG cc_start: 0.5088 (tmm160) cc_final: 0.4730 (tpt90) REVERT: G 45 MET cc_start: 0.9359 (tmm) cc_final: 0.9066 (tmm) REVERT: G 94 ASN cc_start: 0.9228 (p0) cc_final: 0.8995 (p0) REVERT: G 336 TYR cc_start: 0.8833 (t80) cc_final: 0.8260 (t80) REVERT: G 406 ASP cc_start: 0.9179 (m-30) cc_final: 0.8512 (p0) REVERT: G 543 LEU cc_start: 0.9297 (tp) cc_final: 0.9077 (tp) REVERT: G 574 ASN cc_start: 0.9306 (t0) cc_final: 0.9063 (t0) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1532 time to fit residues: 38.4176 Evaluate side-chains 113 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 6 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 254 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 152 optimal weight: 40.0000 chunk 173 optimal weight: 10.0000 chunk 59 optimal weight: 30.0000 chunk 160 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 216 optimal weight: 5.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN F 430 ASN F 432 ASN ** F 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 470 HIS ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.064782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.053795 restraints weight = 227902.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.054836 restraints weight = 151272.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.055536 restraints weight = 112240.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.056038 restraints weight = 89941.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.056337 restraints weight = 77175.343| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 22494 Z= 0.291 Angle : 0.771 9.290 30411 Z= 0.415 Chirality : 0.046 0.192 3187 Planarity : 0.005 0.069 4003 Dihedral : 6.158 30.319 3079 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 28.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.25 % Favored : 89.68 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.15 % Twisted Proline : 0.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.15), residues: 2803 helix: -1.40 (0.21), residues: 499 sheet: -1.06 (0.19), residues: 727 loop : -1.41 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 407 TYR 0.029 0.003 TYR B 668 PHE 0.041 0.003 PHE F 172 TRP 0.040 0.002 TRP A 877 HIS 0.011 0.002 HIS G 470 Details of bonding type rmsd covalent geometry : bond 0.00615 (22450) covalent geometry : angle 0.76849 (30327) SS BOND : bond 0.00471 ( 42) SS BOND : angle 1.47672 ( 84) hydrogen bonds : bond 0.04464 ( 658) hydrogen bonds : angle 7.56648 ( 1779) Misc. bond : bond 0.00121 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LEU cc_start: 0.9532 (mp) cc_final: 0.9186 (tt) REVERT: A 407 ARG cc_start: 0.8908 (tmm-80) cc_final: 0.8625 (tmm-80) REVERT: A 777 ASP cc_start: 0.8705 (t0) cc_final: 0.8438 (t0) REVERT: A 880 VAL cc_start: 0.9310 (t) cc_final: 0.8968 (t) REVERT: B 154 TYR cc_start: 0.8620 (m-80) cc_final: 0.8371 (m-80) REVERT: B 161 TYR cc_start: 0.8133 (p90) cc_final: 0.7353 (p90) REVERT: B 410 LEU cc_start: 0.8766 (tp) cc_final: 0.8249 (tp) REVERT: B 464 PHE cc_start: 0.7289 (m-80) cc_final: 0.7044 (m-10) REVERT: F 26 ARG cc_start: 0.4704 (tmm160) cc_final: 0.4402 (tpt90) REVERT: G 336 TYR cc_start: 0.8812 (t80) cc_final: 0.8191 (t80) REVERT: G 399 LYS cc_start: 0.9597 (mmmm) cc_final: 0.9357 (mmmm) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1517 time to fit residues: 35.2085 Evaluate side-chains 113 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 97 optimal weight: 9.9990 chunk 72 optimal weight: 0.0870 chunk 261 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 169 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 overall best weight: 3.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.066720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.055699 restraints weight = 221061.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.056734 restraints weight = 147418.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.057342 restraints weight = 109699.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.057917 restraints weight = 89516.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.058283 restraints weight = 76234.300| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22494 Z= 0.158 Angle : 0.646 8.642 30411 Z= 0.346 Chirality : 0.044 0.237 3187 Planarity : 0.004 0.061 4003 Dihedral : 5.721 32.101 3079 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.71 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.15 % Twisted Proline : 0.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.16), residues: 2803 helix: -1.14 (0.22), residues: 498 sheet: -0.99 (0.19), residues: 718 loop : -1.27 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 843 TYR 0.021 0.002 TYR B 204 PHE 0.038 0.002 PHE F 172 TRP 0.030 0.002 TRP A 877 HIS 0.009 0.001 HIS F 44 Details of bonding type rmsd covalent geometry : bond 0.00342 (22450) covalent geometry : angle 0.64361 (30327) SS BOND : bond 0.00279 ( 42) SS BOND : angle 1.28391 ( 84) hydrogen bonds : bond 0.03658 ( 658) hydrogen bonds : angle 7.13101 ( 1779) Misc. bond : bond 0.00041 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.7083 (mmm) cc_final: 0.6694 (mmm) REVERT: A 376 TYR cc_start: 0.8181 (p90) cc_final: 0.7849 (p90) REVERT: A 407 ARG cc_start: 0.8896 (tmm-80) cc_final: 0.8410 (tmm-80) REVERT: A 727 ASN cc_start: 0.8432 (p0) cc_final: 0.7758 (p0) REVERT: A 777 ASP cc_start: 0.8815 (t0) cc_final: 0.8067 (t0) REVERT: A 880 VAL cc_start: 0.9161 (t) cc_final: 0.8752 (t) REVERT: B 154 TYR cc_start: 0.8593 (m-80) cc_final: 0.8330 (m-80) REVERT: B 161 TYR cc_start: 0.8086 (p90) cc_final: 0.7285 (p90) REVERT: B 410 LEU cc_start: 0.8828 (tp) cc_final: 0.8351 (tp) REVERT: B 464 PHE cc_start: 0.7211 (m-80) cc_final: 0.6930 (m-80) REVERT: F 26 ARG cc_start: 0.4580 (tmm160) cc_final: 0.3636 (tmt-80) REVERT: F 81 LEU cc_start: 0.6623 (tp) cc_final: 0.6402 (tp) REVERT: F 257 TYR cc_start: 0.5736 (p90) cc_final: 0.5248 (p90) REVERT: G 94 ASN cc_start: 0.9092 (p0) cc_final: 0.8883 (p0) REVERT: G 329 ASP cc_start: 0.9362 (p0) cc_final: 0.9055 (p0) REVERT: G 336 TYR cc_start: 0.8775 (t80) cc_final: 0.8171 (t80) REVERT: G 406 ASP cc_start: 0.9265 (m-30) cc_final: 0.8531 (p0) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1511 time to fit residues: 37.3536 Evaluate side-chains 121 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 234 optimal weight: 8.9990 chunk 267 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 219 optimal weight: 0.9980 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 HIS ** F 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.065182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.054238 restraints weight = 218145.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.055223 restraints weight = 147302.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.055954 restraints weight = 110245.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.056434 restraints weight = 88584.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.056660 restraints weight = 75788.670| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22494 Z= 0.246 Angle : 0.733 8.281 30411 Z= 0.392 Chirality : 0.046 0.249 3187 Planarity : 0.005 0.073 4003 Dihedral : 6.013 30.863 3079 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 25.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.11 % Favored : 89.86 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.15 % Twisted Proline : 0.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.15), residues: 2803 helix: -1.35 (0.21), residues: 494 sheet: -1.17 (0.19), residues: 732 loop : -1.35 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 706 TYR 0.026 0.002 TYR B 668 PHE 0.034 0.003 PHE F 172 TRP 0.038 0.002 TRP A 877 HIS 0.008 0.002 HIS F 625 Details of bonding type rmsd covalent geometry : bond 0.00521 (22450) covalent geometry : angle 0.72959 (30327) SS BOND : bond 0.00367 ( 42) SS BOND : angle 1.50702 ( 84) hydrogen bonds : bond 0.04199 ( 658) hydrogen bonds : angle 7.38339 ( 1779) Misc. bond : bond 0.00023 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 TYR cc_start: 0.8127 (p90) cc_final: 0.7829 (p90) REVERT: A 727 ASN cc_start: 0.8297 (p0) cc_final: 0.7487 (p0) REVERT: A 781 HIS cc_start: 0.8819 (t-90) cc_final: 0.8486 (t-90) REVERT: A 880 VAL cc_start: 0.9157 (t) cc_final: 0.8831 (t) REVERT: B 161 TYR cc_start: 0.8063 (p90) cc_final: 0.7324 (p90) REVERT: B 410 LEU cc_start: 0.8730 (tp) cc_final: 0.8164 (tp) REVERT: B 464 PHE cc_start: 0.7213 (m-80) cc_final: 0.6994 (m-80) REVERT: F 26 ARG cc_start: 0.4939 (tmm160) cc_final: 0.4490 (tpt90) REVERT: F 344 ASN cc_start: 0.8514 (m110) cc_final: 0.8181 (m110) REVERT: G 94 ASN cc_start: 0.9143 (p0) cc_final: 0.8931 (p0) REVERT: G 329 ASP cc_start: 0.9359 (p0) cc_final: 0.9117 (p0) REVERT: G 406 ASP cc_start: 0.9217 (m-30) cc_final: 0.8528 (p0) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1619 time to fit residues: 38.0442 Evaluate side-chains 112 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 269 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 274 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 264 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 HIS G 171 ASN ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.066470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.055306 restraints weight = 212193.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.056348 restraints weight = 140958.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.057118 restraints weight = 104800.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.057673 restraints weight = 83511.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.058067 restraints weight = 70247.405| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22494 Z= 0.151 Angle : 0.649 8.367 30411 Z= 0.345 Chirality : 0.044 0.247 3187 Planarity : 0.004 0.061 4003 Dihedral : 5.701 30.669 3079 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.04 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.15 % Twisted Proline : 0.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.16), residues: 2803 helix: -1.21 (0.22), residues: 497 sheet: -1.05 (0.19), residues: 731 loop : -1.25 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 843 TYR 0.020 0.002 TYR B 668 PHE 0.036 0.002 PHE F 172 TRP 0.037 0.002 TRP A 877 HIS 0.007 0.001 HIS F 44 Details of bonding type rmsd covalent geometry : bond 0.00328 (22450) covalent geometry : angle 0.64578 (30327) SS BOND : bond 0.00327 ( 42) SS BOND : angle 1.34437 ( 84) hydrogen bonds : bond 0.03595 ( 658) hydrogen bonds : angle 7.02329 ( 1779) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 TYR cc_start: 0.8196 (p90) cc_final: 0.7857 (p90) REVERT: A 727 ASN cc_start: 0.8219 (p0) cc_final: 0.7448 (p0) REVERT: A 781 HIS cc_start: 0.8798 (t-90) cc_final: 0.8562 (t-90) REVERT: A 880 VAL cc_start: 0.9162 (t) cc_final: 0.8766 (t) REVERT: B 161 TYR cc_start: 0.7940 (p90) cc_final: 0.7249 (p90) REVERT: F 128 MET cc_start: 0.9218 (pmm) cc_final: 0.8980 (pmm) REVERT: G 94 ASN cc_start: 0.9108 (p0) cc_final: 0.8892 (p0) REVERT: G 399 LYS cc_start: 0.9598 (mmmm) cc_final: 0.9333 (mmmm) REVERT: G 406 ASP cc_start: 0.9230 (m-30) cc_final: 0.8458 (p0) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1423 time to fit residues: 34.5328 Evaluate side-chains 116 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 144 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 197 optimal weight: 0.0270 chunk 230 optimal weight: 4.9990 chunk 278 optimal weight: 1.9990 chunk 260 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 226 optimal weight: 0.0010 chunk 112 optimal weight: 6.9990 chunk 235 optimal weight: 20.0000 chunk 243 optimal weight: 6.9990 overall best weight: 1.5248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 360 GLN ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.067853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.056685 restraints weight = 211476.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.057780 restraints weight = 141097.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.058518 restraints weight = 104049.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.059086 restraints weight = 83347.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.059411 restraints weight = 70145.786| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22494 Z= 0.121 Angle : 0.622 8.710 30411 Z= 0.330 Chirality : 0.043 0.248 3187 Planarity : 0.004 0.057 4003 Dihedral : 5.327 29.788 3079 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.46 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.16), residues: 2803 helix: -0.86 (0.22), residues: 491 sheet: -0.91 (0.19), residues: 732 loop : -1.17 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 541 TYR 0.021 0.001 TYR A 791 PHE 0.036 0.001 PHE F 172 TRP 0.035 0.002 TRP A 877 HIS 0.007 0.001 HIS F 554 Details of bonding type rmsd covalent geometry : bond 0.00265 (22450) covalent geometry : angle 0.62003 (30327) SS BOND : bond 0.00285 ( 42) SS BOND : angle 1.21898 ( 84) hydrogen bonds : bond 0.03327 ( 658) hydrogen bonds : angle 6.65837 ( 1779) Misc. bond : bond 0.00031 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 TYR cc_start: 0.8043 (p90) cc_final: 0.7720 (p90) REVERT: A 727 ASN cc_start: 0.8022 (p0) cc_final: 0.7237 (p0) REVERT: A 781 HIS cc_start: 0.8865 (t-90) cc_final: 0.8520 (t-90) REVERT: A 880 VAL cc_start: 0.9103 (t) cc_final: 0.8668 (t) REVERT: B 161 TYR cc_start: 0.7841 (p90) cc_final: 0.7283 (p90) REVERT: F 128 MET cc_start: 0.9230 (pmm) cc_final: 0.8959 (pmm) REVERT: F 344 ASN cc_start: 0.8305 (m110) cc_final: 0.8066 (m110) REVERT: G 45 MET cc_start: 0.9295 (tmm) cc_final: 0.9078 (tmm) REVERT: G 94 ASN cc_start: 0.9125 (p0) cc_final: 0.8889 (p0) REVERT: G 285 LEU cc_start: 0.9260 (tt) cc_final: 0.8805 (mt) REVERT: G 399 LYS cc_start: 0.9627 (mmmm) cc_final: 0.9370 (mtmt) REVERT: G 406 ASP cc_start: 0.9248 (m-30) cc_final: 0.8420 (p0) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1494 time to fit residues: 38.5445 Evaluate side-chains 125 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 238 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 209 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 HIS ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 ASN ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.066579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.055612 restraints weight = 223959.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.056660 restraints weight = 149436.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.057386 restraints weight = 111139.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.057938 restraints weight = 88920.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.058246 restraints weight = 74900.475| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22494 Z= 0.165 Angle : 0.650 8.360 30411 Z= 0.344 Chirality : 0.043 0.224 3187 Planarity : 0.004 0.058 4003 Dihedral : 5.467 31.722 3079 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.61 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.15 % Twisted Proline : 0.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.16), residues: 2803 helix: -0.93 (0.22), residues: 486 sheet: -0.86 (0.19), residues: 721 loop : -1.20 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 346 TYR 0.021 0.002 TYR B 668 PHE 0.034 0.002 PHE F 172 TRP 0.041 0.002 TRP A 877 HIS 0.006 0.001 HIS F 44 Details of bonding type rmsd covalent geometry : bond 0.00357 (22450) covalent geometry : angle 0.64736 (30327) SS BOND : bond 0.00315 ( 42) SS BOND : angle 1.27585 ( 84) hydrogen bonds : bond 0.03571 ( 658) hydrogen bonds : angle 6.79560 ( 1779) Misc. bond : bond 0.00023 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4065.50 seconds wall clock time: 71 minutes 39.19 seconds (4299.19 seconds total)