Starting phenix.real_space_refine on Mon Jun 23 23:55:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8x_36967/06_2025/8k8x_36967.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8x_36967/06_2025/8k8x_36967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k8x_36967/06_2025/8k8x_36967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8x_36967/06_2025/8k8x_36967.map" model { file = "/net/cci-nas-00/data/ceres_data/8k8x_36967/06_2025/8k8x_36967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8x_36967/06_2025/8k8x_36967.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 17625 2.51 5 N 5000 2.21 5 O 5220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.96s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27880 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "C" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "B" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "A" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "E" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Time building chain proxies: 16.30, per 1000 atoms: 0.58 Number of scatterers: 27880 At special positions: 0 Unit cell: (127.92, 157.44, 182.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 5220 8.00 N 5000 7.00 C 17625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.44 Conformation dependent library (CDL) restraints added in 3.4 seconds 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6600 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 57 sheets defined 54.3% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'D' and resid 4 through 9 removed outlier: 3.529A pdb=" N LEU D 8 " --> pdb=" O SER D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 58 through 68 Processing helix chain 'D' and resid 97 through 111 Processing helix chain 'D' and resid 111 through 120 Processing helix chain 'D' and resid 121 through 153 removed outlier: 3.559A pdb=" N ALA D 153 " --> pdb=" O GLU D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 221 removed outlier: 4.050A pdb=" N ASN D 212 " --> pdb=" O HIS D 208 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG D 213 " --> pdb=" O TYR D 209 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 224 through 242 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 273 through 279 Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 322 through 333 Processing helix chain 'D' and resid 363 through 372 removed outlier: 3.887A pdb=" N GLY D 369 " --> pdb=" O GLU D 365 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU D 370 " --> pdb=" O ALA D 366 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 379 Processing helix chain 'D' and resid 393 through 407 Processing helix chain 'D' and resid 412 through 428 Processing helix chain 'D' and resid 436 through 452 Processing helix chain 'D' and resid 456 through 471 Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 543 through 557 Processing helix chain 'D' and resid 584 through 597 Processing helix chain 'D' and resid 621 through 636 Processing helix chain 'D' and resid 649 through 654 removed outlier: 3.664A pdb=" N ALA D 652 " --> pdb=" O ALA D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 666 Processing helix chain 'D' and resid 676 through 686 Processing helix chain 'D' and resid 694 through 713 removed outlier: 3.938A pdb=" N HIS D 713 " --> pdb=" O LEU D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 719 removed outlier: 3.652A pdb=" N GLU D 719 " --> pdb=" O GLU D 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 96 through 119 removed outlier: 4.392A pdb=" N HIS C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASN C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 153 removed outlier: 3.998A pdb=" N ALA C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 221 removed outlier: 4.144A pdb=" N ASN C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 224 through 242 removed outlier: 3.614A pdb=" N GLU C 229 " --> pdb=" O ARG C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 273 through 279 Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 300 through 305 removed outlier: 3.666A pdb=" N ARG C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'C' and resid 363 through 372 removed outlier: 4.037A pdb=" N GLY C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.691A pdb=" N SER C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU C 378 " --> pdb=" O PRO C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 407 Processing helix chain 'C' and resid 412 through 428 Processing helix chain 'C' and resid 436 through 451 Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.757A pdb=" N SER C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 543 through 557 Processing helix chain 'C' and resid 585 through 597 Processing helix chain 'C' and resid 621 through 636 removed outlier: 3.605A pdb=" N LYS C 625 " --> pdb=" O ALA C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 654 removed outlier: 3.895A pdb=" N ALA C 652 " --> pdb=" O ALA C 649 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 654 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 666 Processing helix chain 'C' and resid 676 through 686 Processing helix chain 'C' and resid 694 through 718 removed outlier: 3.646A pdb=" N GLU C 716 " --> pdb=" O GLY C 712 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG C 718 " --> pdb=" O ASP C 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 32 through 45 Processing helix chain 'B' and resid 58 through 70 removed outlier: 3.733A pdb=" N THR B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 70 " --> pdb=" O TYR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 120 removed outlier: 4.381A pdb=" N HIS B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASN B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 152 Processing helix chain 'B' and resid 173 through 221 removed outlier: 4.321A pdb=" N ASN B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 224 through 242 Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 273 through 279 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 363 through 372 removed outlier: 3.852A pdb=" N GLU B 368 " --> pdb=" O PRO B 364 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 380 removed outlier: 3.890A pdb=" N SER B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 407 Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 436 through 452 Processing helix chain 'B' and resid 456 through 471 removed outlier: 3.811A pdb=" N SER B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 485 Processing helix chain 'B' and resid 532 through 534 No H-bonds generated for 'chain 'B' and resid 532 through 534' Processing helix chain 'B' and resid 543 through 557 Processing helix chain 'B' and resid 584 through 597 Processing helix chain 'B' and resid 621 through 636 removed outlier: 3.665A pdb=" N LYS B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 654 removed outlier: 3.915A pdb=" N ALA B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 Processing helix chain 'B' and resid 676 through 686 Processing helix chain 'B' and resid 694 through 717 Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 58 through 69 Processing helix chain 'A' and resid 97 through 119 removed outlier: 4.084A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASN A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 152 removed outlier: 3.725A pdb=" N LEU A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 221 removed outlier: 4.160A pdb=" N ASN A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 224 through 242 Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 363 through 372 removed outlier: 4.165A pdb=" N GLY A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 393 through 407 Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 436 through 452 Processing helix chain 'A' and resid 456 through 471 removed outlier: 3.878A pdb=" N SER A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 543 through 557 removed outlier: 3.561A pdb=" N TYR A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 597 Processing helix chain 'A' and resid 621 through 636 removed outlier: 3.533A pdb=" N LYS A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 removed outlier: 4.073A pdb=" N ALA A 652 " --> pdb=" O ALA A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 694 through 716 removed outlier: 3.860A pdb=" N GLU A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 58 through 69 removed outlier: 3.706A pdb=" N THR E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 4.097A pdb=" N HIS E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASN E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 152 Processing helix chain 'E' and resid 173 through 221 removed outlier: 4.203A pdb=" N ASN E 212 " --> pdb=" O HIS E 208 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG E 213 " --> pdb=" O TYR E 209 " (cutoff:3.500A) Proline residue: E 216 - end of helix Processing helix chain 'E' and resid 224 through 242 Processing helix chain 'E' and resid 246 through 251 removed outlier: 4.096A pdb=" N ARG E 251 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 279 Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 314 through 320 removed outlier: 3.627A pdb=" N GLU E 320 " --> pdb=" O SER E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 333 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 373 through 380 Processing helix chain 'E' and resid 393 through 407 Processing helix chain 'E' and resid 412 through 427 Processing helix chain 'E' and resid 436 through 452 Processing helix chain 'E' and resid 456 through 471 Processing helix chain 'E' and resid 471 through 485 removed outlier: 4.304A pdb=" N GLU E 475 " --> pdb=" O SER E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 557 removed outlier: 3.613A pdb=" N TYR E 557 " --> pdb=" O LEU E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 597 Processing helix chain 'E' and resid 621 through 636 Processing helix chain 'E' and resid 649 through 654 removed outlier: 4.067A pdb=" N ALA E 652 " --> pdb=" O ALA E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 666 removed outlier: 3.730A pdb=" N LEU E 661 " --> pdb=" O ARG E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 676 through 686 Processing helix chain 'E' and resid 694 through 718 removed outlier: 3.640A pdb=" N GLU E 716 " --> pdb=" O GLY E 712 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP E 717 " --> pdb=" O HIS E 713 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 2 through 3 removed outlier: 4.684A pdb=" N ILE D 671 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN D 642 " --> pdb=" O HIS D 670 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N TYR D 672 " --> pdb=" O GLN D 642 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL D 644 " --> pdb=" O TYR D 672 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL D 674 " --> pdb=" O VAL D 644 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU D 646 " --> pdb=" O VAL D 674 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA D 605 " --> pdb=" O ILE D 645 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 266 through 268 removed outlier: 6.547A pdb=" N VAL D 267 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ASP D 313 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU D 310 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL D 361 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU D 312 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N HIS D 48 " --> pdb=" O PHE D 380 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 382 " --> pdb=" O HIS D 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 77 through 82 Processing sheet with id=AA4, first strand: chain 'D' and resid 156 through 160 Processing sheet with id=AA5, first strand: chain 'D' and resid 284 through 286 Processing sheet with id=AA6, first strand: chain 'D' and resid 334 through 335 Processing sheet with id=AA7, first strand: chain 'D' and resid 389 through 391 Processing sheet with id=AA8, first strand: chain 'D' and resid 410 through 411 removed outlier: 7.282A pdb=" N GLN D 410 " --> pdb=" O LEU D 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 494 through 496 Processing sheet with id=AB1, first strand: chain 'D' and resid 498 through 504 Processing sheet with id=AB2, first strand: chain 'D' and resid 609 through 610 Processing sheet with id=AB3, first strand: chain 'C' and resid 266 through 268 removed outlier: 6.484A pdb=" N VAL C 267 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ASP C 313 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU C 310 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL C 361 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU C 312 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N HIS C 48 " --> pdb=" O PHE C 380 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C 382 " --> pdb=" O HIS C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 77 through 82 removed outlier: 3.801A pdb=" N VAL C 88 " --> pdb=" O GLU C 348 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AB7, first strand: chain 'C' and resid 334 through 335 Processing sheet with id=AB8, first strand: chain 'C' and resid 389 through 391 Processing sheet with id=AB9, first strand: chain 'C' and resid 410 through 411 removed outlier: 7.484A pdb=" N GLN C 410 " --> pdb=" O LEU C 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AC2, first strand: chain 'C' and resid 498 through 504 removed outlier: 6.796A pdb=" N ILE C 529 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N PHE C 571 " --> pdb=" O ILE C 529 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 583 through 584 removed outlier: 4.580A pdb=" N ALA C 583 " --> pdb=" O VAL C 610 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 604 through 606 removed outlier: 6.760A pdb=" N GLN C 642 " --> pdb=" O HIS C 670 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N TYR C 672 " --> pdb=" O GLN C 642 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL C 644 " --> pdb=" O TYR C 672 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL C 674 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU C 646 " --> pdb=" O VAL C 674 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 266 through 268 removed outlier: 6.682A pdb=" N VAL B 267 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ASP B 313 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU B 310 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B 361 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU B 312 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR B 50 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 77 through 82 Processing sheet with id=AC7, first strand: chain 'B' and resid 156 through 160 Processing sheet with id=AC8, first strand: chain 'B' and resid 280 through 281 Processing sheet with id=AC9, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AD1, first strand: chain 'B' and resid 334 through 335 Processing sheet with id=AD2, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AD3, first strand: chain 'B' and resid 410 through 411 removed outlier: 7.394A pdb=" N GLN B 410 " --> pdb=" O LEU B 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AD5, first strand: chain 'B' and resid 498 through 504 removed outlier: 6.694A pdb=" N ILE B 529 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N PHE B 571 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 604 through 606 removed outlier: 5.827A pdb=" N VAL B 644 " --> pdb=" O TYR B 672 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B 674 " --> pdb=" O VAL B 644 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 646 " --> pdb=" O VAL B 674 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 609 through 610 removed outlier: 3.684A pdb=" N ALA B 609 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 2 through 3 removed outlier: 4.650A pdb=" N ILE A 671 " --> pdb=" O LEU A 3 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 266 through 269 removed outlier: 4.215A pdb=" N ASP A 313 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N HIS A 48 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ARG A 383 " --> pdb=" O HIS A 48 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR A 50 " --> pdb=" O ARG A 383 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLU A 385 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL A 52 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 76 through 82 Processing sheet with id=AE2, first strand: chain 'A' and resid 156 through 160 Processing sheet with id=AE3, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AE4, first strand: chain 'A' and resid 284 through 286 Processing sheet with id=AE5, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AE6, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AE7, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AE8, first strand: chain 'A' and resid 498 through 504 removed outlier: 3.756A pdb=" N SER A 501 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE A 529 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N PHE A 571 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 583 through 584 removed outlier: 4.116A pdb=" N ALA A 583 " --> pdb=" O VAL A 610 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 266 through 268 Processing sheet with id=AF2, first strand: chain 'E' and resid 77 through 82 Processing sheet with id=AF3, first strand: chain 'E' and resid 156 through 160 Processing sheet with id=AF4, first strand: chain 'E' and resid 280 through 281 Processing sheet with id=AF5, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AF6, first strand: chain 'E' and resid 334 through 335 Processing sheet with id=AF7, first strand: chain 'E' and resid 389 through 391 Processing sheet with id=AF8, first strand: chain 'E' and resid 410 through 411 removed outlier: 7.389A pdb=" N GLN E 410 " --> pdb=" O LEU E 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'E' and resid 494 through 495 Processing sheet with id=AG1, first strand: chain 'E' and resid 498 through 503 removed outlier: 7.283A pdb=" N ILE E 529 " --> pdb=" O LEU E 569 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 583 through 584 removed outlier: 4.275A pdb=" N ALA E 583 " --> pdb=" O VAL E 610 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 604 through 606 removed outlier: 6.312A pdb=" N ALA E 605 " --> pdb=" O ILE E 645 " (cutoff:3.500A) 1568 hydrogen bonds defined for protein. 4485 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: 11.32 Time building geometry restraints manager: 7.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9698 1.34 - 1.46: 5227 1.46 - 1.57: 13450 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 28435 Sorted by residual: bond pdb=" CA ASN C 650 " pdb=" C ASN C 650 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.80e-02 3.09e+03 2.66e+00 bond pdb=" CB TYR E 575 " pdb=" CG TYR E 575 " ideal model delta sigma weight residual 1.512 1.547 -0.035 2.20e-02 2.07e+03 2.46e+00 bond pdb=" CB TYR A 575 " pdb=" CG TYR A 575 " ideal model delta sigma weight residual 1.512 1.545 -0.033 2.20e-02 2.07e+03 2.25e+00 bond pdb=" CB TYR B 575 " pdb=" CG TYR B 575 " ideal model delta sigma weight residual 1.512 1.544 -0.032 2.20e-02 2.07e+03 2.16e+00 bond pdb=" CB TYR C 575 " pdb=" CG TYR C 575 " ideal model delta sigma weight residual 1.512 1.544 -0.032 2.20e-02 2.07e+03 2.08e+00 ... (remaining 28430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 38083 2.22 - 4.44: 468 4.44 - 6.66: 47 6.66 - 8.88: 5 8.88 - 11.10: 2 Bond angle restraints: 38605 Sorted by residual: angle pdb=" C ASN E 574 " pdb=" N TYR E 575 " pdb=" CA TYR E 575 " ideal model delta sigma weight residual 121.54 130.72 -9.18 1.91e+00 2.74e-01 2.31e+01 angle pdb=" N PRO A 509 " pdb=" CD PRO A 509 " pdb=" CG PRO A 509 " ideal model delta sigma weight residual 103.20 96.86 6.34 1.50e+00 4.44e-01 1.79e+01 angle pdb=" N TYR E 575 " pdb=" CA TYR E 575 " pdb=" CB TYR E 575 " ideal model delta sigma weight residual 110.49 117.31 -6.82 1.69e+00 3.50e-01 1.63e+01 angle pdb=" CA PRO A 509 " pdb=" N PRO A 509 " pdb=" CD PRO A 509 " ideal model delta sigma weight residual 112.00 106.44 5.56 1.40e+00 5.10e-01 1.58e+01 angle pdb=" C TYR E 510 " pdb=" N TRP E 511 " pdb=" CA TRP E 511 " ideal model delta sigma weight residual 121.54 129.12 -7.58 1.91e+00 2.74e-01 1.58e+01 ... (remaining 38600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 15763 17.96 - 35.91: 1042 35.91 - 53.87: 186 53.87 - 71.83: 156 71.83 - 89.78: 123 Dihedral angle restraints: 17270 sinusoidal: 6995 harmonic: 10275 Sorted by residual: dihedral pdb=" CA ASN B 574 " pdb=" C ASN B 574 " pdb=" N TYR B 575 " pdb=" CA TYR B 575 " ideal model delta harmonic sigma weight residual -180.00 -138.28 -41.72 0 5.00e+00 4.00e-02 6.96e+01 dihedral pdb=" CA ASN E 574 " pdb=" C ASN E 574 " pdb=" N TYR E 575 " pdb=" CA TYR E 575 " ideal model delta harmonic sigma weight residual -180.00 -138.50 -41.50 0 5.00e+00 4.00e-02 6.89e+01 dihedral pdb=" CA ASN C 574 " pdb=" C ASN C 574 " pdb=" N TYR C 575 " pdb=" CA TYR C 575 " ideal model delta harmonic sigma weight residual -180.00 -139.52 -40.48 0 5.00e+00 4.00e-02 6.55e+01 ... (remaining 17267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2836 0.032 - 0.063: 1047 0.063 - 0.095: 280 0.095 - 0.126: 134 0.126 - 0.158: 8 Chirality restraints: 4305 Sorted by residual: chirality pdb=" CA ARG D 708 " pdb=" N ARG D 708 " pdb=" C ARG D 708 " pdb=" CB ARG D 708 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" CA VAL E 289 " pdb=" N VAL E 289 " pdb=" C VAL E 289 " pdb=" CB VAL E 289 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CB ILE A 558 " pdb=" CA ILE A 558 " pdb=" CG1 ILE A 558 " pdb=" CG2 ILE A 558 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 4302 not shown) Planarity restraints: 5155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 574 " 0.021 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C ASN D 574 " -0.076 2.00e-02 2.50e+03 pdb=" O ASN D 574 " 0.029 2.00e-02 2.50e+03 pdb=" N TYR D 575 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 574 " 0.021 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C ASN B 574 " -0.076 2.00e-02 2.50e+03 pdb=" O ASN B 574 " 0.029 2.00e-02 2.50e+03 pdb=" N TYR B 575 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 574 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C ASN A 574 " -0.070 2.00e-02 2.50e+03 pdb=" O ASN A 574 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR A 575 " 0.024 2.00e-02 2.50e+03 ... (remaining 5152 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 294 2.65 - 3.21: 26365 3.21 - 3.77: 45653 3.77 - 4.34: 61225 4.34 - 4.90: 100664 Nonbonded interactions: 234201 Sorted by model distance: nonbonded pdb=" OG SER A 593 " pdb=" O LEU A 598 " model vdw 2.085 3.040 nonbonded pdb=" NH2 ARG E 708 " pdb=" OE2 GLU E 711 " model vdw 2.169 3.120 nonbonded pdb=" OG SER B 593 " pdb=" O LEU B 598 " model vdw 2.186 3.040 nonbonded pdb=" O THR B 456 " pdb=" OG SER B 459 " model vdw 2.195 3.040 nonbonded pdb=" O PHE A 221 " pdb=" NH2 ARG A 225 " model vdw 2.196 3.120 ... (remaining 234196 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.120 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 62.090 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 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 0.045 28435 Z= 0.201 Angle : 0.628 11.103 38605 Z= 0.361 Chirality : 0.038 0.158 4305 Planarity : 0.005 0.056 5155 Dihedral : 16.366 89.782 10670 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.32 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 3585 helix: 1.70 (0.12), residues: 1826 sheet: -0.54 (0.23), residues: 453 loop : -0.42 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 205 HIS 0.005 0.001 HIS C 527 PHE 0.017 0.002 PHE C 629 TYR 0.021 0.002 TYR C 420 ARG 0.012 0.000 ARG D 708 Details of bonding type rmsd hydrogen bonds : bond 0.14111 ( 1568) hydrogen bonds : angle 5.73617 ( 4485) covalent geometry : bond 0.00409 (28435) covalent geometry : angle 0.62753 (38605) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 2.958 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 542 PHE cc_start: 0.6744 (m-10) cc_final: 0.6413 (m-10) REVERT: D 582 SER cc_start: 0.8709 (t) cc_final: 0.8370 (m) REVERT: C 56 SER cc_start: 0.8863 (m) cc_final: 0.8601 (p) REVERT: C 195 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8286 (mt-10) REVERT: C 243 GLU cc_start: 0.6835 (pt0) cc_final: 0.6608 (pt0) REVERT: C 327 LYS cc_start: 0.8606 (ttpt) cc_final: 0.8082 (ttpp) REVERT: C 498 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7035 (mt-10) REVERT: C 557 TYR cc_start: 0.6474 (m-80) cc_final: 0.6183 (m-80) REVERT: C 581 ASP cc_start: 0.7496 (p0) cc_final: 0.7193 (p0) REVERT: B 91 LEU cc_start: 0.8241 (tp) cc_final: 0.7759 (mt) REVERT: B 251 ARG cc_start: 0.8141 (mtt180) cc_final: 0.7797 (ttm110) REVERT: B 527 HIS cc_start: 0.6381 (t-90) cc_final: 0.5874 (p90) REVERT: B 641 THR cc_start: 0.8574 (p) cc_final: 0.8331 (t) REVERT: B 679 GLN cc_start: 0.7215 (mt0) cc_final: 0.6946 (mm-40) REVERT: A 312 LEU cc_start: 0.6523 (mt) cc_final: 0.6154 (mp) REVERT: A 356 MET cc_start: 0.7304 (ppp) cc_final: 0.7048 (ppp) REVERT: A 403 TRP cc_start: 0.8121 (t60) cc_final: 0.7913 (t60) REVERT: A 544 LYS cc_start: 0.7325 (tppt) cc_final: 0.6810 (tptp) REVERT: A 688 ARG cc_start: 0.7170 (mtp180) cc_final: 0.6592 (mmm-85) REVERT: A 698 LYS cc_start: 0.7698 (mttm) cc_final: 0.7430 (mmmt) REVERT: A 704 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7244 (pp20) REVERT: A 709 LEU cc_start: 0.7623 (mt) cc_final: 0.7383 (mt) REVERT: E 293 ASN cc_start: 0.7867 (p0) cc_final: 0.7459 (p0) REVERT: E 600 LEU cc_start: 0.6900 (mt) cc_final: 0.6658 (mt) REVERT: E 688 ARG cc_start: 0.5430 (mtp180) cc_final: 0.5165 (mpt180) outliers start: 0 outliers final: 0 residues processed: 428 average time/residue: 0.5521 time to fit residues: 338.9187 Evaluate side-chains 185 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 299 optimal weight: 20.0000 chunk 269 optimal weight: 3.9990 chunk 149 optimal weight: 0.0370 chunk 91 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 278 optimal weight: 9.9990 chunk 107 optimal weight: 0.2980 chunk 169 optimal weight: 0.0770 chunk 207 optimal weight: 0.9990 chunk 322 optimal weight: 7.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 357 GLN C 303 HIS A 60 HIS A 208 HIS E 130 GLN E 396 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.176173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.140191 restraints weight = 55221.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.138816 restraints weight = 48955.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.140479 restraints weight = 45795.186| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28435 Z= 0.127 Angle : 0.565 8.364 38605 Z= 0.288 Chirality : 0.038 0.181 4305 Planarity : 0.005 0.050 5155 Dihedral : 4.199 42.223 4000 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.18 % Favored : 97.71 % Rotamer: Outliers : 0.70 % Allowed : 6.16 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.14), residues: 3585 helix: 1.66 (0.12), residues: 1846 sheet: -0.55 (0.23), residues: 450 loop : -0.23 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 250 HIS 0.009 0.001 HIS A 208 PHE 0.020 0.001 PHE B 221 TYR 0.033 0.002 TYR C 5 ARG 0.007 0.000 ARG E 657 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 1568) hydrogen bonds : angle 4.66151 ( 4485) covalent geometry : bond 0.00274 (28435) covalent geometry : angle 0.56525 (38605) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 244 time to evaluate : 3.113 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: symmetry clash REVERT: D 131 LEU cc_start: 0.8208 (tp) cc_final: 0.7741 (mt) REVERT: C 47 PHE cc_start: 0.8017 (m-10) cc_final: 0.7771 (m-80) REVERT: C 557 TYR cc_start: 0.6453 (m-80) cc_final: 0.6232 (m-80) REVERT: C 581 ASP cc_start: 0.7445 (p0) cc_final: 0.7090 (p0) REVERT: B 1 MET cc_start: 0.7085 (ppp) cc_final: 0.6421 (ptt) REVERT: B 91 LEU cc_start: 0.8453 (tp) cc_final: 0.8247 (tt) REVERT: B 108 LEU cc_start: 0.7833 (mt) cc_final: 0.7561 (mt) REVERT: A 464 ILE cc_start: 0.8506 (mt) cc_final: 0.8207 (mt) REVERT: A 544 LYS cc_start: 0.7718 (tppt) cc_final: 0.7189 (tptp) REVERT: A 688 ARG cc_start: 0.7068 (mtp180) cc_final: 0.6835 (mmm-85) REVERT: E 603 ASP cc_start: 0.6532 (m-30) cc_final: 0.6315 (t0) outliers start: 20 outliers final: 11 residues processed: 259 average time/residue: 0.4595 time to fit residues: 181.6003 Evaluate side-chains 169 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 546 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 200 optimal weight: 4.9990 chunk 305 optimal weight: 10.0000 chunk 252 optimal weight: 20.0000 chunk 217 optimal weight: 30.0000 chunk 161 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 291 optimal weight: 10.0000 chunk 233 optimal weight: 20.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 543 HIS B 573 GLN ** E 527 HIS ** 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 = 0.4274 r_free = 0.4274 target = 0.161348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.113500 restraints weight = 54892.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.112471 restraints weight = 36134.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.113690 restraints weight = 33617.960| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 28435 Z= 0.246 Angle : 0.647 8.772 38605 Z= 0.325 Chirality : 0.042 0.166 4305 Planarity : 0.005 0.059 5155 Dihedral : 4.344 40.360 4000 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.43 % Favored : 97.46 % Rotamer: Outliers : 1.37 % Allowed : 8.98 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.14), residues: 3585 helix: 1.31 (0.12), residues: 1864 sheet: -0.65 (0.23), residues: 450 loop : -0.23 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 290 HIS 0.007 0.001 HIS E 527 PHE 0.027 0.002 PHE E 571 TYR 0.030 0.002 TYR B 575 ARG 0.009 0.001 ARG E 331 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 1568) hydrogen bonds : angle 4.71440 ( 4485) covalent geometry : bond 0.00575 (28435) covalent geometry : angle 0.64656 (38605) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 LEU cc_start: 0.8353 (tp) cc_final: 0.7895 (mt) REVERT: C 327 LYS cc_start: 0.8638 (ttpt) cc_final: 0.8335 (ttpp) REVERT: C 581 ASP cc_start: 0.7516 (p0) cc_final: 0.7201 (p0) REVERT: B 91 LEU cc_start: 0.8594 (tp) cc_final: 0.8204 (tt) REVERT: A 193 GLU cc_start: 0.7373 (tp30) cc_final: 0.6215 (mm-30) REVERT: A 544 LYS cc_start: 0.7665 (tppt) cc_final: 0.7055 (tptp) REVERT: A 688 ARG cc_start: 0.7315 (mtp180) cc_final: 0.6796 (mmm-85) REVERT: A 689 MET cc_start: 0.4831 (mtp) cc_final: 0.4557 (mtp) REVERT: E 205 TRP cc_start: 0.7511 (m100) cc_final: 0.7255 (m-10) REVERT: E 293 ASN cc_start: 0.7994 (p0) cc_final: 0.7757 (p0) REVERT: E 603 ASP cc_start: 0.7441 (m-30) cc_final: 0.6883 (t0) REVERT: E 661 LEU cc_start: 0.8239 (mt) cc_final: 0.8017 (mt) REVERT: E 704 GLU cc_start: 0.3184 (OUTLIER) cc_final: 0.2938 (mp0) outliers start: 39 outliers final: 21 residues processed: 192 average time/residue: 0.4338 time to fit residues: 131.1289 Evaluate side-chains 162 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 3.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 582 SER Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 704 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 278 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 198 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 218 optimal weight: 10.0000 chunk 338 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 268 optimal weight: 9.9990 chunk 292 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 543 HIS D 573 GLN C 696 GLN ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.171578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.137312 restraints weight = 54837.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.133996 restraints weight = 56792.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.135782 restraints weight = 49922.293| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28435 Z= 0.116 Angle : 0.527 9.571 38605 Z= 0.263 Chirality : 0.038 0.164 4305 Planarity : 0.004 0.063 5155 Dihedral : 4.063 39.797 4000 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.92 % Favored : 97.96 % Rotamer: Outliers : 1.30 % Allowed : 10.25 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.14), residues: 3585 helix: 1.59 (0.12), residues: 1854 sheet: -0.55 (0.23), residues: 460 loop : -0.21 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.010 0.001 HIS A 208 PHE 0.017 0.001 PHE A 218 TYR 0.029 0.002 TYR C 575 ARG 0.007 0.000 ARG C 556 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 1568) hydrogen bonds : angle 4.34088 ( 4485) covalent geometry : bond 0.00255 (28435) covalent geometry : angle 0.52745 (38605) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 3.037 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: D 131 LEU cc_start: 0.8257 (tp) cc_final: 0.7910 (mt) REVERT: D 498 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6775 (mm-30) REVERT: D 641 THR cc_start: 0.7811 (p) cc_final: 0.7414 (t) REVERT: C 581 ASP cc_start: 0.7512 (p0) cc_final: 0.7169 (p0) REVERT: B 91 LEU cc_start: 0.8438 (tp) cc_final: 0.8085 (mt) REVERT: A 312 LEU cc_start: 0.8021 (mt) cc_final: 0.7801 (mp) REVERT: A 532 ASP cc_start: 0.6048 (t0) cc_final: 0.5837 (t0) REVERT: A 544 LYS cc_start: 0.7526 (tppt) cc_final: 0.7007 (tptp) REVERT: A 688 ARG cc_start: 0.7065 (mtp180) cc_final: 0.6851 (mmm-85) REVERT: A 689 MET cc_start: 0.5344 (mtp) cc_final: 0.4951 (mtp) REVERT: E 527 HIS cc_start: 0.6497 (t70) cc_final: 0.6272 (t70) outliers start: 37 outliers final: 21 residues processed: 200 average time/residue: 0.4140 time to fit residues: 132.6764 Evaluate side-chains 162 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 700 ARG Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 546 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 349 optimal weight: 8.9990 chunk 332 optimal weight: 20.0000 chunk 176 optimal weight: 10.0000 chunk 336 optimal weight: 40.0000 chunk 244 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 335 optimal weight: 6.9990 chunk 227 optimal weight: 30.0000 chunk 70 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 543 HIS C 602 GLN B 573 GLN A 160 ASN E 668 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.154784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.116627 restraints weight = 53867.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.112438 restraints weight = 52485.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.114111 restraints weight = 46598.572| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 28435 Z= 0.377 Angle : 0.774 10.511 38605 Z= 0.388 Chirality : 0.046 0.169 4305 Planarity : 0.006 0.069 5155 Dihedral : 4.660 40.371 4000 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.60 % Rotamer: Outliers : 2.32 % Allowed : 11.02 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3585 helix: 0.97 (0.12), residues: 1856 sheet: -0.85 (0.24), residues: 446 loop : -0.46 (0.18), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 205 HIS 0.025 0.002 HIS A 208 PHE 0.031 0.003 PHE D 472 TYR 0.034 0.003 TYR C 420 ARG 0.012 0.001 ARG C 631 Details of bonding type rmsd hydrogen bonds : bond 0.04626 ( 1568) hydrogen bonds : angle 4.96057 ( 4485) covalent geometry : bond 0.00882 (28435) covalent geometry : angle 0.77440 (38605) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 151 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 327 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8367 (ttpp) REVERT: C 581 ASP cc_start: 0.7686 (p0) cc_final: 0.7370 (p0) REVERT: B 405 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8664 (mm) REVERT: B 573 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7629 (mt0) REVERT: A 193 GLU cc_start: 0.7157 (tp30) cc_final: 0.6027 (mm-30) REVERT: A 544 LYS cc_start: 0.7694 (tppt) cc_final: 0.7140 (tptp) REVERT: A 554 ARG cc_start: 0.6460 (mtm-85) cc_final: 0.6122 (ttp80) REVERT: A 688 ARG cc_start: 0.7235 (mtp180) cc_final: 0.6876 (mmm-85) REVERT: E 520 ARG cc_start: 0.5078 (mmm160) cc_final: 0.4679 (tpt90) REVERT: E 542 PHE cc_start: 0.6092 (OUTLIER) cc_final: 0.4607 (m-10) REVERT: E 603 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6690 (t70) outliers start: 66 outliers final: 38 residues processed: 209 average time/residue: 0.4264 time to fit residues: 141.0337 Evaluate side-chains 167 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 526 ASP Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 542 PHE Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 603 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 217 optimal weight: 3.9990 chunk 317 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 314 optimal weight: 2.9990 chunk 316 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 322 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 353 optimal weight: 7.9990 chunk 342 optimal weight: 20.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 527 HIS B 527 HIS B 573 GLN B 612 GLN A 208 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.161922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.117716 restraints weight = 54161.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.117813 restraints weight = 38825.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.117853 restraints weight = 27339.642| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28435 Z= 0.131 Angle : 0.550 9.078 38605 Z= 0.274 Chirality : 0.038 0.224 4305 Planarity : 0.004 0.050 5155 Dihedral : 4.192 39.391 4000 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.01 % Favored : 97.88 % Rotamer: Outliers : 1.73 % Allowed : 12.39 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.14), residues: 3585 helix: 1.35 (0.12), residues: 1878 sheet: -0.61 (0.24), residues: 430 loop : -0.50 (0.18), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP E 205 HIS 0.005 0.001 HIS A 60 PHE 0.019 0.001 PHE B 278 TYR 0.041 0.002 TYR A 283 ARG 0.008 0.000 ARG B 280 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 1568) hydrogen bonds : angle 4.38726 ( 4485) covalent geometry : bond 0.00289 (28435) covalent geometry : angle 0.55040 (38605) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 150 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.7325 (tmm) cc_final: 0.6819 (pmm) REVERT: C 498 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6356 (mt-10) REVERT: C 577 SER cc_start: 0.6286 (m) cc_final: 0.6078 (p) REVERT: C 581 ASP cc_start: 0.7403 (p0) cc_final: 0.7065 (p0) REVERT: B 327 LYS cc_start: 0.7472 (pttt) cc_final: 0.7178 (pttm) REVERT: B 405 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8606 (mm) REVERT: A 193 GLU cc_start: 0.7392 (tp30) cc_final: 0.6270 (mm-30) REVERT: A 227 TYR cc_start: 0.5661 (t80) cc_final: 0.5423 (t80) REVERT: A 312 LEU cc_start: 0.7578 (mt) cc_final: 0.7303 (mp) REVERT: A 544 LYS cc_start: 0.7633 (tppt) cc_final: 0.6975 (tptp) REVERT: A 554 ARG cc_start: 0.6505 (mtm-85) cc_final: 0.6095 (tpt90) REVERT: A 688 ARG cc_start: 0.7358 (mtp180) cc_final: 0.6892 (mmm-85) REVERT: E 603 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6559 (t70) outliers start: 49 outliers final: 30 residues processed: 193 average time/residue: 0.3959 time to fit residues: 124.9072 Evaluate side-chains 161 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 603 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 93 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 chunk 322 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 323 optimal weight: 10.0000 chunk 79 optimal weight: 0.0770 chunk 80 optimal weight: 0.2980 chunk 1 optimal weight: 9.9990 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 573 GLN A 208 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.161332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.117042 restraints weight = 54216.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.117005 restraints weight = 43928.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.117181 restraints weight = 30401.945| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28435 Z= 0.147 Angle : 0.551 19.136 38605 Z= 0.272 Chirality : 0.038 0.159 4305 Planarity : 0.004 0.047 5155 Dihedral : 4.092 39.142 4000 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.40 % Favored : 97.52 % Rotamer: Outliers : 1.76 % Allowed : 12.82 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.14), residues: 3585 helix: 1.43 (0.12), residues: 1882 sheet: -0.59 (0.24), residues: 430 loop : -0.48 (0.18), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 205 HIS 0.017 0.001 HIS A 208 PHE 0.038 0.001 PHE D 571 TYR 0.033 0.002 TYR A 283 ARG 0.008 0.000 ARG C 200 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 1568) hydrogen bonds : angle 4.34178 ( 4485) covalent geometry : bond 0.00333 (28435) covalent geometry : angle 0.55103 (38605) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 3.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.7257 (tmm) cc_final: 0.6724 (pmm) REVERT: D 135 PHE cc_start: 0.7608 (m-10) cc_final: 0.6526 (m-10) REVERT: D 641 THR cc_start: 0.7966 (p) cc_final: 0.7547 (t) REVERT: C 581 ASP cc_start: 0.7414 (p0) cc_final: 0.7089 (p0) REVERT: B 237 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.7116 (ttm110) REVERT: B 327 LYS cc_start: 0.7472 (pttt) cc_final: 0.7055 (pttp) REVERT: A 193 GLU cc_start: 0.7359 (tp30) cc_final: 0.6251 (mm-30) REVERT: A 544 LYS cc_start: 0.7624 (tppt) cc_final: 0.6959 (tptp) REVERT: A 554 ARG cc_start: 0.6405 (mtm-85) cc_final: 0.6113 (tpt90) REVERT: A 688 ARG cc_start: 0.7246 (mtp180) cc_final: 0.6876 (mmm-85) REVERT: E 542 PHE cc_start: 0.6017 (OUTLIER) cc_final: 0.4356 (m-80) REVERT: E 603 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6615 (t70) outliers start: 50 outliers final: 34 residues processed: 185 average time/residue: 0.3964 time to fit residues: 119.9739 Evaluate side-chains 166 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 542 PHE Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 603 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 80 optimal weight: 0.6980 chunk 275 optimal weight: 1.9990 chunk 308 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 279 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 336 optimal weight: 40.0000 chunk 42 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 312 optimal weight: 20.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 623 ASN A 208 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.161517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.117000 restraints weight = 54247.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.117320 restraints weight = 39985.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.117410 restraints weight = 29387.429| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28435 Z= 0.143 Angle : 0.545 16.658 38605 Z= 0.270 Chirality : 0.038 0.157 4305 Planarity : 0.004 0.048 5155 Dihedral : 4.028 38.393 4000 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.26 % Favored : 97.63 % Rotamer: Outliers : 1.73 % Allowed : 13.10 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.14), residues: 3585 helix: 1.48 (0.12), residues: 1878 sheet: -0.77 (0.24), residues: 462 loop : -0.30 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 205 HIS 0.022 0.001 HIS A 208 PHE 0.032 0.001 PHE D 571 TYR 0.037 0.002 TYR A 283 ARG 0.012 0.000 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 1568) hydrogen bonds : angle 4.29943 ( 4485) covalent geometry : bond 0.00325 (28435) covalent geometry : angle 0.54510 (38605) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 137 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.7243 (tmm) cc_final: 0.6761 (pmm) REVERT: D 641 THR cc_start: 0.7992 (p) cc_final: 0.7571 (t) REVERT: C 498 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6742 (mt-10) REVERT: C 581 ASP cc_start: 0.7464 (p0) cc_final: 0.7111 (p0) REVERT: B 179 ARG cc_start: 0.6146 (tpt170) cc_final: 0.5516 (mmm160) REVERT: B 237 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.7054 (ttm110) REVERT: A 193 GLU cc_start: 0.7398 (tp30) cc_final: 0.6290 (mm-30) REVERT: A 544 LYS cc_start: 0.7592 (tppt) cc_final: 0.6916 (tptp) REVERT: A 688 ARG cc_start: 0.7242 (mtp180) cc_final: 0.6877 (mmm-85) REVERT: E 542 PHE cc_start: 0.5962 (OUTLIER) cc_final: 0.4320 (m-80) REVERT: E 603 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6681 (t70) outliers start: 49 outliers final: 35 residues processed: 182 average time/residue: 0.3900 time to fit residues: 115.1250 Evaluate side-chains 168 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 623 ASN Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 542 PHE Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 603 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 219 optimal weight: 8.9990 chunk 89 optimal weight: 30.0000 chunk 141 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 256 optimal weight: 9.9990 chunk 306 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 260 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 221 optimal weight: 1.9990 chunk 291 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 413 GLN D 543 HIS C 623 ASN A 208 HIS E 483 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.157957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.109667 restraints weight = 55307.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.110234 restraints weight = 37471.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.110415 restraints weight = 27720.899| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 28435 Z= 0.355 Angle : 0.748 16.129 38605 Z= 0.375 Chirality : 0.045 0.178 4305 Planarity : 0.006 0.066 5155 Dihedral : 4.572 38.172 4000 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.60 % Favored : 96.29 % Rotamer: Outliers : 1.83 % Allowed : 13.31 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3585 helix: 1.09 (0.12), residues: 1850 sheet: -0.95 (0.24), residues: 425 loop : -0.61 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 205 HIS 0.029 0.002 HIS A 208 PHE 0.029 0.003 PHE D 472 TYR 0.035 0.003 TYR A 283 ARG 0.009 0.001 ARG D 631 Details of bonding type rmsd hydrogen bonds : bond 0.04451 ( 1568) hydrogen bonds : angle 4.86517 ( 4485) covalent geometry : bond 0.00826 (28435) covalent geometry : angle 0.74829 (38605) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 127 time to evaluate : 3.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.7410 (tmm) cc_final: 0.6829 (pmm) REVERT: C 327 LYS cc_start: 0.8594 (ttpt) cc_final: 0.8363 (ttpp) REVERT: B 237 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7179 (ttm110) REVERT: A 193 GLU cc_start: 0.7426 (tp30) cc_final: 0.6219 (mm-30) REVERT: A 227 TYR cc_start: 0.5938 (t80) cc_final: 0.5603 (t80) REVERT: A 544 LYS cc_start: 0.7643 (tppt) cc_final: 0.7009 (tptp) REVERT: A 688 ARG cc_start: 0.7194 (mtp180) cc_final: 0.6902 (mmm-85) REVERT: E 520 ARG cc_start: 0.4739 (mmm160) cc_final: 0.4292 (tpt90) REVERT: E 542 PHE cc_start: 0.6127 (OUTLIER) cc_final: 0.4337 (m-10) REVERT: E 603 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.6757 (t70) outliers start: 52 outliers final: 37 residues processed: 174 average time/residue: 0.3953 time to fit residues: 113.4905 Evaluate side-chains 162 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 3.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 526 ASP Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 542 PHE Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 603 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 87 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 308 optimal weight: 0.2980 chunk 110 optimal weight: 0.9990 chunk 266 optimal weight: 6.9990 chunk 275 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 543 HIS C 623 ASN ** A 208 HIS ** 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 = 0.4297 r_free = 0.4297 target = 0.162225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.115962 restraints weight = 54056.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.117904 restraints weight = 36031.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.118326 restraints weight = 24039.105| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28435 Z= 0.117 Angle : 0.554 16.981 38605 Z= 0.274 Chirality : 0.038 0.158 4305 Planarity : 0.004 0.059 5155 Dihedral : 4.130 37.375 4000 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.90 % Favored : 97.99 % Rotamer: Outliers : 1.16 % Allowed : 14.01 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.14), residues: 3585 helix: 1.41 (0.12), residues: 1878 sheet: -0.79 (0.24), residues: 432 loop : -0.50 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 205 HIS 0.019 0.001 HIS A 208 PHE 0.017 0.001 PHE B 278 TYR 0.028 0.002 TYR A 283 ARG 0.008 0.000 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 1568) hydrogen bonds : angle 4.33504 ( 4485) covalent geometry : bond 0.00254 (28435) covalent geometry : angle 0.55399 (38605) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.7290 (tmm) cc_final: 0.6729 (pmm) REVERT: D 291 SER cc_start: 0.7890 (p) cc_final: 0.7325 (m) REVERT: D 641 THR cc_start: 0.8031 (p) cc_final: 0.7615 (t) REVERT: B 179 ARG cc_start: 0.6101 (tpt170) cc_final: 0.5457 (mmm160) REVERT: B 237 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.7025 (ttm110) REVERT: A 193 GLU cc_start: 0.7411 (tp30) cc_final: 0.6224 (mm-30) REVERT: A 227 TYR cc_start: 0.5821 (t80) cc_final: 0.5611 (t80) REVERT: A 688 ARG cc_start: 0.7200 (mtp180) cc_final: 0.6935 (mmm-85) REVERT: E 520 ARG cc_start: 0.4771 (mmm160) cc_final: 0.4283 (tpt90) REVERT: E 603 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6710 (t70) outliers start: 33 outliers final: 27 residues processed: 171 average time/residue: 0.3946 time to fit residues: 109.1110 Evaluate side-chains 160 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 623 ASN Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 603 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 120 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 289 optimal weight: 0.0060 chunk 232 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 171 optimal weight: 0.0470 chunk 223 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 345 optimal weight: 20.0000 chunk 154 optimal weight: 0.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 543 HIS C 623 ASN A 208 HIS ** E 612 GLN ** 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 = 0.4293 r_free = 0.4293 target = 0.159575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.121865 restraints weight = 53601.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.119051 restraints weight = 49481.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.120596 restraints weight = 38005.088| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 28435 Z= 0.111 Angle : 0.545 16.443 38605 Z= 0.269 Chirality : 0.038 0.192 4305 Planarity : 0.004 0.068 5155 Dihedral : 4.018 36.897 4000 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.06 % Favored : 97.82 % Rotamer: Outliers : 1.09 % Allowed : 14.51 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3585 helix: 1.52 (0.12), residues: 1878 sheet: -0.66 (0.25), residues: 432 loop : -0.38 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 205 HIS 0.017 0.001 HIS A 208 PHE 0.021 0.001 PHE A 218 TYR 0.034 0.002 TYR A 283 ARG 0.009 0.000 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 1568) hydrogen bonds : angle 4.25551 ( 4485) covalent geometry : bond 0.00245 (28435) covalent geometry : angle 0.54520 (38605) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8154.32 seconds wall clock time: 142 minutes 3.80 seconds (8523.80 seconds total)