Starting phenix.real_space_refine on Thu Mar 5 07:40:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u84_20677/03_2026/6u84_20677.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u84_20677/03_2026/6u84_20677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u84_20677/03_2026/6u84_20677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u84_20677/03_2026/6u84_20677.map" model { file = "/net/cci-nas-00/data/ceres_data/6u84_20677/03_2026/6u84_20677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u84_20677/03_2026/6u84_20677.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 116 5.16 5 C 13360 2.51 5 N 3452 2.21 5 O 3532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20460 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5115 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 606} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 5115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5115 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 606} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 5115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5115 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 606} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 5115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5115 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 606} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 4.30, per 1000 atoms: 0.21 Number of scatterers: 20460 At special positions: 0 Unit cell: (136.74, 136.74, 114.48, 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 116 16.00 O 3532 8.00 N 3452 7.00 C 13360 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: 1.40 Conformation dependent library (CDL) restraints added in 827.6 milliseconds 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 62.1% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.966A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 94 through 103 removed outlier: 3.637A pdb=" N TYR A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.680A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 147 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 166 through 174 removed outlier: 4.246A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 removed outlier: 3.963A pdb=" N LEU A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.508A pdb=" N THR A 227 " --> pdb=" O TRP A 223 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 297 through 306 removed outlier: 3.601A pdb=" N GLY A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.924A pdb=" N HIS A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 377 through 413 removed outlier: 5.400A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 461 through 466 Processing helix chain 'A' and resid 466 through 492 removed outlier: 6.946A pdb=" N PHE A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.009A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 3.538A pdb=" N THR A 516 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 518' Processing helix chain 'A' and resid 519 through 530 removed outlier: 4.093A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 560 removed outlier: 3.829A pdb=" N ASP A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.633A pdb=" N ALA A 596 " --> pdb=" O SER A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 649 Processing helix chain 'A' and resid 655 through 672 Processing helix chain 'A' and resid 711 through 719 removed outlier: 3.602A pdb=" N THR A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 719 " --> pdb=" O TRP A 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.966A pdb=" N ARG B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 94 through 103 removed outlier: 3.637A pdb=" N TYR B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.681A pdb=" N LYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 147 Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 166 through 174 removed outlier: 4.247A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 185 removed outlier: 3.962A pdb=" N LEU B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.508A pdb=" N THR B 227 " --> pdb=" O TRP B 223 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 260 through 282 Processing helix chain 'B' and resid 297 through 306 removed outlier: 3.601A pdb=" N GLY B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 316 removed outlier: 3.923A pdb=" N HIS B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 377 through 413 removed outlier: 5.399A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 461 through 466 Processing helix chain 'B' and resid 466 through 492 removed outlier: 6.946A pdb=" N PHE B 472 " --> pdb=" O MET B 468 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU B 473 " --> pdb=" O ASP B 469 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 4.008A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.538A pdb=" N THR B 516 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 518' Processing helix chain 'B' and resid 519 through 530 removed outlier: 4.094A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 560 removed outlier: 3.829A pdb=" N ASP B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 removed outlier: 3.634A pdb=" N ALA B 596 " --> pdb=" O SER B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 649 Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 711 through 719 removed outlier: 3.602A pdb=" N THR B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 719 " --> pdb=" O TRP B 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.966A pdb=" N ARG C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 94 through 103 removed outlier: 3.637A pdb=" N TYR C 98 " --> pdb=" O GLY C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.680A pdb=" N LYS C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 166 through 174 removed outlier: 4.246A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 removed outlier: 3.963A pdb=" N LEU C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.508A pdb=" N THR C 227 " --> pdb=" O TRP C 223 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 257 Processing helix chain 'C' and resid 260 through 282 Processing helix chain 'C' and resid 297 through 306 removed outlier: 3.602A pdb=" N GLY C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 316 removed outlier: 3.923A pdb=" N HIS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 377 through 413 removed outlier: 5.399A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 461 through 466 Processing helix chain 'C' and resid 466 through 492 removed outlier: 6.946A pdb=" N PHE C 472 " --> pdb=" O MET C 468 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 4.009A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 removed outlier: 3.538A pdb=" N THR C 516 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 513 through 518' Processing helix chain 'C' and resid 519 through 530 removed outlier: 4.094A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 560 removed outlier: 3.829A pdb=" N ASP C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 removed outlier: 3.633A pdb=" N ALA C 596 " --> pdb=" O SER C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 649 Processing helix chain 'C' and resid 655 through 672 Processing helix chain 'C' and resid 711 through 719 removed outlier: 3.603A pdb=" N THR C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 719 " --> pdb=" O TRP C 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.965A pdb=" N ARG D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 87 " --> pdb=" O VAL D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 94 through 103 removed outlier: 3.637A pdb=" N TYR D 98 " --> pdb=" O GLY D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.681A pdb=" N LYS D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 147 Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 166 through 174 removed outlier: 4.247A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 185 removed outlier: 3.963A pdb=" N LEU D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.508A pdb=" N THR D 227 " --> pdb=" O TRP D 223 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 260 through 282 Processing helix chain 'D' and resid 297 through 306 removed outlier: 3.602A pdb=" N GLY D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 removed outlier: 3.923A pdb=" N HIS D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 368 through 372 Processing helix chain 'D' and resid 377 through 413 removed outlier: 5.399A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 461 through 466 Processing helix chain 'D' and resid 466 through 492 removed outlier: 6.947A pdb=" N PHE D 472 " --> pdb=" O MET D 468 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.008A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.537A pdb=" N THR D 516 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 513 through 518' Processing helix chain 'D' and resid 519 through 530 removed outlier: 4.093A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 560 removed outlier: 3.830A pdb=" N ASP D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 removed outlier: 3.633A pdb=" N ALA D 596 " --> pdb=" O SER D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 649 Processing helix chain 'D' and resid 655 through 672 Processing helix chain 'D' and resid 711 through 719 removed outlier: 3.602A pdb=" N THR D 718 " --> pdb=" O ALA D 714 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 719 " --> pdb=" O TRP D 715 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.575A pdb=" N LYS A 329 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP A 344 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP A 700 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.574A pdb=" N LYS B 329 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP B 344 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THR B 331 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU B 342 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP B 700 " --> pdb=" O VAL B 691 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.574A pdb=" N LYS C 329 " --> pdb=" O ASP C 344 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP C 344 " --> pdb=" O LYS C 329 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP C 700 " --> pdb=" O VAL C 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.574A pdb=" N LYS D 329 " --> pdb=" O ASP D 344 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP D 344 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP D 700 " --> pdb=" O VAL D 691 " (cutoff:3.500A) 1084 hydrogen bonds defined for protein. 3156 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6447 1.34 - 1.46: 5003 1.46 - 1.57: 9346 1.57 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 20976 Sorted by residual: bond pdb=" CB VAL C 356 " pdb=" CG2 VAL C 356 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.94e+00 bond pdb=" CB VAL A 356 " pdb=" CG2 VAL A 356 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.94e+00 bond pdb=" CB VAL B 356 " pdb=" CG2 VAL B 356 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.85e+00 bond pdb=" CB VAL D 356 " pdb=" CG2 VAL D 356 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.85e+00 bond pdb=" CG LEU D 558 " pdb=" CD1 LEU D 558 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 ... (remaining 20971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 24763 1.00 - 2.01: 2925 2.01 - 3.01: 545 3.01 - 4.02: 174 4.02 - 5.02: 49 Bond angle restraints: 28456 Sorted by residual: angle pdb=" C GLU B 332 " pdb=" N TRP B 333 " pdb=" CA TRP B 333 " ideal model delta sigma weight residual 121.89 118.30 3.59 1.74e+00 3.30e-01 4.27e+00 angle pdb=" C GLU A 332 " pdb=" N TRP A 333 " pdb=" CA TRP A 333 " ideal model delta sigma weight residual 121.89 118.30 3.59 1.74e+00 3.30e-01 4.26e+00 angle pdb=" C GLU D 332 " pdb=" N TRP D 333 " pdb=" CA TRP D 333 " ideal model delta sigma weight residual 121.89 118.30 3.59 1.74e+00 3.30e-01 4.26e+00 angle pdb=" C GLU C 332 " pdb=" N TRP C 333 " pdb=" CA TRP C 333 " ideal model delta sigma weight residual 121.89 118.33 3.56 1.74e+00 3.30e-01 4.19e+00 angle pdb=" CA TYR C 271 " pdb=" CB TYR C 271 " pdb=" CG TYR C 271 " ideal model delta sigma weight residual 113.90 117.39 -3.49 1.80e+00 3.09e-01 3.76e+00 ... (remaining 28451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 10841 18.03 - 36.06: 1245 36.06 - 54.10: 210 54.10 - 72.13: 40 72.13 - 90.16: 12 Dihedral angle restraints: 12348 sinusoidal: 4984 harmonic: 7364 Sorted by residual: dihedral pdb=" CA ASN C 247 " pdb=" C ASN C 247 " pdb=" N THR C 248 " pdb=" CA THR C 248 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ASN B 247 " pdb=" C ASN B 247 " pdb=" N THR B 248 " pdb=" CA THR B 248 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ASN D 247 " pdb=" C ASN D 247 " pdb=" N THR D 248 " pdb=" CA THR D 248 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 12345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1882 0.036 - 0.072: 882 0.072 - 0.107: 330 0.107 - 0.143: 80 0.143 - 0.179: 14 Chirality restraints: 3188 Sorted by residual: chirality pdb=" CB VAL C 338 " pdb=" CA VAL C 338 " pdb=" CG1 VAL C 338 " pdb=" CG2 VAL C 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" CB VAL A 338 " pdb=" CA VAL A 338 " pdb=" CG1 VAL A 338 " pdb=" CG2 VAL A 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CB VAL D 338 " pdb=" CA VAL D 338 " pdb=" CG1 VAL D 338 " pdb=" CG2 VAL D 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.85e-01 ... (remaining 3185 not shown) Planarity restraints: 3540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 250 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C LEU C 250 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU C 250 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS C 251 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 250 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.54e+00 pdb=" C LEU A 250 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU A 250 " 0.010 2.00e-02 2.50e+03 pdb=" N HIS A 251 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 250 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.52e+00 pdb=" C LEU D 250 " -0.027 2.00e-02 2.50e+03 pdb=" O LEU D 250 " 0.010 2.00e-02 2.50e+03 pdb=" N HIS D 251 " 0.009 2.00e-02 2.50e+03 ... (remaining 3537 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3763 2.75 - 3.29: 20686 3.29 - 3.83: 33063 3.83 - 4.36: 37465 4.36 - 4.90: 66280 Nonbonded interactions: 161257 Sorted by model distance: nonbonded pdb=" O LEU D 216 " pdb=" OG1 THR D 220 " model vdw 2.214 3.040 nonbonded pdb=" O LEU B 216 " pdb=" OG1 THR B 220 " model vdw 2.215 3.040 nonbonded pdb=" O LEU A 216 " pdb=" OG1 THR A 220 " model vdw 2.215 3.040 nonbonded pdb=" O LEU C 216 " pdb=" OG1 THR C 220 " model vdw 2.215 3.040 nonbonded pdb=" O ILE A 529 " pdb=" ND2 ASN B 639 " model vdw 2.243 3.120 ... (remaining 161252 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.600 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.011 0.066 20976 Z= 0.452 Angle : 0.743 5.023 28456 Z= 0.400 Chirality : 0.047 0.179 3188 Planarity : 0.004 0.033 3540 Dihedral : 15.058 90.159 7588 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.90 % Allowed : 8.77 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.15), residues: 2488 helix: -1.02 (0.12), residues: 1416 sheet: -1.26 (0.62), residues: 64 loop : -2.01 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 560 TYR 0.023 0.003 TYR C 162 PHE 0.025 0.003 PHE A 362 TRP 0.008 0.001 TRP D 715 HIS 0.005 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.01106 (20976) covalent geometry : angle 0.74287 (28456) hydrogen bonds : bond 0.12929 ( 1084) hydrogen bonds : angle 5.60114 ( 3156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 267 time to evaluate : 0.753 Fit side-chains REVERT: A 193 ARG cc_start: 0.8379 (ptp90) cc_final: 0.8114 (ptp-110) REVERT: A 640 MET cc_start: 0.8498 (tmm) cc_final: 0.8187 (ttp) REVERT: A 667 SER cc_start: 0.9184 (t) cc_final: 0.8962 (p) REVERT: B 193 ARG cc_start: 0.8388 (ptp90) cc_final: 0.8115 (ptp-110) REVERT: B 614 GLU cc_start: 0.7028 (pp20) cc_final: 0.6352 (pp20) REVERT: B 640 MET cc_start: 0.8363 (tmm) cc_final: 0.8074 (ttp) REVERT: B 667 SER cc_start: 0.9219 (t) cc_final: 0.8974 (p) REVERT: C 193 ARG cc_start: 0.8381 (ptp90) cc_final: 0.8113 (ptp-110) REVERT: C 614 GLU cc_start: 0.7030 (pp20) cc_final: 0.6353 (pp20) REVERT: C 640 MET cc_start: 0.8365 (tmm) cc_final: 0.8071 (ttp) REVERT: C 667 SER cc_start: 0.9221 (t) cc_final: 0.8973 (p) REVERT: D 193 ARG cc_start: 0.8385 (ptp90) cc_final: 0.8111 (ptp-110) REVERT: D 314 ILE cc_start: 0.8762 (mt) cc_final: 0.8493 (mt) REVERT: D 614 GLU cc_start: 0.7035 (pp20) cc_final: 0.6350 (pp20) REVERT: D 640 MET cc_start: 0.8359 (tmm) cc_final: 0.8071 (ttp) REVERT: D 667 SER cc_start: 0.9220 (t) cc_final: 0.8975 (p) outliers start: 20 outliers final: 12 residues processed: 283 average time/residue: 0.1603 time to fit residues: 67.7056 Evaluate side-chains 216 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 204 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 247 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 269 HIS ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN B 269 HIS ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN C 269 HIS ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN D 269 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.106382 restraints weight = 28474.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.108793 restraints weight = 18143.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.110414 restraints weight = 13404.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.111495 restraints weight = 10867.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.112323 restraints weight = 9350.720| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20976 Z= 0.125 Angle : 0.522 6.992 28456 Z= 0.262 Chirality : 0.036 0.133 3188 Planarity : 0.003 0.030 3540 Dihedral : 4.227 31.728 2772 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.31 % Allowed : 13.38 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2488 helix: 0.81 (0.14), residues: 1448 sheet: -1.15 (0.53), residues: 64 loop : -1.15 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 44 TYR 0.009 0.001 TYR A 228 PHE 0.017 0.001 PHE B 491 TRP 0.024 0.001 TRP D 676 HIS 0.007 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00296 (20976) covalent geometry : angle 0.52160 (28456) hydrogen bonds : bond 0.03543 ( 1084) hydrogen bonds : angle 3.94670 ( 3156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 267 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8868 (t) REVERT: B 190 VAL cc_start: 0.9106 (OUTLIER) cc_final: 0.8898 (t) REVERT: C 190 VAL cc_start: 0.9110 (OUTLIER) cc_final: 0.8903 (t) REVERT: D 190 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8901 (t) REVERT: D 314 ILE cc_start: 0.8923 (mt) cc_final: 0.8707 (mt) outliers start: 29 outliers final: 12 residues processed: 288 average time/residue: 0.1305 time to fit residues: 59.8049 Evaluate side-chains 230 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 214 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 11 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 236 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 182 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.113804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.092467 restraints weight = 30291.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.094729 restraints weight = 19931.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.096268 restraints weight = 15069.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.097387 restraints weight = 12458.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.098014 restraints weight = 10896.872| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 20976 Z= 0.197 Angle : 0.568 8.606 28456 Z= 0.283 Chirality : 0.039 0.118 3188 Planarity : 0.003 0.028 3540 Dihedral : 4.041 22.858 2760 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.12 % Allowed : 17.63 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.17), residues: 2488 helix: 1.32 (0.14), residues: 1424 sheet: -1.21 (0.52), residues: 64 loop : -1.03 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 44 TYR 0.012 0.001 TYR D 271 PHE 0.010 0.001 PHE D 311 TRP 0.016 0.001 TRP A 676 HIS 0.002 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00471 (20976) covalent geometry : angle 0.56777 (28456) hydrogen bonds : bond 0.03839 ( 1084) hydrogen bonds : angle 3.89688 ( 3156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 241 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7592 (tm-30) REVERT: B 453 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9077 (mm) REVERT: B 670 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7610 (tm-30) REVERT: C 453 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9085 (mm) REVERT: C 670 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7609 (tm-30) REVERT: D 314 ILE cc_start: 0.9094 (mt) cc_final: 0.8852 (mt) REVERT: D 453 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9076 (mm) REVERT: D 670 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7612 (tm-30) outliers start: 69 outliers final: 41 residues processed: 302 average time/residue: 0.1225 time to fit residues: 60.9149 Evaluate side-chains 258 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 214 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 84 optimal weight: 4.9990 chunk 176 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 17 optimal weight: 0.0670 chunk 201 optimal weight: 0.9990 chunk 198 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.116276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.094891 restraints weight = 30257.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.097284 restraints weight = 19644.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.098911 restraints weight = 14754.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.099970 restraints weight = 12174.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.100766 restraints weight = 10680.279| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20976 Z= 0.128 Angle : 0.502 7.886 28456 Z= 0.254 Chirality : 0.036 0.119 3188 Planarity : 0.003 0.031 3540 Dihedral : 3.660 14.466 2756 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.98 % Allowed : 18.58 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.17), residues: 2488 helix: 1.62 (0.14), residues: 1432 sheet: -0.64 (0.59), residues: 64 loop : -0.88 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 44 TYR 0.010 0.001 TYR D 228 PHE 0.008 0.001 PHE B 311 TRP 0.010 0.001 TRP B 676 HIS 0.001 0.000 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00304 (20976) covalent geometry : angle 0.50248 (28456) hydrogen bonds : bond 0.03379 ( 1084) hydrogen bonds : angle 3.57793 ( 3156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 253 time to evaluate : 0.690 Fit side-chains REVERT: A 453 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9041 (mm) REVERT: A 636 LEU cc_start: 0.8850 (tp) cc_final: 0.8611 (tt) REVERT: B 636 LEU cc_start: 0.8850 (tp) cc_final: 0.8609 (tt) REVERT: C 453 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9069 (mm) REVERT: C 636 LEU cc_start: 0.8851 (tp) cc_final: 0.8612 (tt) REVERT: D 314 ILE cc_start: 0.9078 (mt) cc_final: 0.8862 (mt) REVERT: D 453 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9069 (mm) REVERT: D 636 LEU cc_start: 0.8851 (tp) cc_final: 0.8613 (tt) outliers start: 66 outliers final: 38 residues processed: 311 average time/residue: 0.1245 time to fit residues: 63.5641 Evaluate side-chains 275 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 234 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 140 optimal weight: 6.9990 chunk 220 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 7 optimal weight: 0.0980 chunk 94 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.117867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.096616 restraints weight = 30037.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.099045 restraints weight = 19368.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.100704 restraints weight = 14474.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.101769 restraints weight = 11880.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.102612 restraints weight = 10372.757| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20976 Z= 0.107 Angle : 0.486 8.529 28456 Z= 0.244 Chirality : 0.035 0.118 3188 Planarity : 0.003 0.030 3540 Dihedral : 3.468 13.812 2756 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.57 % Allowed : 19.62 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.17), residues: 2488 helix: 1.83 (0.14), residues: 1436 sheet: -0.72 (0.56), residues: 64 loop : -0.81 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 44 TYR 0.009 0.001 TYR B 228 PHE 0.007 0.001 PHE B 311 TRP 0.009 0.001 TRP C 660 HIS 0.001 0.000 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00247 (20976) covalent geometry : angle 0.48567 (28456) hydrogen bonds : bond 0.03183 ( 1084) hydrogen bonds : angle 3.41508 ( 3156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 272 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7538 (tm-30) REVERT: B 453 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8974 (mm) REVERT: D 314 ILE cc_start: 0.9075 (mt) cc_final: 0.8862 (mt) REVERT: D 670 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7535 (tm-30) outliers start: 79 outliers final: 50 residues processed: 339 average time/residue: 0.1239 time to fit residues: 69.1398 Evaluate side-chains 279 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 228 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 131 optimal weight: 10.0000 chunk 141 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.115256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.093552 restraints weight = 30096.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.095969 restraints weight = 19327.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.097622 restraints weight = 14420.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.098766 restraints weight = 11858.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.099470 restraints weight = 10335.636| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20976 Z= 0.138 Angle : 0.537 9.409 28456 Z= 0.262 Chirality : 0.036 0.122 3188 Planarity : 0.003 0.034 3540 Dihedral : 3.497 14.436 2756 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.80 % Allowed : 20.25 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.17), residues: 2488 helix: 1.87 (0.14), residues: 1436 sheet: -0.79 (0.54), residues: 64 loop : -0.80 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 193 TYR 0.009 0.001 TYR A 228 PHE 0.018 0.001 PHE C 491 TRP 0.007 0.001 TRP B 676 HIS 0.002 0.000 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00330 (20976) covalent geometry : angle 0.53678 (28456) hydrogen bonds : bond 0.03348 ( 1084) hydrogen bonds : angle 3.48083 ( 3156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 237 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8948 (mm) REVERT: B 453 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8923 (mm) REVERT: C 453 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8925 (mm) REVERT: D 453 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8941 (mm) outliers start: 84 outliers final: 66 residues processed: 313 average time/residue: 0.1271 time to fit residues: 64.9951 Evaluate side-chains 296 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 226 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 28 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 174 optimal weight: 0.8980 chunk 244 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 185 optimal weight: 2.9990 chunk 246 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.102772 restraints weight = 29626.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.105016 restraints weight = 19581.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.106612 restraints weight = 14818.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.107614 restraints weight = 12187.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.108420 restraints weight = 10643.330| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20976 Z= 0.112 Angle : 0.508 10.069 28456 Z= 0.248 Chirality : 0.035 0.118 3188 Planarity : 0.003 0.037 3540 Dihedral : 3.406 13.661 2756 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.89 % Allowed : 20.98 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.17), residues: 2488 helix: 2.02 (0.14), residues: 1436 sheet: -0.88 (0.53), residues: 64 loop : -0.76 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 193 TYR 0.008 0.001 TYR A 228 PHE 0.019 0.001 PHE A 491 TRP 0.008 0.001 TRP D 660 HIS 0.002 0.000 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00264 (20976) covalent geometry : angle 0.50816 (28456) hydrogen bonds : bond 0.03142 ( 1084) hydrogen bonds : angle 3.34899 ( 3156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 256 time to evaluate : 0.905 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: A 190 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8949 (t) REVERT: A 453 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8939 (mm) REVERT: B 190 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8957 (t) REVERT: B 453 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8938 (mm) REVERT: C 190 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8959 (t) REVERT: C 453 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8913 (mm) REVERT: D 190 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8966 (t) REVERT: D 453 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8911 (mm) outliers start: 86 outliers final: 70 residues processed: 334 average time/residue: 0.1238 time to fit residues: 68.5261 Evaluate side-chains 305 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 227 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 182 optimal weight: 6.9990 chunk 239 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 245 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 193 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.116293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.095672 restraints weight = 30263.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.097897 restraints weight = 19948.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.099327 restraints weight = 15033.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.100426 restraints weight = 12476.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.101104 restraints weight = 10908.854| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20976 Z= 0.214 Angle : 0.614 10.821 28456 Z= 0.304 Chirality : 0.039 0.126 3188 Planarity : 0.003 0.041 3540 Dihedral : 3.704 15.625 2756 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.34 % Allowed : 21.93 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2488 helix: 1.78 (0.14), residues: 1436 sheet: -0.97 (0.53), residues: 64 loop : -0.80 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 193 TYR 0.011 0.002 TYR C 271 PHE 0.020 0.001 PHE D 491 TRP 0.009 0.001 TRP A 333 HIS 0.002 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00513 (20976) covalent geometry : angle 0.61377 (28456) hydrogen bonds : bond 0.03771 ( 1084) hydrogen bonds : angle 3.67413 ( 3156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 234 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7682 (t80) cc_final: 0.7472 (t80) REVERT: A 453 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8983 (mm) REVERT: B 98 TYR cc_start: 0.7682 (t80) cc_final: 0.7475 (t80) REVERT: B 453 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8973 (mm) REVERT: C 98 TYR cc_start: 0.7680 (t80) cc_final: 0.7477 (t80) REVERT: C 453 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8978 (mm) REVERT: D 98 TYR cc_start: 0.7683 (t80) cc_final: 0.7478 (t80) REVERT: D 453 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8975 (mm) outliers start: 96 outliers final: 68 residues processed: 318 average time/residue: 0.1224 time to fit residues: 64.6635 Evaluate side-chains 301 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 229 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 138 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 169 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.115504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.093882 restraints weight = 30106.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.096332 restraints weight = 19291.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.097968 restraints weight = 14369.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.099106 restraints weight = 11799.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.099833 restraints weight = 10271.476| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20976 Z= 0.130 Angle : 0.549 11.367 28456 Z= 0.271 Chirality : 0.036 0.122 3188 Planarity : 0.003 0.042 3540 Dihedral : 3.528 14.081 2756 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.80 % Allowed : 22.38 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.17), residues: 2488 helix: 1.91 (0.14), residues: 1436 sheet: -0.99 (0.53), residues: 64 loop : -0.74 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 517 TYR 0.012 0.001 TYR B 105 PHE 0.021 0.001 PHE A 491 TRP 0.009 0.001 TRP C 660 HIS 0.001 0.000 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00308 (20976) covalent geometry : angle 0.54867 (28456) hydrogen bonds : bond 0.03317 ( 1084) hydrogen bonds : angle 3.47213 ( 3156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 233 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8882 (mm) REVERT: A 492 MET cc_start: 0.7376 (ttt) cc_final: 0.7171 (ttt) REVERT: B 453 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8883 (mm) REVERT: B 492 MET cc_start: 0.7315 (ttt) cc_final: 0.7105 (ttt) REVERT: C 453 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8878 (mm) REVERT: C 492 MET cc_start: 0.7314 (ttt) cc_final: 0.7103 (ttt) REVERT: D 453 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8874 (mm) REVERT: D 492 MET cc_start: 0.7311 (ttt) cc_final: 0.7099 (ttt) outliers start: 84 outliers final: 73 residues processed: 309 average time/residue: 0.1123 time to fit residues: 58.4459 Evaluate side-chains 304 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 227 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 223 TRP Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 TRP Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 223 TRP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 223 TRP Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 152 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 197 optimal weight: 0.9990 chunk 228 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.118070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.097455 restraints weight = 30038.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.099723 restraints weight = 19669.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.101288 restraints weight = 14899.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.102311 restraints weight = 12306.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.103086 restraints weight = 10762.826| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20976 Z= 0.112 Angle : 0.541 11.855 28456 Z= 0.267 Chirality : 0.035 0.119 3188 Planarity : 0.003 0.043 3540 Dihedral : 3.401 13.262 2756 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.11 % Allowed : 22.29 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.17), residues: 2488 helix: 2.01 (0.14), residues: 1436 sheet: -0.90 (0.53), residues: 64 loop : -0.70 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 563 TYR 0.008 0.001 TYR A 228 PHE 0.023 0.001 PHE B 491 TRP 0.010 0.001 TRP D 660 HIS 0.001 0.000 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00261 (20976) covalent geometry : angle 0.54053 (28456) hydrogen bonds : bond 0.03121 ( 1084) hydrogen bonds : angle 3.41874 ( 3156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 237 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8883 (mm) REVERT: A 492 MET cc_start: 0.7479 (ttt) cc_final: 0.7246 (ttt) REVERT: B 453 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8888 (mm) REVERT: B 492 MET cc_start: 0.7470 (ttt) cc_final: 0.7240 (ttt) REVERT: C 453 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8857 (mm) REVERT: C 492 MET cc_start: 0.7474 (ttt) cc_final: 0.7239 (ttt) REVERT: D 453 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8857 (mm) REVERT: D 492 MET cc_start: 0.7471 (ttt) cc_final: 0.7235 (ttt) outliers start: 91 outliers final: 75 residues processed: 320 average time/residue: 0.1175 time to fit residues: 63.5279 Evaluate side-chains 306 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 227 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 223 TRP Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 TRP Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 223 TRP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 223 TRP Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 65 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 186 optimal weight: 0.8980 chunk 51 optimal weight: 0.0970 chunk 18 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 199 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 overall best weight: 1.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.122158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.101712 restraints weight = 30345.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.104001 restraints weight = 19536.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.105566 restraints weight = 14634.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.106634 restraints weight = 12025.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.107363 restraints weight = 10461.220| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20976 Z= 0.157 Angle : 0.578 11.756 28456 Z= 0.286 Chirality : 0.037 0.142 3188 Planarity : 0.003 0.043 3540 Dihedral : 3.501 14.372 2756 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.89 % Allowed : 22.78 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.17), residues: 2488 helix: 1.95 (0.14), residues: 1436 sheet: -0.91 (0.53), residues: 64 loop : -0.70 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 517 TYR 0.012 0.001 TYR C 105 PHE 0.023 0.001 PHE A 491 TRP 0.008 0.001 TRP A 333 HIS 0.002 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00376 (20976) covalent geometry : angle 0.57788 (28456) hydrogen bonds : bond 0.03452 ( 1084) hydrogen bonds : angle 3.53013 ( 3156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2735.93 seconds wall clock time: 48 minutes 15.03 seconds (2895.03 seconds total)